container build already running since 7 days and doesn't finish or give error

[stebo85]

Link to Container Collection Log, Build, or Collection (in that order)

https://github.com/CAIsr/singularity-minc-v2-develop https://singularity-hub.org/collections/352/

Behavior when Building Locally

the build works perfectly and everything works as expected

Error on Singularity Hub

the build does not finish

What do you think is going on?

the download of external packages might be extremely slow or is timing out for every download?

[vsoch]

I think this build got lost in a server restart - the instance finished, sent the response, and it was not fully received (meaning the builder is done / gone but the main application not updated). Would you mind canceling, and committing again to restart? Also, it looks like your %files section in your Singularity spec file is empty!

[vsoch]

hey @stebo85 - I see that it's building again, and from what I can tell the instance is active, possibly running out of memory / space because I'm unable to shell into it. I notice you build the entire revusive clone of submodules:

git clone --recursive https://github.com/BIC-MNI/minc-toolkit-v2.git minc-toolkit-v2 -b develop-1.9.15
  cd minc-toolkit-v2
  mkdir build && cd build

I was looking at the number of installs and compiles needed for this and holy crap no wonder it is taking 7 days! I think the first thing to try is using an already Dockerized version of minc-tools and then adding onto that? And try increasing the size of the build in the instance. Thanks!

[yarikoptic]

Hi @vsoch Found this one so decided to comment on instead of breeding a new one. I have a build which runs already for > 12h, and typically here locally it takes just an hour or so: https://singularity-hub.org/collections/67/

I guess if there was some way to see build logs of the RUNNING build -- it could help identify why it is stuck and cancel it in such cases, instead of pestering you ;)

[vsoch]

It must be due to calculating the size - have you timed it when providing a size so it doesn't need to estimate?

[yarikoptic]

oh -- I didn't ... I guess I will need to read on that ;)

[yarikoptic]

tricky point -- "Image size:?" does not give idea in what units to specify -- MB, GB? I will assume it is in megabytes so will say 12000 to be on a safe side.

[vsoch]

ah yes, same convention as with singularity. I'll make sure to have this specified for next release!

[vsoch]

okay, change is in!

[yarikoptic]

even with specified size, and toggling some debug output somewhere is settings it is still "Running" since Aug 12 (https://singularity-hub.org/collections/67/)

[vsoch]

Here is the full log, for neurodebian I was actually able to shell into the instance. You mean to use singularity 2.2? also, I noticed that

Environment message level found to be DEBUG
INFO:shub_builder:Singularity 2.2 being used.
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/dobuild HTTP/1.1" 200 4
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/debug HTTP/1.1" 200 7
INFO:shub_builder:DEBUG True
WARNING:shub_builder:Build directory not set, using /tmp/tmpgzd2el0m
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/repo_url HTTP/1.1" 200 46
INFO:shub_builder:repo_url is set to https://www.github.com/neurodebian/neurodebian
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/repo_id HTTP/1.1" 200 7
INFO:shub_builder:repo_id is set to 1091819
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/response_url HTTP/1.1" 200 54
INFO:shub_builder:response_url is set to https://singularity-hub.org/hooks/build/google/receive
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/bucket_name HTTP/1.1" 200 24
INFO:shub_builder:bucket_name is set to singularity-hub-regional
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/token HTTP/1.1" 200 36
INFO:shub_builder:token is set to 0bd3e4e2-9f6a-456c-a510-62189cb69ba7
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/commit HTTP/1.1" 200 40
INFO:shub_builder:commit is set to cb25afb804c79a4d8e0ee2de3e5754f319ccbdde
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/secret HTTP/1.1" 200 36
INFO:shub_builder:secret is set to 7dfa746d-5b9f-41bb-912b-1268a7dff9cb
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/size HTTP/1.1" 200 5
INFO:shub_builder:size is set to 12000
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/branch HTTP/1.1" 200 6
INFO:shub_builder:branch is set to master
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/spec_file HTTP/1.1" 200 11
INFO:shub_builder:spec_file is set to Singularity
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/padding HTTP/1.1" 200 3
INFO:shub_builder:padding is set to 200
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/logging_url HTTP/1.1" 200 53
INFO:shub_builder:logging_url is set to https://singularity-hub.org/hooks/build/google/finish
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/logfile HTTP/1.1" 200 14
INFO:shub_builder:logfile is set to /tmp/.shub-log
Cloning into '/tmp/tmpgzd2el0m'...
INFO:shub_builder:Checking out branch master
Already on 'master'
Your branch is up-to-date with 'origin/master'.
INFO:shub_builder:Checking out commit cb25afb804c79a4d8e0ee2de3e5754f319ccbdde
INFO:shub_builder:Found spec file Singularity in repository
DEBUG:shub_builder:Building in directory /tmp/tmpgzd2el0m
DEBUG:shub_builder:Spec file set to Singularity
DEBUG:shub_builder:Spec file for build should be in /tmp/tmpgzd2el0m/Singularity
VERBOSE [U=0,P=2133]       message.c:52:message_init()                : Set messagelevel to: 5
VERBOSE [U=0,P=2133]       config_parser.c:113:singularity_config_parse(): Initialize configuration file: /usr/local/etc/singularity/singularity.conf
DEBUG   [U=0,P=2133]       config_parser.c:125:singularity_config_parse(): Starting parse of configuration file /usr/local/etc/singularity/singularity.conf
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key allow setuid = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key allow pid ns = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key allow user image = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key protected image mode = 'none'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key enable overlay = 'no'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key config passwd = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key config group = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key config resolv_conf = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key mount proc = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key mount sys = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key mount dev = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key mount home = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key mount tmp = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key mount hostfs = 'no'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key bind path = '/etc/hosts'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key user bind control = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key mount slave = 'yes'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key container dir = '/var/lib/singularity/mnt'
VERBOSE [U=0,P=2133]       config_parser.c:176:singularity_config_parse(): Got config key singularity user = 'singularity'
DEBUG   [U=0,P=2133]       config_parser.c:184:singularity_config_parse(): Finished parsing configuration file '/usr/local/etc/singularity/singularity.conf'
DEBUG   [U=0,P=2133]       privilege.c:73:singularity_priv_init()     : Called singularity_priv_init(void)
VERBOSE [U=0,P=2133]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_TARGET_UID'
DEBUG   [U=0,P=2133]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_TARGET_UID
VERBOSE [U=0,P=2133]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_TARGET_UID
VERBOSE [U=0,P=2133]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_TARGET_GID'
DEBUG   [U=0,P=2133]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_TARGET_GID
VERBOSE [U=0,P=2133]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_TARGET_GID
DEBUG   [U=0,P=2133]       privilege.c:138:singularity_priv_init()    : Returning singularity_priv_init(void)
DEBUG   [U=0,P=2133]       simage.c:77:main()                         : Running /usr/local/libexec/singularity/simage create workflow
DEBUG   [U=0,P=2133]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=2133]       create.c:47:singularity_image_create()     : Creating new sparse image at: /tmp/tmpgzd2el0m/image
DEBUG   [U=0,P=2133]       create.c:54:singularity_image_create()     : Opening image 'w'
VERBOSE [U=0,P=2133]       create.c:61:singularity_image_create()     : Writing image header
VERBOSE [U=0,P=2133]       create.c:64:singularity_image_create()     : Expanding image to 12000MB
VERBOSE [U=0,P=2133]       create.c:74:singularity_image_create()     : Making image executable
DEBUG   [U=0,P=2133]       create.c:80:singularity_image_create()     : Returning image_create(/tmp/tmpgzd2el0m/image, 12000) = 0
VERBOSE [U=0,P=2132]       message.c:52:message_init()                : Set messagelevel to: 5
VERBOSE [U=0,P=2132]       config_parser.c:113:singularity_config_parse(): Initialize configuration file: /usr/local/etc/singularity/singularity.conf
DEBUG   [U=0,P=2132]       config_parser.c:125:singularity_config_parse(): Starting parse of configuration file /usr/local/etc/singularity/singularity.conf
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key allow setuid = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key allow pid ns = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key allow user image = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key protected image mode = 'none'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key enable overlay = 'no'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key config passwd = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key config group = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key config resolv_conf = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key mount proc = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key mount sys = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key mount dev = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key mount home = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key mount tmp = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key mount hostfs = 'no'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key bind path = '/etc/hosts'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key user bind control = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key mount slave = 'yes'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key container dir = '/var/lib/singularity/mnt'
VERBOSE [U=0,P=2132]       config_parser.c:176:singularity_config_parse(): Got config key singularity user = 'singularity'
DEBUG   [U=0,P=2132]       config_parser.c:184:singularity_config_parse(): Finished parsing configuration file '/usr/local/etc/singularity/singularity.conf'
DEBUG   [U=0,P=2132]       privilege.c:73:singularity_priv_init()     : Called singularity_priv_init(void)
VERBOSE [U=0,P=2132]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_TARGET_UID'
DEBUG   [U=0,P=2132]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_TARGET_UID
VERBOSE [U=0,P=2132]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_TARGET_UID
VERBOSE [U=0,P=2132]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_TARGET_GID'
DEBUG   [U=0,P=2132]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_TARGET_GID
VERBOSE [U=0,P=2132]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_TARGET_GID
DEBUG   [U=0,P=2132]       privilege.c:138:singularity_priv_init()    : Returning singularity_priv_init(void)
DEBUG   [U=0,P=2132]       simage.c:77:main()                         : Running /usr/local/libexec/singularity/simage bind workflow
DEBUG   [U=0,P=2132]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=2132]       bind.c:56:singularity_image_bind()         : Checking calling user
DEBUG   [U=0,P=2132]       util/util.c:104:envar_path()               : Checking environment variable is valid path: 'SINGULARITY_IMAGE'
VERBOSE [U=0,P=2132]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_IMAGE'
DEBUG   [U=0,P=2132]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_IMAGE
DEBUG   [U=0,P=2132]       util/util.c:60:envar()                     : Checking environment variable length (<= 4096): SINGULARITY_IMAGE
DEBUG   [U=0,P=2132]       util/util.c:66:envar()                     : Checking environment variable has allowed characters: SINGULARITY_IMAGE
VERBOSE [U=0,P=2132]       util/util.c:89:envar()                     : Obtained input from environment 'SINGULARITY_IMAGE' = '/tmp/tmpgzd2el0m/image'
VERBOSE [U=0,P=2132]       bind.c:67:singularity_image_bind()         : Evaluating image: /tmp/tmpgzd2el0m/image
VERBOSE [U=0,P=2132]       bind.c:69:singularity_image_bind()         : Checking if container image exists
VERBOSE [U=0,P=2132]       bind.c:75:singularity_image_bind()         : Checking if container can be opened read/write
DEBUG   [U=0,P=2132]       privilege.c:73:singularity_priv_init()     : Called singularity_priv_init(void)
VERBOSE [U=0,P=2132]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_TARGET_UID'
DEBUG   [U=0,P=2132]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_TARGET_UID
VERBOSE [U=0,P=2132]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_TARGET_UID
VERBOSE [U=0,P=2132]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_TARGET_GID'
DEBUG   [U=0,P=2132]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_TARGET_GID
VERBOSE [U=0,P=2132]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_TARGET_GID
DEBUG   [U=0,P=2132]       privilege.c:138:singularity_priv_init()    : Returning singularity_priv_init(void)
DEBUG   [U=0,P=2132]       sessiondir.c:60:singularity_sessiondir_init(): Checking Singularity configuration for 'sessiondir prefix'
DEBUG   [U=0,P=2132]       util/util.c:104:envar_path()               : Checking environment variable is valid path: 'SINGULARITY_SESSIONDIR'
VERBOSE [U=0,P=2132]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_SESSIONDIR'
DEBUG   [U=0,P=2132]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_SESSIONDIR
VERBOSE [U=0,P=2132]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_SESSIONDIR
DEBUG   [U=0,P=2132]       config_parser.c:230:_singularity_config_get_value_impl(): No configuration entry found for 'sessiondir prefix'; returning default value '/tmp/.singularity-session-'
DEBUG   [U=0,P=2132]       sessiondir.c:81:singularity_sessiondir_init(): Set sessiondir to: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=2132]       util/file.c:263:s_mkpath()                 : Creating directory: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=2132]       sessiondir.c:97:singularity_sessiondir_init(): Opening sessiondir file descriptor
DEBUG   [U=0,P=2132]       sessiondir.c:103:singularity_sessiondir_init(): Setting shared flock() on session directory
DEBUG   [U=0,P=2132]       util/util.c:94:envar_defined()             : Checking if environment variable is defined: SINGULARITY_NOSESSIONCLEANUP
VERBOSE [U=0,P=2132]       util/util.c:96:envar_defined()             : Environment variable is undefined: SINGULARITY_NOSESSIONCLEANUP
DEBUG   [U=0,P=2132]       util/util.c:94:envar_defined()             : Checking if environment variable is defined: SINGULARITY_NOCLEANUP
VERBOSE [U=0,P=2132]       util/util.c:96:envar_defined()             : Environment variable is undefined: SINGULARITY_NOCLEANUP
DEBUG   [U=0,P=2132]       fork.c:77:prepare_fork()                   : Creating parent/child coordination pipes.
VERBOSE [U=0,P=2132]       fork.c:153:singularity_fork()              : Forking child process
VERBOSE [U=0,P=2132]       fork.c:171:singularity_fork()              : Hello from parent process
DEBUG   [U=0,P=2132]       fork.c:190:singularity_fork()              : Assigning sigaction()s
DEBUG   [U=0,P=2132]       fork.c:221:singularity_fork()              : Creating generic signal pipes
DEBUG   [U=0,P=2132]       fork.c:229:singularity_fork()              : Creating sigchld signal pipes
DEBUG   [U=0,P=2132]       fork.c:260:singularity_fork()              : Waiting on signal from watchdog
VERBOSE [U=0,P=2204]       fork.c:157:singularity_fork()              : Hello from child process
DEBUG   [U=0,P=2204]       fork.c:160:singularity_fork()              : Closing watchdog write pipe
DEBUG   [U=0,P=2204]       fork.c:167:singularity_fork()              : Child process is returning control to process thread
DEBUG   [U=0,P=2204]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(mount slave, yes)
DEBUG   [U=0,P=2204]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value mount slave='yes'
DEBUG   [U=0,P=2204]       config_parser.c:303:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(mount slave, yes) = 1
DEBUG   [U=0,P=2204]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
DEBUG   [U=0,P=2204]       mnt.c:53:singularity_ns_mnt_unshare()      : Virtualizing FS namespace
DEBUG   [U=0,P=2204]       mnt.c:60:singularity_ns_mnt_unshare()      : Virtualizing mount namespace
DEBUG   [U=0,P=2204]       mnt.c:69:singularity_ns_mnt_unshare()      : Making mounts slave
DEBUG   [U=0,P=2204]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=2204]       bind.c:88:singularity_image_bind()         : Binding container to loop interface
DEBUG   [U=0,P=2204]       sessiondir.c:172:singularity_sessiondir_get(): Returning: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=2204]       loop-control.c:65:singularity_loop_bind_with_offset(): Opening image loop device file: /tmp/.singularity-session-0.2049.271187/image_loop_dev
DEBUG   [U=0,P=2204]       loop-control.c:71:singularity_loop_bind_with_offset(): Requesting exclusive flock() on loop_dev lockfile
DEBUG   [U=0,P=2204]       loop-control.c:95:singularity_loop_bind_with_offset(): Calculating image offset
VERBOSE [U=0,P=2204]       image.c:77:singularity_image_offset()      : Calculating image offset
VERBOSE [U=0,P=2204]       image.c:86:singularity_image_offset()      : Found image at an offset of 31 bytes
DEBUG   [U=0,P=2204]       image.c:91:singularity_image_offset()      : Returning image_offset(image_fp) = 31
DEBUG   [U=0,P=2204]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
DEBUG   [U=0,P=2204]       loop-control.c:106:singularity_loop_bind_with_offset(): Finding next available loop device...
VERBOSE [U=0,P=2204]       loop-control.c:138:singularity_loop_bind_with_offset(): Found available loop device: /dev/loop0
DEBUG   [U=0,P=2204]       loop-control.c:140:singularity_loop_bind_with_offset(): Setting loop device flags
DEBUG   [U=0,P=2204]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
VERBOSE [U=0,P=2204]       loop-control.c:150:singularity_loop_bind_with_offset(): Using loop device: /dev/loop0
DEBUG   [U=0,P=2204]       loop-control.c:152:singularity_loop_bind_with_offset(): Writing active loop device name (/dev/loop0) to loop file cache: /tmp/.singularity-session-0.2049.271187/image_loop_dev
DEBUG   [U=0,P=2204]       util/file.c:349:fileput()                  : Called fileput(/tmp/.singularity-session-0.2049.271187/image_loop_dev, /dev/loop0)
DEBUG   [U=0,P=2204]       loop-control.c:158:singularity_loop_bind_with_offset(): Resetting exclusive flock() to shared on image_loop_file
DEBUG   [U=0,P=2204]       loop-control.c:161:singularity_loop_bind_with_offset(): Returning singularity_loop_bind(image_fp) = loop_fp
VERBOSE [U=0,P=2204]       bind.c:95:singularity_image_bind()         : Setting SINGULARITY_LOOPDEV to '/dev/loop0'
DEBUG   [U=0,P=2204]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=2204]       simage.c:77:main()                         : Running bind /usr/local/libexec/singularity/helpers/image-create.sh workflow
DEBUG   [U=0,P=2204]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
DEBUG   [U=0,P=2204]       privilege.c:311:singularity_priv_drop_perm(): Called singularity_priv_drop_perm(void)
VERBOSE [U=0,P=2204]       privilege.c:324:singularity_priv_drop_perm(): Calling user is root, no privileges to drop
DEBUG   [U=0,P=2204]       fork.c:77:prepare_fork()                   : Creating parent/child coordination pipes.
VERBOSE [U=0,P=2204]       fork.c:153:singularity_fork()              : Forking child process
VERBOSE [U=0,P=2204]       fork.c:171:singularity_fork()              : Hello from parent process
DEBUG   [U=0,P=2204]       fork.c:190:singularity_fork()              : Assigning sigaction()s
DEBUG   [U=0,P=2204]       fork.c:221:singularity_fork()              : Creating generic signal pipes
DEBUG   [U=0,P=2204]       fork.c:229:singularity_fork()              : Creating sigchld signal pipes
DEBUG   [U=0,P=2204]       fork.c:260:singularity_fork()              : Waiting on signal from watchdog
VERBOSE [U=0,P=2206]       fork.c:157:singularity_fork()              : Hello from child process
DEBUG   [U=0,P=2206]       fork.c:160:singularity_fork()              : Closing watchdog write pipe
DEBUG   [U=0,P=2206]       fork.c:167:singularity_fork()              : Child process is returning control to process thread
DEBUG   [U=0,P=2204]       fork.c:287:singularity_fork()              : Parent process is exiting
DEBUG   [U=0,P=2204]       fork.c:328:singularity_fork_exec()         : Waiting on child process
DEBUG   [U=0,P=2132]       fork.c:287:singularity_fork()              : Parent process is exiting
DEBUG   [U=0,P=2132]       util/util.c:104:envar_path()               : Checking environment variable is valid path: 'SINGULARITY_RUNDIR'
VERBOSE [U=0,P=2132]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_RUNDIR'
DEBUG   [U=0,P=2132]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_RUNDIR
VERBOSE [U=0,P=2132]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_RUNDIR
DEBUG   [U=0,P=2132]       sessiondir.c:117:singularity_sessiondir_init(): Cleanup thread waiting on child...
DEBUG   [U=0,P=2132]       sessiondir.c:122:singularity_sessiondir_init(): Child exited with status 0.
DEBUG   [U=0,P=2132]       sessiondir.c:128:singularity_sessiondir_init(): Checking to see if we are the last process running in this sessiondir
VERBOSE [U=0,P=2132]       sessiondir.c:130:singularity_sessiondir_init(): Cleaning sessiondir: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=2132]       util/file.c:285:s_rmdir()                  : Removing directory: /tmp/.singularity-session-0.2049.271187
VERBOSE [U=0,P=7375]       message.c:52:message_init()                : Set messagelevel to: 5
VERBOSE [U=0,P=7375]       config_parser.c:113:singularity_config_parse(): Initialize configuration file: /usr/local/etc/singularity/singularity.conf
DEBUG   [U=0,P=7375]       config_parser.c:125:singularity_config_parse(): Starting parse of configuration file /usr/local/etc/singularity/singularity.conf
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key allow setuid = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key allow pid ns = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key allow user image = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key protected image mode = 'none'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key enable overlay = 'no'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key config passwd = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key config group = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key config resolv_conf = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key mount proc = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key mount sys = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key mount dev = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key mount home = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key mount tmp = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key mount hostfs = 'no'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key bind path = '/etc/hosts'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key user bind control = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key mount slave = 'yes'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key container dir = '/var/lib/singularity/mnt'
VERBOSE [U=0,P=7375]       config_parser.c:176:singularity_config_parse(): Got config key singularity user = 'singularity'
DEBUG   [U=0,P=7375]       config_parser.c:184:singularity_config_parse(): Finished parsing configuration file '/usr/local/etc/singularity/singularity.conf'
DEBUG   [U=0,P=7375]       privilege.c:73:singularity_priv_init()     : Called singularity_priv_init(void)
VERBOSE [U=0,P=7375]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_TARGET_UID'
DEBUG   [U=0,P=7375]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_TARGET_UID
VERBOSE [U=0,P=7375]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_TARGET_UID
VERBOSE [U=0,P=7375]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_TARGET_GID'
DEBUG   [U=0,P=7375]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_TARGET_GID
VERBOSE [U=0,P=7375]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_TARGET_GID
DEBUG   [U=0,P=7375]       privilege.c:138:singularity_priv_init()    : Returning singularity_priv_init(void)
DEBUG   [U=0,P=7375]       simage.c:77:main()                         : Running /usr/local/libexec/singularity/simage bootstrap workflow
DEBUG   [U=0,P=7375]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7375]       bootstrap.c:48:singularity_bootstrap()     : Preparing to bootstrap image with definition file: /tmp/tmpgzd2el0m/Singularity
DEBUG   [U=0,P=7375]       bootstrap.c:51:singularity_bootstrap()     : Opening singularity bootdef file: /tmp/tmpgzd2el0m/Singularity
VERBOSE [U=0,P=7375]       bootdef_parser.c:52:singularity_bootdef_open(): Opening bootstrap definition file: /tmp/tmpgzd2el0m/Singularity
DEBUG   [U=0,P=7375]       bootstrap.c:58:singularity_bootstrap()     : Initializing container directory
DEBUG   [U=0,P=7375]       sessiondir.c:60:singularity_sessiondir_init(): Checking Singularity configuration for 'sessiondir prefix'
DEBUG   [U=0,P=7375]       util/util.c:104:envar_path()               : Checking environment variable is valid path: 'SINGULARITY_SESSIONDIR'
VERBOSE [U=0,P=7375]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_SESSIONDIR'
DEBUG   [U=0,P=7375]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_SESSIONDIR
VERBOSE [U=0,P=7375]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_SESSIONDIR
DEBUG   [U=0,P=7375]       config_parser.c:230:_singularity_config_get_value_impl(): No configuration entry found for 'sessiondir prefix'; returning default value '/tmp/.singularity-session-'
DEBUG   [U=0,P=7375]       sessiondir.c:81:singularity_sessiondir_init(): Set sessiondir to: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=7375]       util/file.c:263:s_mkpath()                 : Creating directory: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=7375]       sessiondir.c:97:singularity_sessiondir_init(): Opening sessiondir file descriptor
DEBUG   [U=0,P=7375]       sessiondir.c:103:singularity_sessiondir_init(): Setting shared flock() on session directory
DEBUG   [U=0,P=7375]       util/util.c:94:envar_defined()             : Checking if environment variable is defined: SINGULARITY_NOSESSIONCLEANUP
VERBOSE [U=0,P=7375]       util/util.c:96:envar_defined()             : Environment variable is undefined: SINGULARITY_NOSESSIONCLEANUP
DEBUG   [U=0,P=7375]       util/util.c:94:envar_defined()             : Checking if environment variable is defined: SINGULARITY_NOCLEANUP
VERBOSE [U=0,P=7375]       util/util.c:96:envar_defined()             : Environment variable is undefined: SINGULARITY_NOCLEANUP
DEBUG   [U=0,P=7375]       fork.c:77:prepare_fork()                   : Creating parent/child coordination pipes.
VERBOSE [U=0,P=7375]       fork.c:153:singularity_fork()              : Forking child process
VERBOSE [U=0,P=7375]       fork.c:171:singularity_fork()              : Hello from parent process
DEBUG   [U=0,P=7375]       fork.c:190:singularity_fork()              : Assigning sigaction()s
DEBUG   [U=0,P=7375]       fork.c:221:singularity_fork()              : Creating generic signal pipes
DEBUG   [U=0,P=7375]       fork.c:229:singularity_fork()              : Creating sigchld signal pipes
DEBUG   [U=0,P=7375]       fork.c:260:singularity_fork()              : Waiting on signal from watchdog
VERBOSE [U=0,P=7376]       fork.c:157:singularity_fork()              : Hello from child process
DEBUG   [U=0,P=7376]       fork.c:160:singularity_fork()              : Closing watchdog write pipe
DEBUG   [U=0,P=7376]       fork.c:167:singularity_fork()              : Child process is returning control to process thread
DEBUG   [U=0,P=7376]       user.c:47:singularity_ns_user_configured() : Checking if user namespaces are configured.
VERBOSE [U=0,P=7376]       user.c:55:singularity_ns_user_configured() : Not virtualizing USER namespace: running as root
VERBOSE [U=0,P=7376]       user.c:87:singularity_ns_user_unshare()    : Skipping USER namespace creation...
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(mount slave, yes)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value mount slave='yes'
DEBUG   [U=0,P=7376]       config_parser.c:303:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(mount slave, yes) = 1
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
DEBUG   [U=0,P=7376]       mnt.c:53:singularity_ns_mnt_unshare()      : Virtualizing FS namespace
DEBUG   [U=0,P=7376]       mnt.c:60:singularity_ns_mnt_unshare()      : Virtualizing mount namespace
DEBUG   [U=0,P=7376]       mnt.c:69:singularity_ns_mnt_unshare()      : Making mounts slave
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       bootstrap.c:64:singularity_bootstrap()     : Mounting container rootfs
DEBUG   [U=0,P=7376]       rootfs.c:71:singularity_rootfs_init()      : Checking on container source type
DEBUG   [U=0,P=7376]       rootfs.c:79:singularity_rootfs_init()      : Figuring out where to mount Singularity container
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value container dir='/var/lib/singularity/mnt'
VERBOSE [U=0,P=7376]       rootfs.c:82:singularity_rootfs_init()      : Set image mount path to: /var/lib/singularity/mnt
DEBUG   [U=0,P=7376]       image.c:77:rootfs_image_init()             : Inializing container rootfs image subsystem
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(allow user image, yes)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value allow user image='yes'
DEBUG   [U=0,P=7376]       config_parser.c:303:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(allow user image, yes) = 1
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value protected image mode='none'
DEBUG   [U=0,P=7376]       image.c:92:rootfs_image_init()             : Protected image mode set to none.
DEBUG   [U=0,P=7376]       util/util.c:94:envar_defined()             : Checking if environment variable is defined: SINGULARITY_WRITABLE
VERBOSE [U=0,P=7376]       util/util.c:99:envar_defined()             : Environment variable is defined: SINGULARITY_WRITABLE
DEBUG   [U=0,P=7376]       util/util.c:94:envar_defined()             : Checking if environment variable is defined: SINGULARITY_NOIMAGELOCK
VERBOSE [U=0,P=7376]       util/util.c:99:envar_defined()             : Environment variable is defined: SINGULARITY_NOIMAGELOCK
DEBUG   [U=0,P=7376]       image.c:114:rootfs_image_init()            : Obtaining exclusive write lock on image
VERBOSE [U=0,P=7376]       image.c:48:singularity_image_check()       : Checking file is a Singularity image
DEBUG   [U=0,P=7376]       image.c:59:singularity_image_check()       : Checking if first line matches key
VERBOSE [U=0,P=7376]       image.c:62:singularity_image_check()       : File is a valid Singularity image
DEBUG   [U=0,P=7376]       rootfs.c:110:singularity_rootfs_mount()    : Checking 'container dir' mount location: /var/lib/singularity/mnt
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       rootfs.c:113:singularity_rootfs_mount()    : Creating container dir: /var/lib/singularity/mnt
DEBUG   [U=0,P=7376]       util/file.c:263:s_mkpath()                 : Creating directory: /var/lib/singularity
DEBUG   [U=0,P=7376]       util/file.c:263:s_mkpath()                 : Creating directory: /var/lib/singularity/mnt
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:121:singularity_rootfs_mount()    : Checking for rootfs_source directory: /var/lib/singularity/mnt/source
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       rootfs.c:124:singularity_rootfs_mount()    : Creating container destination dir: /var/lib/singularity/mnt/source
DEBUG   [U=0,P=7376]       util/file.c:263:s_mkpath()                 : Creating directory: /var/lib/singularity/mnt/source
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:132:singularity_rootfs_mount()    : Checking for overlay_mount directory: /var/lib/singularity/mnt/overlay
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       rootfs.c:135:singularity_rootfs_mount()    : Creating container mount dir: /var/lib/singularity/mnt/overlay
DEBUG   [U=0,P=7376]       util/file.c:263:s_mkpath()                 : Creating directory: /var/lib/singularity/mnt/overlay
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:143:singularity_rootfs_mount()    : Checking for overlay_final directory: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       rootfs.c:146:singularity_rootfs_mount()    : Creating overlay final dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       util/file.c:263:s_mkpath()                 : Creating directory: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       image.c:174:rootfs_image_mount()           : Binding image to loop device
DEBUG   [U=0,P=7376]       sessiondir.c:172:singularity_sessiondir_get(): Returning: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=7376]       loop-control.c:65:singularity_loop_bind_with_offset(): Opening image loop device file: /tmp/.singularity-session-0.2049.271187/image_loop_dev
DEBUG   [U=0,P=7376]       loop-control.c:71:singularity_loop_bind_with_offset(): Requesting exclusive flock() on loop_dev lockfile
DEBUG   [U=0,P=7376]       loop-control.c:95:singularity_loop_bind_with_offset(): Calculating image offset
VERBOSE [U=0,P=7376]       image.c:77:singularity_image_offset()      : Calculating image offset
VERBOSE [U=0,P=7376]       image.c:86:singularity_image_offset()      : Found image at an offset of 31 bytes
DEBUG   [U=0,P=7376]       image.c:91:singularity_image_offset()      : Returning image_offset(image_fp) = 31
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
DEBUG   [U=0,P=7376]       loop-control.c:106:singularity_loop_bind_with_offset(): Finding next available loop device...
VERBOSE [U=0,P=7376]       loop-control.c:138:singularity_loop_bind_with_offset(): Found available loop device: /dev/loop0
DEBUG   [U=0,P=7376]       loop-control.c:140:singularity_loop_bind_with_offset(): Setting loop device flags
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
VERBOSE [U=0,P=7376]       loop-control.c:150:singularity_loop_bind_with_offset(): Using loop device: /dev/loop0
DEBUG   [U=0,P=7376]       loop-control.c:152:singularity_loop_bind_with_offset(): Writing active loop device name (/dev/loop0) to loop file cache: /tmp/.singularity-session-0.2049.271187/image_loop_dev
DEBUG   [U=0,P=7376]       util/file.c:349:fileput()                  : Called fileput(/tmp/.singularity-session-0.2049.271187/image_loop_dev, /dev/loop0)
DEBUG   [U=0,P=7376]       loop-control.c:158:singularity_loop_bind_with_offset(): Resetting exclusive flock() to shared on image_loop_file
DEBUG   [U=0,P=7376]       loop-control.c:161:singularity_loop_bind_with_offset(): Returning singularity_loop_bind(image_fp) = loop_fp
VERBOSE [U=0,P=7376]       image.c:185:rootfs_image_mount()           : Mounting image in read/write
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:174:singularity_rootfs_mount()    : OverlayFS enabled by host build
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(enable overlay, no)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value enable overlay='no'
DEBUG   [U=0,P=7376]       config_parser.c:308:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(enable overlay, no) = 0
VERBOSE [U=0,P=7376]       rootfs.c:176:singularity_rootfs_mount()    : Not enabling overlayFS via configuration
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       rootfs.c:225:singularity_rootfs_mount()    : Binding the ROOTFS_SOURCE to OVERLAY_FINAL (/var/lib/singularity/mnt/source->/var/lib/singularity/mnt/final)
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       bootdef_parser.c:122:singularity_bootdef_get_value(): No bootstrap definition file entry found for 'DistType'
VERBOSE [U=0,P=7376]       bootstrap.c:84:singularity_bootstrap()     : Running bootstrap driver v2
VERBOSE [U=0,P=7376]       bootstrap.c:149:singularity_bootstrap_script_run(): Searching for %pre bootstrap script
VERBOSE [U=0,P=7376]       bootdef_parser.c:193:singularity_bootdef_section_get(): Attempting to find and return script defined by section %pre
VERBOSE [U=0,P=7376]       bootdef_parser.c:152:singularity_bootdef_section_find(): Searching for section %pre
VERBOSE [U=0,P=7376]       bootdef_parser.c:68:singularity_bootdef_rewind(): Rewinding bootstrap definition file
DEBUG   [U=0,P=7376]       bootdef_parser.c:161:singularity_bootdef_section_find(): Scanning file for start of %pre section
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: BootStrap to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: OSVersion to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: MirrorURL to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: #MirrorURL to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: runscript to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: /bin/bash to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: post to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: sed to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: wget to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: bash to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: curl to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: npm to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: rm to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: mkdir to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: pre
DEBUG   [U=0,P=7376]       bootdef_parser.c:175:singularity_bootdef_section_find(): Unable to find %pre section
DEBUG   [U=0,P=7376]       bootdef_parser.c:195:singularity_bootdef_section_get(): Unable to find section: %pre in bootstrap definition file
VERBOSE [U=0,P=7376]       bootstrap.c:151:singularity_bootstrap_script_run(): No %pre bootstrap script found, skipping
VERBOSE [U=0,P=7376]       bootdef_parser.c:68:singularity_bootdef_rewind(): Rewinding bootstrap definition file
VERBOSE [U=0,P=7376]       bootdef_parser.c:114:singularity_bootdef_get_value(): Got bootstrap definition key BootStrap(: 'debootstrap')
VERBOSE [U=0,P=7376]       bootstrap.c:186:bootstrap_module_init()    : Running bootstrap module debootstrap
DEBUG   [U=0,P=7376]       fork.c:77:prepare_fork()                   : Creating parent/child coordination pipes.
VERBOSE [U=0,P=7376]       fork.c:153:singularity_fork()              : Forking child process
VERBOSE [U=0,P=7376]       fork.c:171:singularity_fork()              : Hello from parent process
DEBUG   [U=0,P=7376]       fork.c:190:singularity_fork()              : Assigning sigaction()s
DEBUG   [U=0,P=7376]       fork.c:221:singularity_fork()              : Creating generic signal pipes
DEBUG   [U=0,P=7376]       fork.c:229:singularity_fork()              : Creating sigchld signal pipes
DEBUG   [U=0,P=7376]       fork.c:260:singularity_fork()              : Waiting on signal from watchdog
VERBOSE [U=0,P=7382]       fork.c:157:singularity_fork()              : Hello from child process
DEBUG   [U=0,P=7382]       fork.c:160:singularity_fork()              : Closing watchdog write pipe
DEBUG   [U=0,P=7382]       fork.c:167:singularity_fork()              : Child process is returning control to process thread
DEBUG   [U=0,P=7376]       fork.c:287:singularity_fork()              : Parent process is exiting
DEBUG   [U=0,P=7376]       fork.c:328:singularity_fork_exec()         : Waiting on child process
DEBUG   [U=0,P=7376]       rootfs.c:238:singularity_rootfs_check()    : Checking if container has /bin/sh...
DEBUG   [U=0,P=7376]       util/file.c:295:copy_file()                : Called copy_file(/etc/hosts, /var/lib/singularity/mnt/final/etc/hosts)
DEBUG   [U=0,P=7376]       util/file.c:302:copy_file()                : Opening source file: /etc/hosts
DEBUG   [U=0,P=7376]       util/file.c:308:copy_file()                : Opening destination file: /var/lib/singularity/mnt/final/etc/hosts
DEBUG   [U=0,P=7376]       util/file.c:315:copy_file()                : Calling fstat() on source file descriptor: 12
DEBUG   [U=0,P=7376]       util/file.c:323:copy_file()                : Cloning permission string of source to dest
DEBUG   [U=0,P=7376]       util/file.c:331:copy_file()                : Copying file data...
DEBUG   [U=0,P=7376]       util/file.c:336:copy_file()                : Done copying data, closing file pointers
DEBUG   [U=0,P=7376]       util/file.c:340:copy_file()                : Returning copy_file(/etc/hosts, /var/lib/singularity/mnt/final/etc/hosts) = 0
DEBUG   [U=0,P=7376]       util/file.c:295:copy_file()                : Called copy_file(/etc/resolv.conf, /var/lib/singularity/mnt/final/etc/resolv.conf)
DEBUG   [U=0,P=7376]       util/file.c:302:copy_file()                : Opening source file: /etc/resolv.conf
DEBUG   [U=0,P=7376]       util/file.c:308:copy_file()                : Opening destination file: /var/lib/singularity/mnt/final/etc/resolv.conf
DEBUG   [U=0,P=7376]       util/file.c:315:copy_file()                : Calling fstat() on source file descriptor: 12
DEBUG   [U=0,P=7376]       util/file.c:323:copy_file()                : Cloning permission string of source to dest
DEBUG   [U=0,P=7376]       util/file.c:331:copy_file()                : Copying file data...
DEBUG   [U=0,P=7376]       util/file.c:336:copy_file()                : Done copying data, closing file pointers
DEBUG   [U=0,P=7376]       util/file.c:340:copy_file()                : Returning copy_file(/etc/resolv.conf, /var/lib/singularity/mnt/final/etc/resolv.conf) = 0
DEBUG   [U=0,P=7376]       util/file.c:349:fileput()                  : Called fileput(/var/lib/singularity/mnt/final/etc/mtab, singularity / rootfs rw 0 0)
VERBOSE [U=0,P=7376]       bootstrap.c:241:bootstrap_copy_script()    : Attempting to copy %runscript script into /singularity in container.
VERBOSE [U=0,P=7376]       bootdef_parser.c:193:singularity_bootdef_section_get(): Attempting to find and return script defined by section %runscript
VERBOSE [U=0,P=7376]       bootdef_parser.c:152:singularity_bootdef_section_find(): Searching for section %runscript
VERBOSE [U=0,P=7376]       bootdef_parser.c:68:singularity_bootdef_rewind(): Rewinding bootstrap definition file
DEBUG   [U=0,P=7376]       bootdef_parser.c:161:singularity_bootdef_section_find(): Scanning file for start of %runscript section
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: BootStrap to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: OSVersion to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: MirrorURL to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: #MirrorURL to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: runscript to section name: runscript
DEBUG   [U=0,P=7376]       bootdef_parser.c:169:singularity_bootdef_section_find(): Found %runscript section, returning 0.
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     echo "Welcome to the NeuroDebian v 2.2 (Debian stretch) environment"
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Welcome to the NeuroDebian v 2.2 (Debian stretch) environment"
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     echo "Please source /etc/fsl/fsl.sh if you need FSL, /etc/afni/afni.sh if you need AFNI"
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Welcome to the NeuroDebian v 2.2 (Debian stretch) environment"
echo "Please source /etc/fsl/fsl.sh if you need FSL, /etc/afni/afni.sh if you need AFNI"
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     /bin/bash
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Welcome to the NeuroDebian v 2.2 (Debian stretch) environment"
echo "Please source /etc/fsl/fsl.sh if you need FSL, /etc/afni/afni.sh if you need AFNI"
/bin/bash
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line: 
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Welcome to the NeuroDebian v 2.2 (Debian stretch) environment"
echo "Please source /etc/fsl/fsl.sh if you need FSL, /etc/afni/afni.sh if you need AFNI"
/bin/bash

DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line: %post
DEBUG   [U=0,P=7376]       util/file.c:349:fileput()                  : Called fileput(/var/lib/singularity/mnt/final/singularity, 
echo "Welcome to the NeuroDebian v 2.2 (Debian stretch) environment"
echo "Please source /etc/fsl/fsl.sh if you need FSL, /etc/afni/afni.sh if you need AFNI"
/bin/bash
)
VERBOSE [U=0,P=7376]       bootstrap.c:241:bootstrap_copy_script()    : Attempting to copy %test script into /.test in container.
VERBOSE [U=0,P=7376]       bootdef_parser.c:193:singularity_bootdef_section_get(): Attempting to find and return script defined by section %test
VERBOSE [U=0,P=7376]       bootdef_parser.c:152:singularity_bootdef_section_find(): Searching for section %test
VERBOSE [U=0,P=7376]       bootdef_parser.c:68:singularity_bootdef_rewind(): Rewinding bootstrap definition file
DEBUG   [U=0,P=7376]       bootdef_parser.c:161:singularity_bootdef_section_find(): Scanning file for start of %test section
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: BootStrap to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: OSVersion to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: MirrorURL to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: #MirrorURL to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: runscript to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: /bin/bash to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: post to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: sed to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: wget to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: bash to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: curl to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: npm to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: rm to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: mkdir to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: test
DEBUG   [U=0,P=7376]       bootdef_parser.c:175:singularity_bootdef_section_find(): Unable to find %test section
DEBUG   [U=0,P=7376]       bootdef_parser.c:195:singularity_bootdef_section_get(): Unable to find section: %test in bootstrap definition file
VERBOSE [U=0,P=7376]       bootstrap.c:244:bootstrap_copy_script()    : Definition file does not contain test, skipping.
VERBOSE [U=0,P=7376]       bootstrap.c:241:bootstrap_copy_script()    : Attempting to copy %environment script into /environment in container.
VERBOSE [U=0,P=7376]       bootdef_parser.c:193:singularity_bootdef_section_get(): Attempting to find and return script defined by section %environment
VERBOSE [U=0,P=7376]       bootdef_parser.c:152:singularity_bootdef_section_find(): Searching for section %environment
VERBOSE [U=0,P=7376]       bootdef_parser.c:68:singularity_bootdef_rewind(): Rewinding bootstrap definition file
DEBUG   [U=0,P=7376]       bootdef_parser.c:161:singularity_bootdef_section_find(): Scanning file for start of %environment section
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: BootStrap to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: OSVersion to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: MirrorURL to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: #MirrorURL to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: runscript to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: /bin/bash to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: post to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: sed to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: wget to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: bash to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: curl to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: npm to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: rm to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: mkdir to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: environment
DEBUG   [U=0,P=7376]       bootdef_parser.c:175:singularity_bootdef_section_find(): Unable to find %environment section
DEBUG   [U=0,P=7376]       bootdef_parser.c:195:singularity_bootdef_section_get(): Unable to find section: %environment in bootstrap definition file
VERBOSE [U=0,P=7376]       bootstrap.c:244:bootstrap_copy_script()    : Definition file does not contain environment, skipping.
VERBOSE [U=0,P=7376]       bootstrap.c:108:singularity_bootstrap()    : Copying default environment file instead of user specified environment
DEBUG   [U=0,P=7376]       util/file.c:295:copy_file()                : Called copy_file(/usr/local/libexec/singularity/defaults/environment, /var/lib/singularity/mnt/final/environment)
DEBUG   [U=0,P=7376]       util/file.c:302:copy_file()                : Opening source file: /usr/local/libexec/singularity/defaults/environment
DEBUG   [U=0,P=7376]       util/file.c:308:copy_file()                : Opening destination file: /var/lib/singularity/mnt/final/environment
DEBUG   [U=0,P=7376]       util/file.c:315:copy_file()                : Calling fstat() on source file descriptor: 12
DEBUG   [U=0,P=7376]       util/file.c:323:copy_file()                : Cloning permission string of source to dest
DEBUG   [U=0,P=7376]       util/file.c:331:copy_file()                : Copying file data...
DEBUG   [U=0,P=7376]       util/file.c:336:copy_file()                : Done copying data, closing file pointers
DEBUG   [U=0,P=7376]       util/file.c:340:copy_file()                : Returning copy_file(/usr/local/libexec/singularity/defaults/environment, /var/lib/singularity/mnt/final/environment) = 0
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       sessiondir.c:172:singularity_sessiondir_get(): Returning: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=7376]       passwd.c:54:singularity_file_passwd()      : Called singularity_file_passwd_create()
VERBOSE [U=0,P=7376]       passwd.c:57:singularity_file_passwd()      : Not updating passwd file, running as root!
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       sessiondir.c:172:singularity_sessiondir_get(): Returning: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=7376]       group.c:56:singularity_file_group()        : Called singularity_file_group_create()
VERBOSE [U=0,P=7376]       group.c:59:singularity_file_group()        : Not updating group file, running as root!
DEBUG   [U=0,P=7376]       resolvconf.c:47:singularity_file_resolvconf(): Checking configuration option
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(config resolv_conf, yes)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value config resolv_conf='yes'
DEBUG   [U=0,P=7376]       config_parser.c:303:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(config resolv_conf, yes) = 1
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       file-bind.c:41:container_file_bind()       : Called file_bind(/etc/resolv.conf, /etc/resolv.conf()
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       file-bind.c:61:container_file_bind()       : Binding file '/etc/resolv.conf' to '/var/lib/singularity/mnt/final/etc/resolv.conf'
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       entrypoint.c:38:singularity_file_entrypoint(): Copying entrypoint file: run
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       util/file.c:368:filecat()                  : Called filecat(/usr/local/libexec/singularity/defaults/run)
DEBUG   [U=0,P=7376]       util/file.c:349:fileput()                  : Called fileput(/var/lib/singularity/mnt/final/.run, #!/bin/sh
. /environment
if test -x /singularity; then
    exec /singularity "$@"
else
    echo "No Singularity runscript found, executing /bin/sh"
    exec /bin/sh "$@"
fi)
DEBUG   [U=0,P=7376]       entrypoint.c:38:singularity_file_entrypoint(): Copying entrypoint file: exec
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       util/file.c:368:filecat()                  : Called filecat(/usr/local/libexec/singularity/defaults/exec)
DEBUG   [U=0,P=7376]       util/file.c:349:fileput()                  : Called fileput(/var/lib/singularity/mnt/final/.exec, #!/bin/sh
. /environment
exec "$@")
DEBUG   [U=0,P=7376]       entrypoint.c:38:singularity_file_entrypoint(): Copying entrypoint file: shell
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       util/file.c:368:filecat()                  : Called filecat(/usr/local/libexec/singularity/defaults/shell)
DEBUG   [U=0,P=7376]       util/file.c:349:fileput()                  : Called fileput(/var/lib/singularity/mnt/final/.shell, #!/bin/sh
. /environment
if test -n "$SHELL" -a -x "$SHELL"; then
    exec "$SHELL" "$@"
else
    echo "ERROR: Shell does not exist in container: $SHELL" 1>&2
    echo "ERROR: Using /bin/sh instead..." 1>&2
fi
if test -x /bin/sh; then
    SHELL=/bin/sh
    export SHELL
    exec /bin/sh "$@"
else
    echo "ERROR: /bin/sh does not exist in container" 1>&2
fi
exit 1)
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(mount hostfs, no)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value mount hostfs='no'
DEBUG   [U=0,P=7376]       config_parser.c:308:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(mount hostfs, no) = 0
DEBUG   [U=0,P=7376]       hostfs.c:52:singularity_mount_hostfs()     : Not mounting host file systems per configuration
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       util/util.c:94:envar_defined()             : Checking if environment variable is defined: SINGULARITY_CONTAIN
VERBOSE [U=0,P=7376]       util/util.c:96:envar_defined()             : Environment variable is undefined: SINGULARITY_CONTAIN
DEBUG   [U=0,P=7376]       binds.c:48:singularity_mount_binds()       : Checking configuration file for 'bind path'
VERBOSE [U=0,P=7376]       binds.c:62:singularity_mount_binds()       : Found 'bind path' = /etc/hosts, /etc/hosts
DEBUG   [U=0,P=7376]       binds.c:69:singularity_mount_binds()       : Checking if bind point is already mounted: /etc/hosts
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       mount-util.c:42:check_mounted()            : Opening /proc/mounts
DEBUG   [U=0,P=7376]       mount-util.c:48:check_mounted()            : Iterating through /proc/mounts
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       binds.c:111:singularity_mount_binds()      : Binding '/etc/hosts' to '/var/lib/singularity/mnt/final//etc/hosts'
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       kernelfs.c:43:singularity_mount_kernelfs() : Checking configuration file for 'mount proc'
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(mount proc, yes)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value mount proc='yes'
DEBUG   [U=0,P=7376]       config_parser.c:303:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(mount proc, yes) = 1
DEBUG   [U=0,P=7376]       pid.c:46:singularity_ns_pid_enabled()      : Checking PID namespace enabled: -1
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       kernelfs.c:56:singularity_mount_kernelfs() : Bind mounting /proc
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       kernelfs.c:78:singularity_mount_kernelfs() : Checking configuration file for 'mount sys'
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(mount sys, yes)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value mount sys='yes'
DEBUG   [U=0,P=7376]       config_parser.c:303:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(mount sys, yes) = 1
DEBUG   [U=0,P=7376]       user.c:76:singularity_ns_user_enabled()    : User namespaces have not been activated.
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       kernelfs.c:83:singularity_mount_kernelfs() : Mounting /sys
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value mount dev='yes'
DEBUG   [U=0,P=7376]       dev.c:102:singularity_mount_dev()          : Checking configuration file for 'mount dev'
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(mount dev, yes)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value mount dev='yes'
DEBUG   [U=0,P=7376]       config_parser.c:303:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(mount dev, yes) = 1
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       dev.c:106:singularity_mount_dev()          : Bind mounting /dev
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(mount tmp, yes)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value mount tmp='yes'
DEBUG   [U=0,P=7376]       config_parser.c:303:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(mount tmp, yes) = 1
DEBUG   [U=0,P=7376]       util/util.c:94:envar_defined()             : Checking if environment variable is defined: SINGULARITY_CONTAIN
VERBOSE [U=0,P=7376]       util/util.c:96:envar_defined()             : Environment variable is undefined: SINGULARITY_CONTAIN
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       tmp.c:78:singularity_mount_tmp()           : Mounting directory: /tmp
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       tmp.c:104:singularity_mount_tmp()          : Mounting directory: /var/tmp
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       sessiondir.c:172:singularity_sessiondir_get(): Returning: /tmp/.singularity-session-0.2049.271187
DEBUG   [U=0,P=7376]       config_parser.c:297:_singularity_config_get_bool_char_impl(: Called singularity_config_get_bool(mount home, yes)
DEBUG   [U=0,P=7376]       config_parser.c:242:_singularity_config_get_value_impl(): Returning configuration value mount home='yes'
DEBUG   [U=0,P=7376]       config_parser.c:303:_singularity_config_get_bool_char_impl(: Return singularity_config_get_bool(mount home, yes) = 1
DEBUG   [U=0,P=7376]       home.c:53:singularity_mount_home()         : Obtaining user's homedir
DEBUG   [U=0,P=7376]       util/util.c:104:envar_path()               : Checking environment variable is valid path: 'SINGULARITY_HOME'
VERBOSE [U=0,P=7376]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_HOME'
DEBUG   [U=0,P=7376]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_HOME
VERBOSE [U=0,P=7376]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_HOME
VERBOSE [U=0,P=7376]       util/util.c:297:get_homedir()              : Set the home directory (via getpwuid) to: /root
DEBUG   [U=0,P=7376]       util/util.c:104:envar_path()               : Checking environment variable is valid path: 'SINGULARITY_HOME'
VERBOSE [U=0,P=7376]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_HOME'
DEBUG   [U=0,P=7376]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_HOME
VERBOSE [U=0,P=7376]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_HOME
DEBUG   [U=0,P=7376]       util/util.c:94:envar_defined()             : Checking if environment variable is defined: SINGULARITY_CONTAIN
VERBOSE [U=0,P=7376]       util/util.c:96:envar_defined()             : Environment variable is undefined: SINGULARITY_CONTAIN
VERBOSE [U=0,P=7376]       home.c:100:singularity_mount_home()        : Set base the home directory source to: /root
DEBUG   [U=0,P=7376]       home.c:106:singularity_mount_home()        : Checking if home directory is already mounted: /root
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       mount-util.c:42:check_mounted()            : Opening /proc/mounts
DEBUG   [U=0,P=7376]       mount-util.c:48:check_mounted()            : Iterating through /proc/mounts
DEBUG   [U=0,P=7376]       util/file.c:263:s_mkpath()                 : Creating directory: /tmp/.singularity-session-0.2049.271187/root
DEBUG   [U=0,P=7376]       home.c:123:singularity_mount_home()        : Checking permissions on home directory: /root
DEBUG   [U=0,P=7376]       home.c:130:singularity_mount_home()        : Trying to create home dir within container
DEBUG   [U=0,P=7376]       rootfs.c:59:singularity_rootfs_overlay_enabled(): Returning singularity_rootfs_overlay: 0
DEBUG   [U=0,P=7376]       util/file.c:409:basedir()                  : Obtaining basedir for: /root
DEBUG   [U=0,P=7376]       util/file.c:412:basedir()                  : Iterating basedir: /root
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       home.c:154:singularity_mount_home()        : Mounting home directory to stage: /root->/tmp/.singularity-session-0.2049.271187/root
VERBOSE [U=0,P=7376]       home.c:166:singularity_mount_home()        : Mounting staged home directory into container: /tmp/.singularity-session-0.2049.271187/root->/var/lib/singularity/mnt/final/root
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       userbinds.c:45:singularity_mount_userbinds(): Checking for environment variable 'SINGULARITY_BINDPATH'
DEBUG   [U=0,P=7376]       util/util.c:104:envar_path()               : Checking environment variable is valid path: 'SINGULARITY_BINDPATH'
VERBOSE [U=0,P=7376]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_BINDPATH'
DEBUG   [U=0,P=7376]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_BINDPATH
VERBOSE [U=0,P=7376]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_BINDPATH
DEBUG   [U=0,P=7376]       userbinds.c:154:singularity_mount_userbinds(): No user bind mounts specified.
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       scratch.c:53:singularity_mount_scratch()   : Getting SINGULARITY_SCRATCHDIR from environment
DEBUG   [U=0,P=7376]       util/util.c:104:envar_path()               : Checking environment variable is valid path: 'SINGULARITY_SCRATCHDIR'
VERBOSE [U=0,P=7376]       util/util.c:52:envar()                     : Checking input from environment: 'SINGULARITY_SCRATCHDIR'
DEBUG   [U=0,P=7376]       util/util.c:54:envar()                     : Checking environment variable is defined: SINGULARITY_SCRATCHDIR
VERBOSE [U=0,P=7376]       util/util.c:56:envar()                     : Environment variable is NULL: SINGULARITY_SCRATCHDIR
DEBUG   [U=0,P=7376]       scratch.c:55:singularity_mount_scratch()   : Not mounting scratch directory: Not requested
DEBUG   [U=0,P=7376]       rootfs.c:64:singularity_rootfs_dir()       : Returning singularity_rootfs_dir: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       cwd.c:51:singularity_mount_cwd()           : Checking to see if we should mount current working directory
DEBUG   [U=0,P=7376]       cwd.c:53:singularity_mount_cwd()           : Getting current working directory
DEBUG   [U=0,P=7376]       cwd.c:60:singularity_mount_cwd()           : Checking if current directory exists in container
DEBUG   [U=0,P=7376]       util/file.c:68:file_devino()               : Called file_devino(/tmp/tmpgzd2el0m)
DEBUG   [U=0,P=7376]       util/file.c:78:file_devino()               : Returning file_devino(/tmp/tmpgzd2el0m) = 2049.271074
DEBUG   [U=0,P=7376]       util/file.c:68:file_devino()               : Called file_devino(/var/lib/singularity/mnt/final/tmp/tmpgzd2el0m)
DEBUG   [U=0,P=7376]       util/file.c:78:file_devino()               : Returning file_devino(/var/lib/singularity/mnt/final/tmp/tmpgzd2el0m) = 2049.271074
DEBUG   [U=0,P=7376]       cwd.c:65:singularity_mount_cwd()           : Checking if container's cwd == host's cwd
VERBOSE [U=0,P=7376]       cwd.c:67:singularity_mount_cwd()           : Not mounting current directory: location already available within container
VERBOSE [U=0,P=7376]       bootstrap.c:149:singularity_bootstrap_script_run(): Searching for %setup bootstrap script
VERBOSE [U=0,P=7376]       bootdef_parser.c:193:singularity_bootdef_section_get(): Attempting to find and return script defined by section %setup
VERBOSE [U=0,P=7376]       bootdef_parser.c:152:singularity_bootdef_section_find(): Searching for section %setup
VERBOSE [U=0,P=7376]       bootdef_parser.c:68:singularity_bootdef_rewind(): Rewinding bootstrap definition file
DEBUG   [U=0,P=7376]       bootdef_parser.c:161:singularity_bootdef_section_find(): Scanning file for start of %setup section
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: BootStrap to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: OSVersion to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: MirrorURL to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: #MirrorURL to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: runscript to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: /bin/bash to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: post to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: sed to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: wget to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: bash to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: curl to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: eatmydata to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: npm to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: rm to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: apt-get to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: mkdir to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: chmod to section name: setup
DEBUG   [U=0,P=7376]       bootdef_parser.c:175:singularity_bootdef_section_find(): Unable to find %setup section
DEBUG   [U=0,P=7376]       bootdef_parser.c:195:singularity_bootdef_section_get(): Unable to find section: %setup in bootstrap definition file
VERBOSE [U=0,P=7376]       bootstrap.c:151:singularity_bootstrap_script_run(): No %setup bootstrap script found, skipping
DEBUG   [U=0,P=7376]       privilege.c:154:singularity_priv_escalate(): Running as root, not changing privileges
VERBOSE [U=0,P=7376]       rootfs.c:251:singularity_rootfs_chroot()   : Entering container file system root: /var/lib/singularity/mnt/final
DEBUG   [U=0,P=7376]       privilege.c:257:singularity_priv_drop()    : Running as root, not changing privileges
DEBUG   [U=0,P=7376]       rootfs.c:258:singularity_rootfs_chroot()   : Changing dir to '/' within the new root
VERBOSE [U=0,P=7376]       bootstrap.c:149:singularity_bootstrap_script_run(): Searching for %post bootstrap script
VERBOSE [U=0,P=7376]       bootdef_parser.c:193:singularity_bootdef_section_get(): Attempting to find and return script defined by section %post
VERBOSE [U=0,P=7376]       bootdef_parser.c:152:singularity_bootdef_section_find(): Searching for section %post
VERBOSE [U=0,P=7376]       bootdef_parser.c:68:singularity_bootdef_rewind(): Rewinding bootstrap definition file
DEBUG   [U=0,P=7376]       bootdef_parser.c:161:singularity_bootdef_section_find(): Scanning file for start of %post section
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: BootStrap to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: OSVersion to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: MirrorURL to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: #MirrorURL to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: # to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: runscript to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: echo to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: /bin/bash to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:166:singularity_bootdef_section_find(): Comparing token: post to section name: post
DEBUG   [U=0,P=7376]       bootdef_parser.c:169:singularity_bootdef_section_find(): Found %post section, returning 0.
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     echo "Configuring the environment"
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # For build-dep
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     apt-get update
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     apt-get -y install eatmydata 
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # eatmydata apt-get -y build-dep git
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13/tools/nd-configurerepo
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     bash /tmp/nd-configurerepo
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     chmod a+r -R /etc/apt
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     eatmydata apt-get -y install git git-annex-standalone datalad python-nipype virtualenv dcm2niix python-dcmstack python-configparser python-funcsigs python-pytest connectome-workbench python-mvpa2 python-nilearn fsl-core fsl-atlases fsl-first-data mricron afni fsleyes ants convert3d heudiconv
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line: 
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # for bids-validator
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     curl -sL https://deb.nodesource.com/setup_6.x | bash - && \
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:        eatmydata apt-get install -y nodejs
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     npm install -g bids-validator@0.22.0
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     chmod a+rX -R /usr/lib/node_modules/
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line: 
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     chmod a+rX -R /etc/apt/sources.list.d
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     rm -rf /tmp/* /var/tmp/*
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     apt-get clean
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line: 
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # and wipe out apt lists since not to be used RW for further tuning
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # find /var/lib/apt/lists/ -type f -delete
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # /usr/bin/find /var/lib/apt/lists/ -type f -name \*Packages\* -o -name \*Contents\*
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # complicates later interrogation - thus disabled
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line: 
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # Create some additional bind mount directories present on various compute boxes we have
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     # access to, to ease deployment
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     mkdir -p /afs /inbox /ihome /opt /data /backup /apps /srv /scratch
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)DEBUG   [U=0,P=7376]       bootdef_parser.c:202:singularity_bootdef_section_get(): Reading line:     chmod a+rX /afs /inbox /ihome /opt /data /backup /apps /srv /scratch
DEBUG   [U=0,P=7376]       bootdef_parser.c:208:singularity_bootdef_section_get(): script: 
echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13(TRUNCATED...)VERBOSE [U=0,P=7376]       bootstrap.c:158:singularity_bootstrap_script_run(): Running %post bootstrap script
/bin/sh-c

echo "Configuring the environment"
sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
# For build-dep
# sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
apt-get update
apt-get -y install eatmydata 
eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
# eatmydata apt-get -y build-dep git
wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f(TRUNCATED...)DEBUG   [U=0,P=7376]       fork.c:77:prepare_fork()                   : Creating parent/child coordination pipes.
VERBOSE [U=0,P=7376]       fork.c:153:singularity_fork()              : Forking child process
VERBOSE [U=0,P=7376]       fork.c:171:singularity_fork()              : Hello from parent process
DEBUG   [U=0,P=7376]       fork.c:190:singularity_fork()              : Assigning sigaction()s
DEBUG   [U=0,P=7376]       fork.c:221:singularity_fork()              : Creating generic signal pipes
DEBUG   [U=0,P=7376]       fork.c:229:singularity_fork()              : Creating sigchld signal pipes
DEBUG   [U=0,P=7376]       fork.c:260:singularity_fork()              : Waiting on signal from watchdog
VERBOSE [U=0,P=19581]      fork.c:157:singularity_fork()              : Hello from child process
DEBUG   [U=0,P=19581]      fork.c:160:singularity_fork()              : Closing watchdog write pipe
DEBUG   [U=0,P=19581]      fork.c:167:singularity_fork()              : Child process is returning control to process thread
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
debconf: delaying package configuration, since apt-utils is not installed
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
debconf: delaying package configuration, since apt-utils is not installed
I: Command netselect (from package netselect) is N/A.
I: Use with --install to get all necessary packages installed automatically
I: netselect (apt-get install netselect) needed to select the 'best' mirror was not found
I: Selecting the default repository: http://neuro.debian.net/debian
I: Generating /etc/apt/sources.list.d/neurodebian.sources.list
I: Fetching the key from the server
I: Updating APT listings, might take a few minutes
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
debconf: delaying package configuration, since apt-utils is not installed

and then it just stops. There doesn't seem to be any activity:

here is disk usage:

vanessa@shub-builder-1091819-2413:~$ df
Filesystem     1K-blocks     Used Available Use% Mounted on
udev             1887156        0   1887156   0% /dev
tmpfs             378872     5352    373520   2% /run
/dev/sda1       50758760 14302332  36440044  29% /
tmpfs            1894344        0   1894344   0% /dev/shm
tmpfs               5120        0      5120   0% /run/lock
tmpfs            1894344        0   1894344   0% /sys/fs/cgroup
tmpfs             378872        0    378872   0% /run/user/100

there seems to be an image... but it's doing something?

vanessa@shub-builder-1091819-2413:~$ sudo singularity shell /tmp/tmpgzd2el0m/image
ERROR  : Failed to mount image in (read only): Device or resource busy
ABORT  : Retval = 255
vanessa@shub-builder-1091819-2413:~$ 

I'm glad that at least for this case we have an instance to help debug! What should we look at or try next? Have you tried this build with a (non 2.2) older version?

[yarikoptic]

I thought we are all using singularity 2.3.1 everywhere now, so not sure about 2.2 questions

that "Device or resource busy" -- may be related to https://github.com/singularityware/singularity/issues/471 ?

re stuck one -- when I run locally, I am getting a bit more verbose output (I wonder why you don't have those outputs from having 'set -x' which I though singularity ? sets): http://www.onerussian.com/tmp/neurodebian-v2.2-test.img.log After the last line you have it indeed should through many installations of the packages which takes time, but shouldn't be that long.

It could be that some debconf dialog (e.g. to configure popularity contest) pops up for some reason (I think having DEBIAN_FRONTEND=noninteractive should have avoided it and it is set in libexec/bootstrap-scripts/deffile-sections.sh in 2.3.1 but I remember it some times still getting into my way on older debian releases)

[vsoch]

If you want to change the builder to 2.3.1, it's up to you the collection owner to do so! maybe try that? it's a setting under the collection builder settings

[yarikoptic]

Ah I didn't realize it was configurable and expected the most recent and greatest to be used, at least by default. I will give it a shot

[vsoch]

sounds good! I would also change it to specify the larger of the two instances. Let me know if/when it's hanging and I'll go in to investigate.

[yarikoptic]

@vsoch would you be so kind to check current logs for the https://singularity-hub.org/collections/67/ which is Running since yesterday I believe. probably stuck again -- would need to figure out why

[vsoch]

ah I think the bug is revealed! There is something in your build process that is cleaning up tmp. The problem is that /tmp is where the image is being built, and where the repo is cloned, etc, so when you delete it you stop everything. The offending line is here andere is the log in full:

Environment message level found to be DEBUG
INFO:shub_builder:Singularity 2.3-master.gf737013 being used.
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/dobuild HTTP/1.1" 200 4
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/debug HTTP/1.1" 200 7
INFO:shub_builder:DEBUG True
WARNING:shub_builder:Build directory not set, using /tmp/tmpfcuqaxvu
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/repo_url HTTP/1.1" 200 46
INFO:shub_builder:repo_url is set to https://www.github.com/neurodebian/neurodebian
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/repo_id HTTP/1.1" 200 7
INFO:shub_builder:repo_id is set to 1091819
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/response_url HTTP/1.1" 200 54
INFO:shub_builder:response_url is set to https://singularity-hub.org/hooks/build/google/receive
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/bucket_name HTTP/1.1" 200 24
INFO:shub_builder:bucket_name is set to singularity-hub-regional
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/token HTTP/1.1" 200 36
INFO:shub_builder:token is set to 0bd3e4e2-9f6a-456c-a510-62189cb69ba7
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/commit HTTP/1.1" 200 40
INFO:shub_builder:commit is set to 3de1c0b1fee8c242370540cbceb029cb8ed8da3d
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/secret HTTP/1.1" 200 36
INFO:shub_builder:secret is set to ffe72bf5-31fe-43bb-baf4-07ec150e71f8
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/size HTTP/1.1" 200 5
INFO:shub_builder:size is set to 12000
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/branch HTTP/1.1" 200 6
INFO:shub_builder:branch is set to master
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/spec_file HTTP/1.1" 200 11
INFO:shub_builder:spec_file is set to Singularity
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/padding HTTP/1.1" 200 3
INFO:shub_builder:padding is set to 200
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/logging_url HTTP/1.1" 200 53
INFO:shub_builder:logging_url is set to https://singularity-hub.org/hooks/build/google/finish
DEBUG:urllib3.connectionpool:Starting new HTTP connection (1): metadata.google.internal
DEBUG:urllib3.connectionpool:http://metadata.google.internal:80 "GET /computeMetadata/v1/instance/attributes/logfile HTTP/1.1" 200 14
INFO:shub_builder:logfile is set to /tmp/.shub-log
Cloning into '/tmp/tmpfcuqaxvu'...
INFO:shub_builder:Checking out branch master
Already on 'master'
Your branch is up-to-date with 'origin/master'.
INFO:shub_builder:Checking out commit 3de1c0b1fee8c242370540cbceb029cb8ed8da3d
INFO:shub_builder:Found spec file Singularity in repository
DEBUG:shub_builder:Building in directory /tmp/tmpfcuqaxvu
DEBUG:shub_builder:Spec file set to Singularity
DEBUG:shub_builder:Spec file for build should be in /tmp/tmpfcuqaxvu/Singularity
Enabling debugging
Ending argument loop
Singularity version: 2.3-master.gf737013
Exec'ing: /usr/local/libexec/singularity/cli/create.exec
VERBOSE [U=0,P=2529]       message_init()                            Set messagelevel to: 5
VERBOSE [U=0,P=2529]       singularity_config_parse()                Initialize configuration file: /usr/local/etc/singularity/singularity.conf
DEBUG   [U=0,P=2529]       singularity_config_parse()                Starting parse of configuration file /usr/local/etc/singularity/singularity.conf
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key allow setuid = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key max loop devices = '256'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key allow pid ns = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key config passwd = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key config group = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key config resolv_conf = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key mount proc = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key mount sys = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key mount dev = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key mount home = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key mount tmp = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key mount hostfs = 'no'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key bind path = '/etc/localtime'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key bind path = '/etc/hosts'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key user bind control = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key enable overlay = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key mount slave = 'yes'
VERBOSE [U=0,P=2529]       singularity_config_parse()                Got config key sessiondir max size = '16'
DEBUG   [U=0,P=2529]       singularity_config_parse()                Finished parsing configuration file '/usr/local/etc/singularity/singularity.conf'
VERBOSE [U=0,P=2529]       singularity_registry_init()               Initializing Singularity Registry
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'WRITABLE' = '1'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(WRITABLE, 1) = 0
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'LIBEXECDIR' = '/usr/local/libexec'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(libexecdir, /usr/local/libexec) = 0
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'COMMAND' = 'create'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(COMMAND, create) = 0
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'IMAGESIZE' = '12000'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(IMAGESIZE, 12000) = 0
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'MESSAGELEVEL' = '5'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(MESSAGELEVEL, 5) = 0
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'VERSION' = '2.3-master.gf737013'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(version, 2.3-master.gf737013) = 0
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'LOCALSTATEDIR' = '/usr/local/var'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(localstatedir, /usr/local/var) = 0
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'SYSCONFDIR' = '/usr/local/etc'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(sysconfdir, /usr/local/etc) = 0
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'BINDIR' = '/usr/local/bin'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(bindir, /usr/local/bin) = 0
VERBOSE [U=0,P=2529]       singularity_registry_set()                Adding value to registry: 'IMAGE' = '/tmp/tmpfcuqaxvu/image'
DEBUG   [U=0,P=2529]       singularity_registry_set()                Returning singularity_registry_set(IMAGE, /tmp/tmpfcuqaxvu/image) = 0
DEBUG   [U=0,P=2529]       singularity_registry_get()                Returning NULL on 'HOME'
DEBUG   [U=0,P=2529]       singularity_registry_get()                Returning NULL on 'TARGET_UID'
DEBUG   [U=0,P=2529]       singularity_registry_get()                Returning NULL on 'TARGET_GID'
DEBUG   [U=0,P=2529]       singularity_priv_init()                   Initializing user info
DEBUG   [U=0,P=2529]       singularity_priv_init()                   Set the calling user's username to: root
DEBUG   [U=0,P=2529]       singularity_priv_init()                   Marking uinfo structure as ready
DEBUG   [U=0,P=2529]       singularity_priv_init()                   Obtaining home directory
VERBOSE [U=0,P=2529]       singularity_priv_init()                   Set home (via getpwuid()) to: /root
VERBOSE [U=0,P=2529]       singularity_suid_init()                   Running SUID program workflow
VERBOSE [U=0,P=2529]       singularity_suid_init()                   Checking program has appropriate permissions
VERBOSE [U=0,P=2529]       singularity_suid_init()                   Checking configuration file is properly owned by root
VERBOSE [U=0,P=2529]       singularity_suid_init()                   Checking if singularity.conf allows us to run as suid
DEBUG   [U=0,P=2529]       singularity_config_get_bool_char_impl()   Called singularity_config_get_bool(allow setuid, yes)
DEBUG   [U=0,P=2529]       singularity_config_get_value_impl()       Returning configuration value allow setuid='yes'
DEBUG   [U=0,P=2529]       singularity_config_get_bool_char_impl()   Return singularity_config_get_bool(allow setuid, yes) = 1
DEBUG   [U=0,P=2529]       singularity_registry_get()                Returning NULL on 'NOSUID'
DEBUG   [U=0,P=2529]       singularity_priv_drop()                   Running as root, not changing privileges
DEBUG   [U=0,P=2529]       singularity_registry_get()                Returning value from registry: 'IMAGESIZE' = '12000'
VERBOSE [U=0,P=2529]       main()                                    Converted size string to long int: 12000
DEBUG   [U=0,P=2529]       singularity_registry_get()                Returning value from registry: 'IMAGE' = '/tmp/tmpfcuqaxvu/image'
DEBUG   [U=0,P=2529]       singularity_config_get_value_impl()       No configuration entry found for 'limit container owners'; returning default value 'NULL'
DEBUG   [U=0,P=2529]       singularity_config_get_value_impl()       No configuration entry found for 'limit container paths'; returning default value 'NULL'
DEBUG   [U=0,P=2529]       singularity_image_open()                  Opening file descriptor to image: /tmp/tmpfcuqaxvu/image
VERBOSE [U=0,P=2529]       singularity_image_create()                Writing image header
VERBOSE [U=0,P=2529]       singularity_image_create()                Growing image to 12000MB
VERBOSE [U=0,P=2529]       singularity_image_create()                Making image executable
DEBUG   [U=0,P=2529]       singularity_config_get_value_impl()       Returning configuration value max loop devices='256'
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Entered singularity_image_bind()
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Converting max_loop_devs_string to int: '256'
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Converted max_loop_devs_string to int: '256' -> 256
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Checking if this image has been properly opened
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Checking if image is valid file
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Checking if image is already bound to a loop device
DEBUG   [U=0,P=2529]       singularity_registry_get()                Returning value from registry: 'WRITABLE' = '1'
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Setting loopdev open to: O_RDWR
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Setting LO_FLAGS_AUTOCLEAR
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Calculating image offset
VERBOSE [U=0,P=2529]       singularity_image_check()                 Checking that file pointer is a Singularity image
DEBUG   [U=0,P=2529]       singularity_image_check()                 First line of image(fd=4): #!/usr/bin/env run-singularity

DEBUG   [U=0,P=2529]       singularity_image_check()                 Checking if first line matches key
VERBOSE [U=0,P=2529]       singularity_image_check()                 File is a valid Singularity image
VERBOSE [U=0,P=2529]       singularity_image_offset()                Calculating image offset
VERBOSE [U=0,P=2529]       singularity_image_offset()                Found image at an offset of 31 bytes
DEBUG   [U=0,P=2529]       singularity_image_offset()                Returning image_offset(image_fp) = 31
DEBUG   [U=0,P=2529]       singularity_priv_escalate()               Running as root, not changing privileges
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Finding next available loop device...
VERBOSE [U=0,P=2529]       singularity_image_bind()                  Found available loop device: /dev/loop0
DEBUG   [U=0,P=2529]       singularity_image_bind()                  Setting loop device flags
DEBUG   [U=0,P=2529]       singularity_priv_drop()                   Running as root, not changing privileges
VERBOSE [U=0,P=2529]       singularity_image_bind()                  Using loop device: /dev/loop0
DEBUG   [U=0,P=2529]       main()                                    Cleaning environment
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_WRITABLE
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SHELL
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: TERM
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_libexecdir
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_COMMAND
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_IMAGESIZE
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: USER
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_MESSAGELEVEL
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SUDO_USER
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SUDO_UID
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: USERNAME
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_version
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: PATH
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: MAIL
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_localstatedir
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: PWD
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: LANG
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: HOME
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SUDO_COMMAND
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SHLVL
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_sysconfdir
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: LOGNAME
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_bindir
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SUDO_GID
DEBUG   [U=0,P=2529]       envclean()                                Unsetting environment variable: SINGULARITY_IMAGE
DEBUG   [U=0,P=2529]       singularity_priv_escalate()               Running as root, not changing privileges
DEBUG   [U=0,P=2529]       prepare_fork()                            Creating parent/child coordination pipes.
VERBOSE [U=0,P=2529]       singularity_fork()                        Forking child process
VERBOSE [U=0,P=2529]       singularity_fork()                        Hello from parent process
DEBUG   [U=0,P=2529]       singularity_fork()                        Assigning sigaction()s
DEBUG   [U=0,P=2529]       singularity_fork()                        Creating generic signal pipes
DEBUG   [U=0,P=2529]       singularity_fork()                        Creating sigchld signal pipes
DEBUG   [U=0,P=2529]       singularity_fork()                        Dropping permissions
DEBUG   [U=0,P=2529]       singularity_priv_drop()                   Running as root, not changing privileges
DEBUG   [U=0,P=2529]       singularity_fork()                        Waiting on signal from watchdog
VERBOSE [U=0,P=2532]       singularity_fork()                        Hello from child process
DEBUG   [U=0,P=2532]       singularity_fork()                        Closing watchdog write pipe
DEBUG   [U=0,P=2532]       singularity_fork()                        Child process is returning control to process thread
DEBUG   [U=0,P=2532]       singularity_fork_exec()                   fork argv[0] = /sbin/mkfs.ext3
DEBUG   [U=0,P=2532]       singularity_fork_exec()                   fork argv[1] = -q
DEBUG   [U=0,P=2532]       singularity_fork_exec()                   fork argv[2] = /dev/loop0
VERBOSE [U=0,P=2532]       singularity_fork_exec()                   Running child program: /sbin/mkfs.ext3
DEBUG   [U=0,P=2529]       singularity_fork()                        Parent process is exiting
DEBUG   [U=0,P=2529]       singularity_fork_exec()                   Waiting on child process
DEBUG   [U=0,P=2529]       singularity_fork_exec()                   Returning from singularity_fork_exec with: 0
DEBUG   [U=0,P=2529]       singularity_priv_drop()                   Running as root, not changing privileges
Enabling debugging
Ending argument loop
Singularity version: 2.3-master.gf737013
Exec'ing: /usr/local/libexec/singularity/cli/bootstrap.exec
VERBOSE [U=0,P=2543]       message_init()                            Set messagelevel to: 5
VERBOSE [U=0,P=2543]       singularity_config_parse()                Initialize configuration file: /usr/local/etc/singularity/singularity.conf
DEBUG   [U=0,P=2543]       singularity_config_parse()                Starting parse of configuration file /usr/local/etc/singularity/singularity.conf
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key allow setuid = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key max loop devices = '256'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key allow pid ns = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key config passwd = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key config group = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key config resolv_conf = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key mount proc = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key mount sys = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key mount dev = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key mount home = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key mount tmp = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key mount hostfs = 'no'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key bind path = '/etc/localtime'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key bind path = '/etc/hosts'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key user bind control = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key enable overlay = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key mount slave = 'yes'
VERBOSE [U=0,P=2543]       singularity_config_parse()                Got config key sessiondir max size = '16'
DEBUG   [U=0,P=2543]       singularity_config_parse()                Finished parsing configuration file '/usr/local/etc/singularity/singularity.conf'
VERBOSE [U=0,P=2543]       singularity_registry_init()               Initializing Singularity Registry
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'WRITABLE' = '1'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(WRITABLE, 1) = 0
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'LIBEXECDIR' = '/usr/local/libexec'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(libexecdir, /usr/local/libexec) = 0
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'COMMAND' = 'bootstrap'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(COMMAND, bootstrap) = 0
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'MESSAGELEVEL' = '5'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(MESSAGELEVEL, 5) = 0
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'VERSION' = '2.3-master.gf737013'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(version, 2.3-master.gf737013) = 0
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'LOCALSTATEDIR' = '/usr/local/var'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(localstatedir, /usr/local/var) = 0
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'SYSCONFDIR' = '/usr/local/etc'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(sysconfdir, /usr/local/etc) = 0
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'BINDIR' = '/usr/local/bin'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(bindir, /usr/local/bin) = 0
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'BUILDDEF' = '/tmp/tmpfcuqaxvu/Singularity'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(BUILDDEF, /tmp/tmpfcuqaxvu/Singularity) = 0
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'IMAGE' = '/tmp/tmpfcuqaxvu/image'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(IMAGE, /tmp/tmpfcuqaxvu/image) = 0
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning NULL on 'HOME'
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning NULL on 'TARGET_UID'
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning NULL on 'TARGET_GID'
DEBUG   [U=0,P=2543]       singularity_priv_init()                   Initializing user info
DEBUG   [U=0,P=2543]       singularity_priv_init()                   Set the calling user's username to: root
DEBUG   [U=0,P=2543]       singularity_priv_init()                   Marking uinfo structure as ready
DEBUG   [U=0,P=2543]       singularity_priv_init()                   Obtaining home directory
VERBOSE [U=0,P=2543]       singularity_priv_init()                   Set home (via getpwuid()) to: /root
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_WRITABLE
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SHELL
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: TERM
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_libexecdir
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_COMMAND
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: USER
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_MESSAGELEVEL
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SUDO_USER
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SUDO_UID
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: USERNAME
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_version
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: PATH
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: MAIL
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_localstatedir
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: PWD
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: LANG
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: HOME
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SUDO_COMMAND
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SHLVL
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_sysconfdir
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: LOGNAME
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_bindir
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_BUILDDEF
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SUDO_GID
DEBUG   [U=0,P=2543]       envclean()                                Unsetting environment variable: SINGULARITY_IMAGE
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'WRITABLE' = '1'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(WRITABLE, 1) = 0
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning value from registry: 'IMAGE' = '/tmp/tmpfcuqaxvu/image'
DEBUG   [U=0,P=2543]       singularity_config_get_value_impl()       No configuration entry found for 'limit container owners'; returning default value 'NULL'
DEBUG   [U=0,P=2543]       singularity_config_get_value_impl()       No configuration entry found for 'limit container paths'; returning default value 'NULL'
DEBUG   [U=0,P=2543]       singularity_image_open()                  Opening file descriptor to image: /tmp/tmpfcuqaxvu/image
DEBUG   [U=0,P=2543]       singularity_suid_enabled()                Executable is not SUID
DEBUG   [U=0,P=2543]       singularity_runtime_ns()                  Calling: _singularity_runtime_ns_mnt()
DEBUG   [U=0,P=2543]       singularity_config_get_bool_char_impl()   Called singularity_config_get_bool(mount slave, yes)
DEBUG   [U=0,P=2543]       singularity_config_get_value_impl()       Returning configuration value mount slave='yes'
DEBUG   [U=0,P=2543]       singularity_config_get_bool_char_impl()   Return singularity_config_get_bool(mount slave, yes) = 1
DEBUG   [U=0,P=2543]       singularity_priv_escalate()               Running as root, not changing privileges
DEBUG   [U=0,P=2543]       singularity_runtime_ns_mnt()              Virtualizing FS namespace
DEBUG   [U=0,P=2543]       singularity_runtime_ns_mnt()              Virtualizing mount namespace
DEBUG   [U=0,P=2543]       singularity_runtime_ns_mnt()              Making mounts slave
DEBUG   [U=0,P=2543]       singularity_priv_drop()                   Running as root, not changing privileges
DEBUG   [U=0,P=2543]       singularity_config_get_value_impl()       Returning configuration value max loop devices='256'
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Entered singularity_image_bind()
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Converting max_loop_devs_string to int: '256'
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Converted max_loop_devs_string to int: '256' -> 256
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Checking if this image has been properly opened
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Checking if image is valid file
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Checking if image is already bound to a loop device
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning value from registry: 'WRITABLE' = '1'
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Setting loopdev open to: O_RDWR
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Setting LO_FLAGS_AUTOCLEAR
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Calculating image offset
VERBOSE [U=0,P=2543]       singularity_image_check()                 Checking that file pointer is a Singularity image
DEBUG   [U=0,P=2543]       singularity_image_check()                 First line of image(fd=4): #!/usr/bin/env run-singularity

DEBUG   [U=0,P=2543]       singularity_image_check()                 Checking if first line matches key
VERBOSE [U=0,P=2543]       singularity_image_check()                 File is a valid Singularity image
VERBOSE [U=0,P=2543]       singularity_image_offset()                Calculating image offset
VERBOSE [U=0,P=2543]       singularity_image_offset()                Found image at an offset of 31 bytes
DEBUG   [U=0,P=2543]       singularity_image_offset()                Returning image_offset(image_fp) = 31
DEBUG   [U=0,P=2543]       singularity_priv_escalate()               Running as root, not changing privileges
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Finding next available loop device...
VERBOSE [U=0,P=2543]       singularity_image_bind()                  Found available loop device: /dev/loop0
DEBUG   [U=0,P=2543]       singularity_image_bind()                  Setting loop device flags
DEBUG   [U=0,P=2543]       singularity_priv_drop()                   Running as root, not changing privileges
VERBOSE [U=0,P=2543]       singularity_image_bind()                  Using loop device: /dev/loop0
VERBOSE [U=0,P=2543]       singularity_runtime_rootfs()              Set container directory to: /usr/local/var/singularity/mnt/container
DEBUG   [U=0,P=2543]       singularity_runtime_rootfs()              Checking for container directory
DEBUG   [U=0,P=2543]       singularity_runtime_rootfs()              Returning container_directory: /usr/local/var/singularity/mnt/container
DEBUG   [U=0,P=2543]       chk_mode()                                Checking exact mode (40755) on: /usr/local/var/singularity/mnt/container
DEBUG   [U=0,P=2543]       chk_mode()                                Found appropriate mode on file: /usr/local/var/singularity/mnt/container
VERBOSE [U=0,P=2543]       singularity_image_mount()                 Checking what kind of image we are mounting
DEBUG   [U=0,P=2543]       singularity_image_mount_squashfs_check()  Image does not appear to be of type '.sqsh': /tmp/tmpfcuqaxvu/image
DEBUG   [U=0,P=2543]       singularity_image_mount_dir_check()       Checking if image is a directory
VERBOSE [U=0,P=2543]       singularity_image_mount_dir_check()       Source path is not a directory: /tmp/tmpfcuqaxvu/image
VERBOSE [U=0,P=2543]       singularity_image_mount()                 Attempting to mount as singularity image
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning value from registry: 'WRITABLE' = '1'
DEBUG   [U=0,P=2543]       singularity_priv_escalate()               Running as root, not changing privileges
VERBOSE [U=0,P=2543]       singularity_image_mount_image_mount()     Mounting /dev/loop0 in read/write to: /usr/local/var/singularity/mnt/container
DEBUG   [U=0,P=2543]       singularity_priv_drop()                   Running as root, not changing privileges
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'PATH' = '/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin'
DEBUG   [U=0,P=2543]       singularity_runtime_rootfs()              Returning container_directory: /usr/local/var/singularity/mnt/container
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'SINGULARITY_ROOTFS' = '/usr/local/var/singularity/mnt/container'
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning value from registry: 'LIBEXECDIR' = '/usr/local/libexec'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'SINGULARITY_libexecdir' = '/usr/local/libexec'
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning value from registry: 'IMAGE' = '/tmp/tmpfcuqaxvu/image'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'SINGULARITY_IMAGE' = '/tmp/tmpfcuqaxvu/image'
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning value from registry: 'BUILDDEF' = '/tmp/tmpfcuqaxvu/Singularity'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'SINGULARITY_BUILDDEF' = '/tmp/tmpfcuqaxvu/Singularity'
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning value from registry: 'MESSAGELEVEL' = '5'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'SINGULARITY_MESSAGELEVEL' = '5'
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning NULL on 'NOTEST'
DEBUG   [U=0,P=2543]       envar_set()                               Unsetting environment variable: SINGULARITY_NOTEST
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning NULL on 'BUILDSECTION'
DEBUG   [U=0,P=2543]       envar_set()                               Unsetting environment variable: SINGULARITY_BUILDSECTION
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning NULL on 'BUILDNOBASE'
DEBUG   [U=0,P=2543]       envar_set()                               Unsetting environment variable: SINGULARITY_BUILDNOBASE
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning value from registry: 'VERSION' = '2.3-master.gf737013'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'SINGULARITY_version' = '2.3-master.gf737013'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'HOME' = '/root'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'LANG' = 'C'
DEBUG   [U=0,P=2543]       singularity_registry_get()                Returning value from registry: 'BUILDDEF' = '/tmp/tmpfcuqaxvu/Singularity'
VERBOSE [U=0,P=2543]       bootstrap_keyval_parse()                  Got bootstrap definition key/val '#  - Due to  https' = '//github.com/singularityware/singularity/issues/471'
DEBUG   [U=0,P=2543]       uppercase()                               Transformed to uppercase: '#  - Due to  https' -> '#  - DUE TO  HTTPS'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: '#  - DUE TO  HTTPS' = '//github.com/singularityware/singularity/issues/471'
VERBOSE [U=0,P=2543]       bootstrap_keyval_parse()                  Got bootstrap definition key/val 'BootStrap' = 'debootstrap'
VERBOSE [U=0,P=2543]       singularity_registry_set()                Adding value to registry: 'DRIVER' = 'debootstrap'
DEBUG   [U=0,P=2543]       singularity_registry_set()                Returning singularity_registry_set(DRIVER, debootstrap) = 0
DEBUG   [U=0,P=2543]       uppercase()                               Transformed to uppercase: 'BootStrap' -> 'BOOTSTRAP'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'BOOTSTRAP' = 'debootstrap'
VERBOSE [U=0,P=2543]       bootstrap_keyval_parse()                  Got bootstrap definition key/val 'OSVersion' = 'stretch'
DEBUG   [U=0,P=2543]       uppercase()                               Transformed to uppercase: 'OSVersion' -> 'OSVERSION'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'OSVERSION' = 'stretch'
VERBOSE [U=0,P=2543]       bootstrap_keyval_parse()                  Got bootstrap definition key/val 'MirrorURL' = 'http://http.debian.net/debian/'
DEBUG   [U=0,P=2543]       uppercase()                               Transformed to uppercase: 'MirrorURL' -> 'MIRRORURL'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: 'MIRRORURL' = 'http://http.debian.net/debian/'
VERBOSE [U=0,P=2543]       bootstrap_keyval_parse()                  Got bootstrap definition key/val '#MirrorURL' = 'http://smaug.datalad.org:3142/debian/'
DEBUG   [U=0,P=2543]       uppercase()                               Transformed to uppercase: '#MirrorURL' -> '#MIRRORURL'
DEBUG   [U=0,P=2543]       envar_set()                               Setting environment variable: '#MIRRORURL' = 'http://smaug.datalad.org:3142/debian/'
VERBOSE [U=0,P=2560]       message_init()                            Set messagelevel to: 5
DEBUG   [U=0,P=2560]       main()                                    Iterating through file looking for sections matching: %pre
VERBOSE [U=0,P=6699]       message_init()                            Set messagelevel to: 5
DEBUG   [U=0,P=6699]       main()                                    Iterating through file looking for sections matching: %runscript
VERBOSE [U=0,P=6713]       message_init()                            Set messagelevel to: 5
DEBUG   [U=0,P=6713]       main()                                    Iterating through file looking for sections matching: %post
+ echo Configuring the environment
+ sed -i -e s, main$, main contrib non-free,g /etc/apt/sources.list
+ apt-get update
+ apt-get -y install eatmydata
debconf: delaying package configuration, since apt-utils is not installed
+ eatmydata apt-get -y install vim wget strace gdb valgrind time ncdu gnupg curl procps
debconf: delaying package configuration, since apt-utils is not installed
+ wget -q -O/tmp/nd-configurerepo https://raw.githubusercontent.com/neurodebian/neurodebian/4d26c8f30433145009aa3f74516da12f560a5a13/tools/nd-configurerepo
+ bash /tmp/nd-configurerepo
I: Command netselect (from package netselect) is N/A.
I: Use with --install to get all necessary packages installed automatically
I: netselect (apt-get install netselect) needed to select the 'best' mirror was not found
I: Selecting the default repository: http://neuro.debian.net/debian
I: Generating /etc/apt/sources.list.d/neurodebian.sources.list
I: Fetching the key from the server
I: Updating APT listings, might take a few minutes
+ chmod a+r -R /etc/apt
+ eatmydata apt-get -y install git git-annex-standalone datalad python-nipype virtualenv dcm2niix python-dcmstack python-configparser python-funcsigs python-pytest connectome-workbench python-mvpa2 python-nilearn fsl-core fsl-atlases fsl-first-data mricron afni fsleyes ants convert3d heudiconv
debconf: delaying package configuration, since apt-utils is not installed
+ bash -
+ curl -sL https://deb.nodesource.com/setup_6.x
Warning: apt-key output should not be parsed (stdout is not a terminal)
+ eatmydata apt-get install -y nodejs
debconf: delaying package configuration, since apt-utils is not installed
+ npm install -g bids-validator@0.22.0
+ chmod a+rX -R /usr/lib/node_modules/
+ chmod a+rX -R /etc/apt/sources.list.d
+ rm -rf /tmp/nd-configurerepo /tmp/npm-13045-0d156422 /tmp/params.pkl /tmp/startup-sthgv1po /tmp/tmpfcuqaxvu /var/tmp/*
+ apt-get clean
+ mkdir -p /afs /inbox /ihome /opt /data /backup /apps /srv /scratch
+ chmod a+rX /afs /inbox /ihome /opt /data /backup /apps /srv /scratch
ERROR: File not found (/tmp/tmpfcuqaxvu/Singularity)

Creating and bootstrapping image...
INFO    [U=0,P=2529]       main()                                    Initializing Singularity image subsystem
INFO    [U=0,P=2529]       main()                                    Opening image file: image
INFO    [U=0,P=2529]       main()                                    Creating 12000MiB image
INFO    [U=0,P=2529]       main()                                    Binding image to loop
INFO    [U=0,P=2529]       main()                                    Creating file system within image
INFO    [U=0,P=2529]       main()                                    Image is done: /tmp/tmpfcuqaxvu/image

INFO    [U=0,P=2543]       main()                                    Sanitizing environment
INFO    [U=0,P=2543]       bootstrap_init()                          Building from bootstrap definition recipe
Adding base Singularity environment to container
W: Cannot check Release signature; keyring file not available /usr/share/keyrings/debian-archive-keyring.gpg
I: Retrieving InRelease 
I: Failed to retrieve InRelease
I: Retrieving Release 
I: Retrieving Packages 
I: Validating Packages 
I: Resolving dependencies of required packages...
I: Resolving dependencies of base packages...
I: Found additional required dependencies: libaudit-common libaudit1 libbz2-1.0 libcap-ng0 libdb5.3 libdebconfclient0 libgcrypt20 libgpg-error0 liblz4-1 libncursesw5 libsemanage-common libsemanage1 libsystemd0 libudev1 libustr-1.0-1 
I: Found additional base dependencies: adduser debian-archive-keyring gpgv libapt-pkg5.0 libstdc++6 
I: Checking component main on http://http.debian.net/debian...
I: Retrieving libacl1 2.2.52-3+b1
I: Validating libacl1 2.2.52-3+b1
I: Retrieving adduser 3.115
I: Validating adduser 3.115
I: Retrieving apt 1.4.7
I: Validating apt 1.4.7
I: Retrieving libapt-pkg5.0 1.4.7
I: Validating libapt-pkg5.0 1.4.7
I: Retrieving libattr1 1:2.4.47-2+b2
I: Validating libattr1 1:2.4.47-2+b2
I: Retrieving libaudit-common 1:2.6.7-2
I: Validating libaudit-common 1:2.6.7-2
I: Retrieving libaudit1 1:2.6.7-2
I: Validating libaudit1 1:2.6.7-2
I: Retrieving base-files 9.9+deb9u1
I: Validating base-files 9.9+deb9u1
I: Retrieving base-passwd 3.5.43
I: Validating base-passwd 3.5.43
I: Retrieving bash 4.4-5
I: Validating bash 4.4-5
I: Retrieving libbz2-1.0 1.0.6-8.1
I: Validating libbz2-1.0 1.0.6-8.1
I: Retrieving libdebconfclient0 0.227
I: Validating libdebconfclient0 0.227
I: Retrieving coreutils 8.26-3
I: Validating coreutils 8.26-3
I: Retrieving dash 0.5.8-2.4
I: Validating dash 0.5.8-2.4
I: Retrieving libdb5.3 5.3.28-12+b1
I: Validating libdb5.3 5.3.28-12+b1
I: Retrieving debconf 1.5.61
I: Validating debconf 1.5.61
I: Retrieving debian-archive-keyring 2017.5
I: Validating debian-archive-keyring 2017.5
I: Retrieving debianutils 4.8.1.1
I: Validating debianutils 4.8.1.1
I: Retrieving diffutils 1:3.5-3
I: Validating diffutils 1:3.5-3
I: Retrieving dpkg 1.18.24
I: Validating dpkg 1.18.24
I: Retrieving e2fslibs 1.43.4-2
I: Validating e2fslibs 1.43.4-2
I: Retrieving e2fsprogs 1.43.4-2
I: Validating e2fsprogs 1.43.4-2
I: Retrieving libcomerr2 1.43.4-2
I: Validating libcomerr2 1.43.4-2
I: Retrieving libss2 1.43.4-2
I: Validating libss2 1.43.4-2
I: Retrieving findutils 4.6.0+git+20161106-2
I: Validating findutils 4.6.0+git+20161106-2
I: Retrieving gcc-6-base 6.3.0-18
I: Validating gcc-6-base 6.3.0-18
I: Retrieving libgcc1 1:6.3.0-18
I: Validating libgcc1 1:6.3.0-18
I: Retrieving libstdc++6 6.3.0-18
I: Validating libstdc++6 6.3.0-18
I: Retrieving libc-bin 2.24-11+deb9u1
I: Validating libc-bin 2.24-11+deb9u1
I: Retrieving libc6 2.24-11+deb9u1
I: Validating libc6 2.24-11+deb9u1
I: Retrieving multiarch-support 2.24-11+deb9u1
I: Validating multiarch-support 2.24-11+deb9u1
I: Retrieving gpgv 2.1.18-6
I: Validating gpgv 2.1.18-6
I: Retrieving grep 2.27-2
I: Validating grep 2.27-2
I: Retrieving gzip 1.6-5+b1
I: Validating gzip 1.6-5+b1
I: Retrieving hostname 3.18+b1
I: Validating hostname 3.18+b1
I: Retrieving init-system-helpers 1.48
I: Validating init-system-helpers 1.48
I: Retrieving libcap-ng0 0.7.7-3+b1
I: Validating libcap-ng0 0.7.7-3+b1
I: Retrieving libgcrypt20 1.7.6-2+deb9u1
I: Validating libgcrypt20 1.7.6-2+deb9u1
I: Retrieving libgpg-error0 1.26-2
I: Validating libgpg-error0 1.26-2
I: Retrieving libselinux1 2.6-3+b1
I: Validating libselinux1 2.6-3+b1
I: Retrieving libsemanage-common 2.6-2
I: Validating libsemanage-common 2.6-2
I: Retrieving libsemanage1 2.6-2
I: Validating libsemanage1 2.6-2
I: Retrieving libsepol1 2.6-2
I: Validating libsepol1 2.6-2
I: Retrieving lsb-base 9.20161125
I: Validating lsb-base 9.20161125
I: Retrieving liblz4-1 0.0~r131-2+b1
I: Validating liblz4-1 0.0~r131-2+b1
I: Retrieving mawk 1.3.3-17+b3
I: Validating mawk 1.3.3-17+b3
I: Retrieving libncursesw5 6.0+20161126-1
I: Validating libncursesw5 6.0+20161126-1
I: Retrieving libtinfo5 6.0+20161126-1
I: Validating libtinfo5 6.0+20161126-1
I: Retrieving ncurses-base 6.0+20161126-1
I: Validating ncurses-base 6.0+20161126-1
I: Retrieving ncurses-bin 6.0+20161126-1
I: Validating ncurses-bin 6.0+20161126-1
I: Retrieving libpam-modules 1.1.8-3.6
I: Validating libpam-modules 1.1.8-3.6
I: Retrieving libpam-modules-bin 1.1.8-3.6
I: Validating libpam-modules-bin 1.1.8-3.6
I: Retrieving libpam-runtime 1.1.8-3.6
I: Validating libpam-runtime 1.1.8-3.6
I: Retrieving libpam0g 1.1.8-3.6
I: Validating libpam0g 1.1.8-3.6
I: Retrieving libpcre3 2:8.39-3
I: Validating libpcre3 2:8.39-3
I: Retrieving perl-base 5.24.1-3+deb9u1
I: Validating perl-base 5.24.1-3+deb9u1
I: Retrieving sed 4.4-1
I: Validating sed 4.4-1
I: Retrieving sensible-utils 0.0.9
I: Validating sensible-utils 0.0.9
I: Retrieving login 1:4.4-4.1
I: Validating login 1:4.4-4.1
I: Retrieving passwd 1:4.4-4.1
I: Validating passwd 1:4.4-4.1
I: Retrieving libsystemd0 232-25+deb9u1
I: Validating libsystemd0 232-25+deb9u1
I: Retrieving libudev1 232-25+deb9u1
I: Validating libudev1 232-25+deb9u1
I: Retrieving sysvinit-utils 2.88dsf-59.9
I: Validating sysvinit-utils 2.88dsf-59.9
I: Retrieving tar 1.29b-1.1
I: Validating tar 1.29b-1.1
I: Retrieving tzdata 2017b-1
I: Validating tzdata 2017b-1
I: Retrieving libustr-1.0-1 1.0.4-6
I: Validating libustr-1.0-1 1.0.4-6
I: Retrieving bsdutils 1:2.29.2-1
I: Validating bsdutils 1:2.29.2-1
I: Retrieving libblkid1 2.29.2-1
I: Validating libblkid1 2.29.2-1
I: Retrieving libfdisk1 2.29.2-1
I: Validating libfdisk1 2.29.2-1
I: Retrieving libmount1 2.29.2-1
I: Validating libmount1 2.29.2-1
I: Retrieving libsmartcols1 2.29.2-1
I: Validating libsmartcols1 2.29.2-1
I: Retrieving libuuid1 2.29.2-1
I: Validating libuuid1 2.29.2-1
I: Retrieving mount 2.29.2-1
I: Validating mount 2.29.2-1
I: Retrieving util-linux 2.29.2-1
I: Validating util-linux 2.29.2-1
I: Retrieving liblzma5 5.2.2-1.2+b1
I: Validating liblzma5 5.2.2-1.2+b1
I: Retrieving zlib1g 1:1.2.8.dfsg-5
I: Validating zlib1g 1:1.2.8.dfsg-5
I: Chosen extractor for .deb packages: dpkg-deb
I: Extracting libacl1...
I: Extracting libattr1...
I: Extracting libaudit-common...
I: Extracting libaudit1...
I: Extracting base-files...
I: Extracting base-passwd...
I: Extracting bash...
I: Extracting libbz2-1.0...
I: Extracting libdebconfclient0...
I: Extracting coreutils...
I: Extracting dash...
I: Extracting libdb5.3...
I: Extracting debconf...
I: Extracting debianutils...
I: Extracting diffutils...
I: Extracting dpkg...
I: Extracting e2fslibs...
I: Extracting e2fsprogs...
I: Extracting libcomerr2...
I: Extracting libss2...
I: Extracting findutils...
I: Extracting gcc-6-base...
I: Extracting libgcc1...
I: Extracting libc-bin...
I: Extracting libc6...
I: Extracting multiarch-support...
I: Extracting grep...
I: Extracting gzip...
I: Extracting hostname...
I: Extracting init-system-helpers...
I: Extracting libcap-ng0...
I: Extracting libgcrypt20...
I: Extracting libgpg-error0...
I: Extracting libselinux1...
I: Extracting libsemanage-common...
I: Extracting libsemanage1...
I: Extracting libsepol1...
I: Extracting lsb-base...
I: Extracting liblz4-1...
I: Extracting mawk...
I: Extracting libncursesw5...
I: Extracting libtinfo5...
I: Extracting ncurses-base...
I: Extracting ncurses-bin...
I: Extracting libpam-modules...
I: Extracting libpam-modules-bin...
I: Extracting libpam-runtime...
I: Extracting libpam0g...
I: Extracting libpcre3...
I: Extracting perl-base...
I: Extracting sed...
I: Extracting sensible-utils...
I: Extracting login...
I: Extracting passwd...
I: Extracting libsystemd0...
I: Extracting libudev1...
I: Extracting sysvinit-utils...
I: Extracting tar...
I: Extracting tzdata...
I: Extracting libustr-1.0-1...
I: Extracting bsdutils...
I: Extracting libblkid1...
I: Extracting libfdisk1...
I: Extracting libmount1...
I: Extracting libsmartcols1...
I: Extracting libuuid1...
I: Extracting mount...
I: Extracting util-linux...
I: Extracting liblzma5...
I: Extracting zlib1g...
I: Installing core packages...
I: Unpacking required packages...
I: Unpacking libacl1:amd64...
I: Unpacking libattr1:amd64...
I: Unpacking libaudit-common...
I: Unpacking libaudit1:amd64...
I: Unpacking base-files...
I: Unpacking base-passwd...
I: Unpacking bash...
I: Unpacking libbz2-1.0:amd64...
I: Unpacking libdebconfclient0:amd64...
I: Unpacking coreutils...
I: Unpacking dash...
I: Unpacking libdb5.3:amd64...
I: Unpacking debconf...
I: Unpacking debianutils...
I: Unpacking diffutils...
I: Unpacking dpkg...
I: Unpacking e2fslibs:amd64...
I: Unpacking e2fsprogs...
I: Unpacking libcomerr2:amd64...
I: Unpacking libss2:amd64...
I: Unpacking findutils...
I: Unpacking gcc-6-base:amd64...
I: Unpacking libgcc1:amd64...
I: Unpacking libc-bin...
I: Unpacking libc6:amd64...
I: Unpacking multiarch-support...
I: Unpacking grep...
I: Unpacking gzip...
I: Unpacking hostname...
I: Unpacking init-system-helpers...
I: Unpacking libcap-ng0:amd64...
I: Unpacking libgcrypt20:amd64...
I: Unpacking libgpg-error0:amd64...
I: Unpacking libselinux1:amd64...
I: Unpacking libsemanage-common...
I: Unpacking libsemanage1:amd64...
I: Unpacking libsepol1:amd64...
I: Unpacking lsb-base...
I: Unpacking liblz4-1:amd64...
I: Unpacking mawk...
I: Unpacking libncursesw5:amd64...
I: Unpacking libtinfo5:amd64...
I: Unpacking ncurses-base...
I: Unpacking ncurses-bin...
I: Unpacking libpam-modules:amd64...
I: Unpacking libpam-modules-bin...
I: Unpacking libpam-runtime...
I: Unpacking libpam0g:amd64...
I: Unpacking libpcre3:amd64...
I: Unpacking perl-base...
I: Unpacking sed...
I: Unpacking sensible-utils...
I: Unpacking login...
I: Unpacking passwd...
I: Unpacking libsystemd0:amd64...
I: Unpacking libudev1:amd64...
I: Unpacking sysvinit-utils...
I: Unpacking tar...
I: Unpacking tzdata...
I: Unpacking libustr-1.0-1:amd64...
I: Unpacking bsdutils...
I: Unpacking libblkid1:amd64...
I: Unpacking libfdisk1:amd64...
I: Unpacking libmount1:amd64...
I: Unpacking libsmartcols1:amd64...
I: Unpacking libuuid1:amd64...
I: Unpacking mount...
I: Unpacking util-linux...
I: Unpacking liblzma5:amd64...
I: Unpacking zlib1g:amd64...
I: Configuring required packages...
I: Configuring gcc-6-base:amd64...
I: Configuring lsb-base...
I: Configuring sensible-utils...
I: Configuring ncurses-base...
I: Configuring libsemanage-common...
I: Configuring libaudit-common...
I: Configuring libc6:amd64...
I: Configuring libbz2-1.0:amd64...
I: Configuring libgpg-error0:amd64...
I: Configuring libc-bin...
I: Configuring libdebconfclient0:amd64...
I: Configuring diffutils...
I: Configuring libcomerr2:amd64...
I: Configuring libcap-ng0:amd64...
I: Configuring libsepol1:amd64...
I: Configuring libgcc1:amd64...
I: Configuring libustr-1.0-1:amd64...
I: Configuring libsmartcols1:amd64...
I: Configuring libaudit1:amd64...
I: Configuring libtinfo5:amd64...
I: Configuring libudev1:amd64...
I: Configuring libattr1:amd64...
I: Configuring libss2:amd64...
I: Configuring liblzma5:amd64...
I: Configuring base-passwd...
I: Configuring e2fslibs:amd64...
I: Configuring liblz4-1:amd64...
I: Configuring debianutils...
I: Configuring libgcrypt20:amd64...
I: Configuring libncursesw5:amd64...
I: Configuring libdb5.3:amd64...
I: Configuring zlib1g:amd64...
I: Configuring hostname...
I: Configuring multiarch-support...
I: Configuring mawk...
I: Configuring libpcre3:amd64...
I: Configuring base-files...
I: Configuring libselinux1:amd64...
I: Configuring findutils...
I: Configuring libacl1:amd64...
I: Configuring ncurses-bin...
I: Configuring sed...
I: Configuring libsystemd0:amd64...
I: Configuring coreutils...
I: Configuring tar...
I: Configuring libsemanage1:amd64...
I: Configuring dpkg...
I: Configuring perl-base...
I: Configuring grep...
I: Configuring debconf...
I: Configuring tzdata...
I: Configuring gzip...
I: Configuring bsdutils...
I: Configuring dash...
I: Configuring init-system-helpers...
I: Configuring libpam0g:amd64...
I: Configuring libpam-modules-bin...
I: Configuring bash...
I: Configuring libpam-modules:amd64...
I: Configuring libpam-runtime...
I: Configuring passwd...
I: Configuring login...
I: Configuring libuuid1:amd64...
I: Configuring libblkid1:amd64...
I: Configuring libmount1:amd64...
I: Configuring mount...
I: Configuring libfdisk1:amd64...
I: Configuring util-linux...
I: Configuring e2fsprogs...
I: Configuring sysvinit-utils...
I: Configuring libc-bin...
I: Unpacking the base system...
I: Unpacking adduser...
I: Unpacking apt...
I: Unpacking libapt-pkg5.0:amd64...
I: Unpacking debian-archive-keyring...
I: Unpacking libstdc++6:amd64...
I: Unpacking gpgv...
I: Configuring the base system...
I: Configuring gpgv...
I: Configuring debian-archive-keyring...
I: Configuring libstdc++6:amd64...
I: Configuring adduser...
I: Configuring libapt-pkg5.0:amd64...
I: Configuring apt...
I: Configuring libc-bin...
I: Base system installed successfully.
User defined %runscript found! Taking priority.
Running post scriptlet
Configuring the environment
Ign:1 http://cdn-fastly.deb.debian.org/debian stretch InRelease
Hit:2 http://cdn-fastly.deb.debian.org/debian stretch Release
Get:3 http://cdn-fastly.deb.debian.org/debian stretch Release.gpg [2373 B]
Get:4 http://cdn-fastly.deb.debian.org/debian stretch/main Translation-en [5393 kB]
Get:5 http://cdn-fastly.deb.debian.org/debian stretch/contrib amd64 Packages [50.9 kB]
Get:6 http://cdn-fastly.deb.debian.org/debian stretch/contrib Translation-en [45.9 kB]
Get:7 http://cdn-fastly.deb.debian.org/debian stretch/non-free amd64 Packages [77.9 kB]
Get:8 http://cdn-fastly.deb.debian.org/debian stretch/non-free Translation-en [79.2 kB]
Fetched 5649 kB in 2s (2169 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
The following additional packages will be installed:
  libeatmydata1
The following NEW packages will be installed:
  eatmydata libeatmydata1
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 29.6 kB of archives.
After this operation, 66.6 kB of additional disk space will be used.
Get:1 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libeatmydata1 amd64 105-5 [14.3 kB]
Get:2 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 eatmydata all 105-5 [15.3 kB]
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(Reading database ... 6317 files and directories currently installed.)
Preparing to unpack .../libeatmydata1_105-5_amd64.deb ...
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Setting up libeatmydata1:amd64 (105-5) ...
Processing triggers for libc-bin (2.24-11+deb9u1) ...
Setting up eatmydata (105-5) ...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  bzip2 ca-certificates dirmngr file gnupg-agent gnupg-l10n krb5-locales
  libassuan0 libbabeltrace-ctf1 libbabeltrace1 libc6-dbg libcurl3 libdw1
  libelf1 libexpat1 libffi6 libglib2.0-0 libglib2.0-data libgmp10 libgnutls30
  libgpm2 libgssapi-krb5-2 libhogweed4 libicu57 libidn11 libidn2-0
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libldap-2.4-2
  libldap-common libmagic-mgc libmagic1 libmpdec2 libncurses5 libnettle6
  libnghttp2-14 libnpth0 libp11-kit0 libpopt0 libprocps6 libpsl5 libpython3.5
  libpython3.5-minimal libpython3.5-stdlib libreadline7 librtmp1 libsasl2-2
  libsasl2-modules libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.0.2
  libssl1.1 libtasn1-6 libunistring0 libxml2 mime-support openssl
  pinentry-curses psmisc publicsuffix readline-common sgml-base
  shared-mime-info valgrind-dbg vim-common vim-runtime xdg-user-dirs xml-core
  xxd xz-utils
Suggested packages:
  bzip2-doc dbus-user-session libpam-systemd pinentry-gnome3 tor gdb-doc
  gdbserver parcimonie xloadimage scdaemon gnutls-bin gpm krb5-doc krb5-user
  libsasl2-modules-gssapi-mit | libsasl2-modules-gssapi-heimdal
  libsasl2-modules-ldap libsasl2-modules-otp libsasl2-modules-sql pinentry-doc
  readline-doc sgml-base-doc valgrind-mpi kcachegrind alleyoop valkyrie ctags
  vim-doc vim-scripts debhelper
The following NEW packages will be installed:
  bzip2 ca-certificates curl dirmngr file gdb gnupg gnupg-agent gnupg-l10n
  krb5-locales libassuan0 libbabeltrace-ctf1 libbabeltrace1 libc6-dbg libcurl3
  libdw1 libelf1 libexpat1 libffi6 libglib2.0-0 libglib2.0-data libgmp10
  libgnutls30 libgpm2 libgssapi-krb5-2 libhogweed4 libicu57 libidn11 libidn2-0
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libldap-2.4-2
  libldap-common libmagic-mgc libmagic1 libmpdec2 libncurses5 libnettle6
  libnghttp2-14 libnpth0 libp11-kit0 libpopt0 libprocps6 libpsl5 libpython3.5
  libpython3.5-minimal libpython3.5-stdlib libreadline7 librtmp1 libsasl2-2
  libsasl2-modules libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.0.2
  libssl1.1 libtasn1-6 libunistring0 libxml2 mime-support ncdu openssl
  pinentry-curses procps psmisc publicsuffix readline-common sgml-base
  shared-mime-info strace time valgrind valgrind-dbg vim vim-common
  vim-runtime wget xdg-user-dirs xml-core xxd xz-utils
0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded.
Need to get 93.9 MB of archives.
After this operation, 384 MB of additional disk space will be used.
Get:1 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 sgml-base all 1.29 [14.8 kB]
Get:2 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libassuan0 amd64 2.4.3-2 [42.5 kB]
Get:3 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 pinentry-curses amd64 1.0.0-2 [50.5 kB]
Get:4 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libnpth0 amd64 1.3-1 [14.6 kB]
Get:5 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB]
Get:6 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB]
Get:7 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 gnupg-agent amd64 2.1.18-6 [554 kB]
Get:8 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libksba8 amd64 1.3.5-2 [99.7 kB]
Get:9 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5 [572 kB]
Get:10 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 gnupg amd64 2.1.18-6 [1126 kB]
Get:11 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libpopt0 amd64 1.16-10+b2 [49.4 kB]
Get:12 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libprocps6 amd64 2:3.3.12-3 [58.1 kB]
Get:13 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libssl1.0.2 amd64 1.0.2l-2 [1294 kB]
Get:14 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0f-3 [1342 kB]
Get:15 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libncurses5 amd64 6.0+20161126-1 [93.4 kB]
Get:16 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 procps amd64 2:3.3.12-3 [249 kB]
Get:17 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 xxd amd64 2:8.0.0197-4 [131 kB]
Get:18 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 vim-common all 2:8.0.0197-4 [159 kB]
Get:19 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB]
Get:20 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b1 [191 kB]
Get:21 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b1 [136 kB]
Get:22 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1 [115 kB]
Get:23 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB]
Get:24 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB]
Get:25 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1 [50.4 kB]
Get:26 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u2 [895 kB]
Get:27 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB]
Get:28 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1 [60.6 kB]
Get:29 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB]
Get:30 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 wget amd64 1.18-5 [800 kB]
Get:31 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 bzip2 amd64 1.0.6-8.1 [47.5 kB]
Get:32 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libmagic-mgc amd64 1:5.30-1 [222 kB]
Get:33 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libmagic1 amd64 1:5.30-1 [111 kB]
Get:34 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 file amd64 1:5.30-1 [63.9 kB]
Get:35 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 krb5-locales all 1.15-1 [93.5 kB]
Get:36 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libgpm2 amd64 1.20.4-6.2+b1 [34.2 kB]
Get:37 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB]
Get:38 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1 [61.7 kB]
Get:39 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1 [119 kB]
Get:40 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1 [311 kB]
Get:41 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1 [154 kB]
Get:42 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3 [68.2 kB]
Get:43 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3 [105 kB]
Get:44 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5 [85.0 kB]
Get:45 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5 [218 kB]
Get:46 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libicu57 amd64 57.1-6 [7701 kB]
Get:47 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libxml2 amd64 2.9.4+dfsg1-2.2 [919 kB]
Get:48 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB]
Get:49 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 xz-utils amd64 5.2.2-1.2+b1 [266 kB]
Get:50 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0f-3 [725 kB]
Get:51 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 ca-certificates all 20161130+nmu1 [196 kB]
Get:52 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1 [79.1 kB]
Get:53 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB]
Get:54 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1 [138 kB]
Get:55 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libcurl3 amd64 7.52.1-5 [291 kB]
Get:56 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 curl amd64 7.52.1-5 [227 kB]
Get:57 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 dirmngr amd64 2.1.18-6 [595 kB]
Get:58 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libelf1 amd64 0.168-1 [157 kB]
Get:59 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libdw1 amd64 0.168-1 [205 kB]
Get:60 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libglib2.0-0 amd64 2.50.3-2 [2691 kB]
Get:61 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libbabeltrace1 amd64 1.5.1-1 [50.1 kB]
Get:62 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libbabeltrace-ctf1 amd64 1.5.1-1 [141 kB]
Get:63 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2 [83.3 kB]
Get:64 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libpython3.5-minimal amd64 3.5.3-1 [573 kB]
Get:65 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libmpdec2 amd64 2.4.2-1 [85.2 kB]
Get:66 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libpython3.5-stdlib amd64 3.5.3-1 [2166 kB]
Get:67 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libpython3.5 amd64 3.5.3-1 [1371 kB]
Get:68 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 gdb amd64 7.12-6 [2722 kB]
Get:69 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libglib2.0-data all 2.50.3-2 [2517 kB]
Get:70 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libsasl2-modules amd64 2.1.27~101-g0780600+dfsg-3 [102 kB]
Get:71 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 ncdu amd64 1.12-1+b1 [41.3 kB]
Get:72 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 psmisc amd64 22.21-2.1+b2 [123 kB]
Get:73 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 shared-mime-info amd64 1.8-1 [731 kB]
Get:74 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 strace amd64 4.15-2 [533 kB]
Get:75 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 time amd64 1.7-25.1+b1 [31.6 kB]
Get:76 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libc6-dbg amd64 2.24-11+deb9u1 [9201 kB]
Get:77 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 valgrind amd64 1:3.12.0~svn20160714-1+b1 [8749 kB]
Get:78 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 vim-runtime all 2:8.0.0197-4 [5409 kB]
Get:79 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 vim amd64 2:8.0.0197-4 [1033 kB]
Get:80 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 xdg-user-dirs amd64 0.15-2+b1 [52.2 kB]
Get:81 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 xml-core all 0.17 [23.2 kB]
Get:82 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 gnupg-l10n all 2.1.18-6 [892 kB]
Get:83 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 publicsuffix all 20170424.0717-1 [98.2 kB]
Get:84 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 valgrind-dbg amd64 1:3.12.0~svn20160714-1+b1 [32.2 MB]
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Setting up fonts-noto-hinted (20161116-1) ...
Setting up liburi-perl (1.71-1) ...
Setting up t1utils (1.39-2) ...
Setting up libatk1.0-0:amd64 (2.22.0-1) ...
Setting up libtext-iconv-perl (1.7-5+b4) ...
Setting up libsnappy1v5:amd64 (1.1.3-3) ...
Setting up qttranslations5-l10n (5.7.1~20161021-1) ...
Setting up dc (1.06.95-9+b3) ...
Setting up libfakeroot:amd64 (1.21-3.1) ...
Setting up python-babel-localedata (2.3.4+dfsg.1-2) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-4) ...
Setting up fonts-ebgaramond (0.016-1) ...
Setting up libltdl7:amd64 (2.4.6-2) ...
Setting up liblwres141:amd64 (1:9.10.3.dfsg.P4-12.3+deb9u1) ...
Setting up libmtdev1:amd64 (1.1.5-1+b1) ...
Setting up docutils-doc (0.13.1+dfsg-2) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up libavc1394-0:amd64 (0.5.4-4+b1) ...
Setting up sphinx-common (1.4.9-2) ...
Setting up fonts-croscore (20161116-1) ...
Setting up libijs-0.35:amd64 (0.35-12) ...
Setting up fsl-resting-connectivity-parcellation-atlases (5.0.7-2) ...
Setting up netpbm (2:10.0-15.3+b2) ...
Setting up libann0 (1.1.2+doc-6) ...
Setting up libvisual-0.4-0:amd64 (0.4.0-10) ...
Setting up libice6:amd64 (2:1.0.9-2) ...
Setting up libfontenc1:amd64 (1:1.1.3-1+b2) ...
Setting up libcolamd2:amd64 (1:4.5.4-1) ...
Setting up libdconf1:amd64 (0.26.0-2+b1) ...
Setting up fsl-oxford-thalamic-connectivity-atlas (5.0.7-2) ...
Setting up libalgorithm-diff-perl (1.19.03-1) ...
Setting up libzvbi-common (0.2.35-13) ...
Setting up libfribidi0:amd64 (0.19.7-1+b1) ...
Setting up liblocale-gettext-perl (1.07-3+b1) ...
Setting up libmpfr4:amd64 (3.1.5-1) ...
Setting up rubygems-integration (1.11) ...
Setting up ttf-bitstream-vera (1.10-8) ...
Setting up libpciaccess0:amd64 (0.13.4-1+b2) ...
Setting up libfftw3-single3:amd64 (3.3.5-3) ...
Setting up python-sympy-doc (1.0-3) ...
Setting up libpotrace0 (1.13-3) ...
Setting up libx11-protocol-perl (0.56-7) ...
Setting up libxml-xpathengine-perl (0.13-1) ...
Setting up libsensors4:amd64 (1:3.4.0-4) ...
Processing triggers for shared-mime-info (1.8-1) ...
Setting up libxkbcommon0:amd64 (0.7.1-1) ...
Setting up libnet-http-perl (6.12-1) ...
Setting up libgudev-1.0-0:amd64 (230-3) ...
Setting up libmpc3:amd64 (1.0.3-1+b2) ...
Setting up libjavascriptcoregtk-4.0-18:amd64 (2.16.3-2) ...
Setting up binutils (2.28-5) ...
Setting up cpp-6 (6.3.0-18) ...
Setting up libcdio-paranoia1:amd64 (0.83-4.3+b1) ...
Setting up libva-drm1:amd64 (1.7.3-2) ...
Setting up libc-dev-bin (2.24-11+deb9u1) ...
Setting up liblua5.2-0:amd64 (5.2.4-1.1+b2) ...
Setting up libdrm-radeon1:amd64 (2.4.74-1) ...
Setting up fonts-gfs-didot (1.1-6) ...
Setting up libgts-bin (0.7.6+darcs121130-4) ...
Setting up libyaml-cpp0.5v5:amd64 (0.5.2-4) ...
Setting up liborc-0.4-0:amd64 (1:0.4.26-2) ...
Setting up libpcre16-3:amd64 (2:8.39-3) ...
Setting up libgme0:amd64 (0.6.0-4) ...
Setting up libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ...
Setting up libcolord2:amd64 (1.3.3-2) ...
Setting up libthai-data (0.1.26-1) ...
Setting up libsodium18:amd64 (1.0.11-2) ...
Setting up libxdmcp6:amd64 (1:1.1.2-3) ...
Setting up fsl-oxford-striatal-atlas (5.0.7-2) ...
Setting up javascript-common (11) ...
Setting up libbdplus0:amd64 (0.1.2-2) ...
Setting up ocl-icd-libopencl1:amd64 (2.2.11-1) ...
Setting up libhdf4-0-alt (4.2.12-3) ...
Setting up libzvbi0:amd64 (0.2.35-13) ...
Setting up fonts-gfs-artemisia (1.1-5) ...
Setting up libdrm-nouveau2:amd64 (2.4.74-1) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libf2c2:amd64 (20130926-2) ...
Setting up bc (1.06.95-9+b3) ...
Setting up ttf-adf-universalis (0.20090423-2) ...
Setting up libsamplerate0:amd64 (0.1.8-8+b2) ...
Setting up libsndio6.1:amd64 (1.1.0-3) ...
Setting up libnl-3-200:amd64 (3.2.27-2) ...
Setting up fonts-dejavu-extra (2.37-1) ...
Setting up fonts-freefont-ttf (20120503-6) ...
Setting up python-django-common (1:1.10.7-2) ...
Setting up ruby-minitest (5.9.0-1) ...
Setting up libvorbis0a:amd64 (1.3.5-4) ...
Setting up libzzip-0-13:amd64 (0.13.62-3.1) ...
Setting up fonts-sil-gentium (20081126:1.03-1) ...
Setting up libsugarext-data (0.110.0-4) ...
Setting up xdg-utils (1.1.1-1) ...
Setting up qhull-bin (2015.2-2) ...
Setting up manpages-dev (4.10-2) ...
Setting up libqt4-test:amd64 (4:4.8.7+dfsg-11) ...
Setting up mricron-data (0.20140804.1~dfsg.1-2) ...
Setting up libmpg123-0:amd64 (1.23.8-1+b1) ...
Setting up hicolor-icon-theme (0.15-1) ...
Setting up libsecret-1-0:amd64 (0.18.5-3.1) ...
Setting up libc6-dev:amd64 (2.24-11+deb9u1) ...
Setting up libslang2:amd64 (2.3.1-5) ...
Setting up cron (3.0pl1-128+b1) ...
Adding group `crontab' (GID 102) ...
Done.
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
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Setting up pigz (2.3.4-1) ...
Setting up lua-lpeg:amd64 (1.0.0-1) ...
Setting up libc-ares2:amd64 (1.12.0-1+deb9u1) ...
Setting up libwww-robotrules-perl (6.01-1) ...
Setting up libwayland-cursor0:amd64 (1.12.0-1) ...
Setting up libopencv-imgproc2.4v5:amd64 (2.4.9.1+dfsg1-2) ...
Setting up libtexluajit2:amd64 (2016.20160513.41080.dfsg-2) ...
Setting up libgsm1:amd64 (1.0.13-4+b2) ...
Setting up fonts-gfs-olga (1.1-5) ...
Setting up libhunspell-1.4-0:amd64 (1.4.1-2+b2) ...
Setting up fsl-harvard-oxford-atlases (5.0.7-2) ...
Setting up libcdt5 (2.38.0-17) ...
Setting up libauthen-sasl-perl (2.1600-1) ...
Setting up libitm1:amd64 (6.3.0-18) ...
Setting up libx11-data (2:1.6.4-3) ...
Setting up libpython2.7-stdlib:amd64 (2.7.13-2) ...
Setting up libqt4-xml:amd64 (4:4.8.7+dfsg-11) ...
Setting up libxau6:amd64 (1:1.0.8-1) ...
Setting up autopoint (0.19.8.1-2) ...
Setting up fuse (2.9.7-1) ...
Setting up libdbus-1-3:amd64 (1.10.18-1) ...
Setting up libgeos-3.5.1 (3.5.1-3) ...
Setting up libdv4:amd64 (1.0.0-11) ...
Setting up libtag1v5-vanilla:amd64 (1.11.1+dfsg.1-0.1) ...
Setting up liblzo2-2:amd64 (2.08-1.2+b2) ...
Setting up liburiparser1:amd64 (0.8.4-1) ...
Setting up fonts-lmodern (2.004.5-3) ...
Setting up libwrap0:amd64 (7.6.q-26) ...
Setting up ruby-power-assert (0.3.0-1) ...
Setting up libavahi-common-data:amd64 (0.6.32-2) ...
Setting up nifti-bin (2.0.0-2+b2) ...
Setting up libcgraph6 (2.38.0-17) ...
Setting up mailutils-common (1:3.1.1-1) ...
Setting up fonts-roboto-hinted (2:0~20160106-2) ...
Setting up popularity-contest (1.64) ...
Setting up fonts-lyx (2.2.2-1) ...
Setting up libsz2:amd64 (0.3.2-1) ...
Setting up afni-atlases (0.20160822-1) ...
Setting up proj-data (4.9.3-1) ...
Setting up libnewmat10ldbl (1.10.4-6) ...
Setting up libwayland-server0:amd64 (1.12.0-1) ...
Setting up netbase (5.4) ...
Setting up libwebp6:amd64 (0.5.2-1) ...
Setting up fsl-bangor-cerebellar-atlas (5.0.7-2) ...
Setting up fsl-mni152-templates (5.0.7-2) ...
Setting up libjsoncpp1:amd64 (1.7.4-3) ...
Setting up libvorbisfile3:amd64 (1.3.5-4) ...
Setting up libhtml-tagset-perl (3.20-3) ...
Setting up libedit2:amd64 (3.1-20160903-3) ...
Setting up libqt5core5a:amd64 (5.7.1+dfsg-3+b1) ...
Setting up libjpeg-turbo-progs (1:1.5.1-2) ...
Setting up libgsasl7 (1.8.0-8+b2) ...
Setting up libpaper1:amd64 (1.1.24+nmu5) ...

Creating config file /etc/papersize with new version
Setting up cpp (4:6.3.0-4) ...
Setting up libblosc1 (1.11.1+ds2-1) ...
Setting up libx265-95:amd64 (2.1-2+b2) ...
Setting up gconf2-common (3.2.6-4) ...

Creating config file /etc/gconf/2/path with new version
Setting up libxerces-c3.1:amd64 (3.1.4+debian-2) ...
Setting up libsm6:amd64 (2:1.2.2-1+b3) ...
Setting up kmod (23-2) ...
Setting up neurodebian-popularity-contest (0.37.6) ...
Setting up libpaper-utils (1.1.24+nmu5) ...
Setting up libqt5dbus5:amd64 (5.7.1+dfsg-3+b1) ...
Setting up libfont-afm-perl (1.20-2) ...
Setting up libproj12 (4.9.3-1) ...
Setting up gir1.2-atk-1.0:amd64 (2.22.0-1) ...
Setting up fontconfig-config (2.11.0-6.7) ...
Setting up libzmq5:amd64 (4.2.1-4) ...
Setting up libgcc-6-dev:amd64 (6.3.0-18) ...
Setting up libtag1v5:amd64 (1.11.1+dfsg.1-0.1) ...
Setting up libisc160:amd64 (1:9.10.3.dfsg.P4-12.3+deb9u1) ...
Setting up libpam-cap:amd64 (1:2.25-1) ...
Setting up libodbc1:amd64 (2.3.4-1) ...
Setting up libstdc++-6-dev:amd64 (6.3.0-18) ...
Setting up libqt5network5:amd64 (5.7.1+dfsg-3+b1) ...
Setting up tex-common (6.06) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libwacom2:amd64 (0.22-1+b1) ...
Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-3) ...
Setting up libmng1:amd64 (1.0.10+dfsg-3.1+b5) ...
Setting up python-matplotlib-data (2.0.0+dfsg1-2) ...
Setting up libglpk40:amd64 (4.61-1) ...
Setting up libltdl-dev:amd64 (2.4.6-2) ...
Setting up libdrm-amdgpu1:amd64 (2.4.74-1) ...
Setting up libfile-which-perl (1.21-1) ...
Setting up libencode-locale-perl (1.05-1) ...
Setting up ruby-test-unit (3.1.7-2) ...
Setting up liberror-perl (0.17024-1) ...
Setting up libdjvulibre21:amd64 (3.5.27.1-7) ...
Setting up dconf-service (0.26.0-2+b1) ...
Setting up gettext (0.19.8.1-2) ...
Setting up libv4l-0:amd64 (1.12.3-1) ...
Setting up libopenmpt0:amd64 (0.2.7386~beta20.3-3+deb9u2) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up dictionaries-common (1.27.2) ...
Setting up rename (0.20-4) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
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Setting up libarchive13:amd64 (3.2.2-2) ...
Setting up libgvpr2 (2.38.0-17) ...
Setting up libcap2-bin (1:2.25-1) ...
Setting up libdbus-glib-1-2:amd64 (0.108-2) ...
Setting up libosmesa6:amd64 (13.0.6-1+b2) ...
Setting up libgdcm2.6:amd64 (2.6.6-3) ...
Setting up libfile-homedir-perl (1.00-1) ...
Setting up lua-json (1.3.3-2) ...
Setting up libipc-system-simple-perl (1.25-3) ...
Setting up libfile-basedir-perl (0.07-1) ...
Setting up libflite1:amd64 (2.0.0-release-3+b1) ...
Setting up liblapack3 (3.7.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libio-html-perl (1.001-1) ...
Setting up libgconf-2-4:amd64 (3.2.6-4+b1) ...
Setting up fonts-lobstertwo (2.0-2) ...
Setting up libllvm3.9:amd64 (1:3.9.1-9) ...
Setting up libgbm1:amd64 (13.0.6-1+b2) ...
Setting up libgfortran-6-dev:amd64 (6.3.0-18) ...
Setting up libtie-ixhash-perl (1.23-2) ...
Setting up libflac8:amd64 (1.3.2-1) ...
Setting up libdpkg-perl (1.18.24) ...
Setting up tex-gyre (20160520-1) ...
Setting up python2.7 (2.7.13-2) ...
Setting up libwebpmux2:amd64 (0.5.2-1) ...
Setting up libnss3:amd64 (2:3.26.2-1.1) ...
Setting up libxfont2:amd64 (1:2.0.1-3) ...
Setting up libharfbuzz0b:amd64 (1.4.2-1) ...
Setting up libdc1394-22:amd64 (2.2.5-1) ...
Setting up libnl-route-3-200:amd64 (3.2.27-2) ...
Setting up preview-latex-style (11.90-1) ...
Setting up autoconf (2.69-10) ...
Setting up libthai0:amd64 (0.1.26-1) ...
Setting up libqt4-sql:amd64 (4:4.8.7+dfsg-11) ...
Setting up exim4-base (4.89-2+deb9u1) ...
exim: DB upgrade, deleting hints-db
Setting up fakeroot (1.21-3.1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up libinput-bin (1.6.3-1) ...
Setting up tcpd (7.6.q-26) ...
Setting up libdsdp-5.8gf (5.8-9.4) ...
Setting up libyaml-tiny-perl (1.70-1) ...
Setting up libsuperlu5:amd64 (5.2.1+dfsg1-2) ...
Setting up libhwloc5:amd64 (1.11.5-1) ...
Setting up libkmlbase1:amd64 (1.3.0-3) ...
Setting up libio-socket-ssl-perl (2.044-1) ...
Setting up libxfont1:amd64 (1:1.5.2-4) ...
Setting up gir1.2-javascriptcoregtk-4.0:amd64 (2.16.3-2) ...
Setting up gcc-6 (6.3.0-18) ...
Setting up fsl-atlases (5.0.7-2) ...
Setting up g++-6 (6.3.0-18) ...
Setting up gconf-service (3.2.6-4+b1) ...
Setting up libogdi3.2 (3.2.0+ds-2) ...
Setting up libpython-stdlib:amd64 (2.7.13-2) ...
Setting up libhwloc-plugins (1.11.5-1) ...
Setting up libalgorithm-merge-perl (0.08-3) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libkmlxsd1:amd64 (1.3.0-3) ...
Setting up libdrm-intel1:amd64 (2.4.74-1) ...
Setting up libgeos-c1v5 (3.5.1-3) ...
Setting up libisccc140:amd64 (1:9.10.3.dfsg.P4-12.3+deb9u1) ...
Setting up libwacom-bin (0.22-1+b1) ...
Setting up dpkg-dev (1.18.24) ...
Setting up libalgorithm-diff-xs-perl (0.04-4+b2) ...
Setting up aria2 (1.30.0-2) ...
Setting up librubberband2:amd64 (1.8.1-7) ...
Setting up libfile-desktopentry-perl (0.22-1) ...
Setting up dcm2niix (1:1.0.20170624+git8-g87d2142-1~nd90+1) ...
Setting up libdcmtk8 (3.6.1~20160216-4) ...
Setting up proj-bin (4.9.3-1) ...
Setting up python-fuse (2:0.2.1-14) ...
Setting up guile-2.0-libs:amd64 (2.0.13+1-4) ...
Setting up tcl8.6 (8.6.6+dfsg-1+b1) ...
Setting up libhtml-parser-perl (3.72-3) ...
Setting up libpython2.7:amd64 (2.7.13-2) ...
Setting up libgeotiff2:amd64 (1.4.2-2+b1) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libqt5sql5:amd64 (5.7.1+dfsg-3+b1) ...
Setting up libquvi-scripts-0.9 (0.9.20131130-1.1) ...
Setting up libjack-jackd2-0:amd64 (1.9.10+20150825git1ed50c92~dfsg-5) ...
Setting up libwebpdemux2:amd64 (0.5.2-1) ...
Setting up libexpat1-dev:amd64 (2.2.0-2) ...
Setting up libspatialite7:amd64 (4.3.0a-5+b1) ...
Setting up libarpack2 (3.4.0-1+b1) ...
Setting up man-db (2.7.6.1-2) ...
Building database of manual pages ...
Setting up libopenal1:amd64 (1:1.17.2-4+b2) ...
Setting up fsl-harvard-oxford-cortical-lateralized-atlas (5.0.7-2) ...
Setting up libpython2.7-dev:amd64 (2.7.13-2) ...
Setting up libkmldom1:amd64 (1.3.0-3) ...
Setting up libavahi-common3:amd64 (0.6.32-2) ...
Setting up exim4-daemon-light (4.89-2+deb9u1) ...
invoke-rc.d: could not determine current runlevel
invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block.
Initializing GnuTLS DH parameter file
Setting up libquvi-0.9-0.9.3:amd64 (0.9.3-1.2) ...
Setting up libavahi-glib1:amd64 (0.6.32-2) ...
Setting up dbus (1.10.18-1) ...
invoke-rc.d: could not determine current runlevel
invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block.
Setting up libvorbisenc2:amd64 (1.3.5-4) ...
Setting up libnewt0.52:amd64 (0.52.19-1+b1) ...
Setting up libcaca0:amd64 (0.99.beta19-2+b2) ...
Setting up aspell (0.60.7~20110707-3+b2) ...
Setting up libtelepathy-glib0:amd64 (0.24.1-1.1) ...
Setting up openssh-client (1:7.4p1-10+deb9u1) ...
Setting up libfile-mimeinfo-perl (0.27-1) ...
Setting up dconf-gsettings-backend:amd64 (0.26.0-2+b1) ...
Setting up python2.7-dev (2.7.13-2) ...
Setting up libkyotocabinet16v5:amd64 (1.2.76-4.2+b1) ...
Setting up libqtdbus4:amd64 (4:4.8.7+dfsg-11) ...
Setting up libxcb1:amd64 (1.12-1) ...
Setting up lmodern (2.004.5-3) ...
Setting up hunspell-en-us (20070829-7) ...
Setting up python (2.7.13-2) ...
Setting up python-contextlib2 (0.5.4-1) ...
Setting up python-gmpy (1.17-3) ...
Setting up libfile-stripnondeterminism-perl (0.034-1) ...
Setting up python-sip (4.18.1+dfsg-2) ...
Setting up python-pyparsing (2.1.10+dfsg1-1) ...
Setting up libxcb-xkb1:amd64 (1.12-1) ...
Setting up libavahi-core7:amd64 (0.6.32-2) ...
Setting up libqt5qml5:amd64 (5.7.1-2+b2) ...
Setting up python-idna (2.2-1) ...
Setting up libtool (2.4.6-2) ...
Setting up libenchant1c2a:amd64 (1.6.0-11+b1) ...
Setting up python-simplejson (3.10.0-1) ...
Setting up libxcb-xinerama0:amd64 (1.12-1) ...
Setting up libmailutils5:amd64 (1:3.1.1-1) ...
Setting up libibverbs1 (1.2.1-2) ...
Setting up libxcb-present0:amd64 (1.12-1) ...
Setting up libpython-dev:amd64 (2.7.13-2) ...
Setting up libfontconfig1:amd64 (2.11.0-6.7+b1) ...
Setting up git-man (1:2.11.0-3+nd1~nd90+1) ...
Setting up libxcb-dri2-0:amd64 (1.12-1) ...
Setting up libxcb-dri3-0:amd64 (1.12-1) ...
Setting up libxcb-glx0:amd64 (1.12-1) ...
Setting up libxcb-randr0:amd64 (1.12-1) ...
Setting up gfortran-6 (6.3.0-18) ...
Setting up libhdf5-cpp-100:amd64 (1.10.0-patch1+docs-3) ...
Setting up python-msgpack (0.4.8-1) ...
Setting up libnm-util2:amd64 (1.6.2-3) ...
Setting up python-functools32 (3.2.3.2-3) ...
Setting up libdns162:amd64 (1:9.10.3.dfsg.P4-12.3+deb9u1) ...
Setting up python-yaml (3.12-1) ...
Setting up python-cssselect (1.0.1-1) ...
Setting up libxcb-xfixes0:amd64 (1.12-1) ...
Setting up libxcb-icccm4:amd64 (0.4.1-1) ...
Setting up libhttp-date-perl (6.02-1) ...
Setting up python-simplegeneric (0.8.1-1) ...
Setting up libxcb-render0:amd64 (1.12-1) ...
Setting up libnetcdf11 (1:4.4.1.1-2) ...
Setting up libnet-smtp-ssl-perl (1.04-1) ...
Setting up python-crypto (2.6.1-7) ...
Setting up python-lz4 (0.8.2+dfsg-2) ...
Setting up libxcb-util0:amd64 (0.3.8-3+b2) ...
Setting up python-sqlparse (0.2.2-1) ...
Setting up python-attr (16.3.0-1) ...
Setting up libgstreamer1.0-0:amd64 (1.10.4-1) ...
Setcap worked! gst-ptp-helper is not suid!
Setting up libharfbuzz-icu0:amd64 (1.4.2-1) ...
Setting up python-snappy (0.5-1.1) ...
Setting up python-dicom (0.9.9-2) ...
Setting up python-traits (4.6.0-1) ...
Setting up po-debconf (1.0.20) ...
Setting up gsettings-desktop-schemas (3.22.0-1) ...
Setting up libnm-glib4:amd64 (1.6.2-3) ...
Setting up libqt4-script:amd64 (4:4.8.7+dfsg-11) ...
Setting up python-reportlab-accel:amd64 (3.3.0-2) ...
Setting up libgtk-3-common (3.22.11-1) ...
Setting up python-reportlab (3.3.0-2) ...
Setting up libqt4-sql-mysql:amd64 (4:4.8.7+dfsg-11) ...
Setting up python-tqdm (4.11.2-1) ...
Setting up python-ply (3.9-1) ...
Setting up python-dev (2.7.13-2) ...
Setting up python-pyasn1 (0.1.9-2) ...
Setting up python-wxversion (3.0.2.0+dfsg-4) ...
Setting up libpoppler64:amd64 (0.48.0-2) ...
Setting up python-cvxopt (1.1.4-1.5) ...
Setting up python-joblib (0.10.3+git55-g660fe5d-1) ...
Setting up libisccfg140:amd64 (1:9.10.3.dfsg.P4-12.3+deb9u1) ...
Setting up whiptail (0.52.19-1+b1) ...
Setting up python-tz (2016.7-0.3) ...
Setting up python-humanize (0.5.1-2) ...
Setting up libx11-6:amd64 (2:1.6.4-3) ...
Setting up libinput10:amd64 (1.6.3-1) ...
Setting up libgl1-mesa-dri:amd64 (13.0.6-1+b2) ...
Setting up tcl (8.6.0+9) ...
Setting up python-imagesize (0.7.1-1) ...
Setting up python-pp (1.6.5-1) ...
Setting up python-twisted-bin:amd64 (16.6.0-2) ...
Setting up xfonts-utils (1:7.7+4) ...
Setting up python-colorama (0.3.7-1) ...
Setting up python-alabaster (0.7.8-1) ...
Setting up librdmacm1 (1.1.0-2) ...
Setting up gcc (4:6.3.0-4) ...
Setting up libarmadillo7 (1:7.600.2+dfsg-2) ...
Setting up python-pkg-resources (33.1.1-1) ...
Setting up python-roman (2.0.0-2) ...
Setting up quvi (0.9.4-1.1+b1) ...
Setting up mailutils (1:3.1.1-1) ...
update-alternatives: using /usr/bin/frm.mailutils to provide /usr/bin/frm (frm) in auto mode
update-alternatives: using /usr/bin/from.mailutils to provide /usr/bin/from (from) in auto mode
update-alternatives: using /usr/bin/messages.mailutils to provide /usr/bin/messages (messages) in auto mode
update-alternatives: using /usr/bin/movemail.mailutils to provide /usr/bin/movemail (movemail) in auto mode
update-alternatives: using /usr/bin/readmsg.mailutils to provide /usr/bin/readmsg (readmsg) in auto mode
update-alternatives: using /usr/bin/dotlock.mailutils to provide /usr/bin/dotlock (dotlock) in auto mode
update-alternatives: using /usr/bin/mail.mailutils to provide /usr/bin/mailx (mailx) in auto mode
Setting up python-pyasn1-modules (0.0.7-0.1) ...
Setting up libxkbcommon-x11-0:amd64 (0.7.1-1) ...
Setting up libxmuu1:amd64 (2:1.1.2-2) ...
Setting up python-markupsafe (0.23-3) ...
Setting up python-numpy (1:1.12.1-3) ...
Setting up python-nipy-lib (0.4.1-1~nd90+1) ...
Setting up python-keyrings.alt (1.3-1) ...
Setting up cython (0.25.2-1) ...
Setting up libhtml-tree-perl (5.03-2) ...
Setting up python-tables-lib (3.3.0-5) ...
Setting up qdbus (4:4.8.7+dfsg-11) ...
Setting up python-pyld (0.6.8-1) ...
Setting up gir1.2-gconf-2.0 (3.2.6-4+b1) ...
Setting up libxcb-sync1:amd64 (1.12-1) ...
Setting up libass5:amd64 (1:0.13.4-2) ...
Setting up libqt5sql5-sqlite:amd64 (5.7.1+dfsg-3+b1) ...
Setting up python-ipython-genutils (0.1.0-2) ...
Setting up python-gobject-2 (2.28.6-13) ...
Setting up libsndfile1:amd64 (1.0.27-3) ...
Setting up python-configparser (3.3.0r2-2) ...
Setting up python-smmap (2.0.1-1) ...
Setting up i965-va-driver:amd64 (1.7.3-1) ...
Setting up python-cffi-backend (1.9.1-2) ...
Setting up python-incremental (16.10.1-3) ...
Setting up python-gi (3.22.0-2) ...
Setting up python-six (1.10.0-3) ...
Setting up python-constantly (15.1.0-1) ...
Setting up python-wcwidth (0.1.7+dfsg1-1) ...
Setting up python-xlrd (1.0.0-1) ...
Setting up python-cbor (0.1.24-1+b1) ...
Setting up python-w3lib (1.14.3-1) ...
Setting up python-pygments (2.2.0+dfsg-1) ...
Setting up python-ptyprocess (0.5.1-1) ...
Setting up libaa1:amd64 (1.4p5-44+b1) ...
Setting up libkmlengine1:amd64 (1.3.0-3) ...
Setting up python-bs4 (4.5.3-1) ...
Setting up python-libsvm (3.21+ds-1.1) ...
Setting up python-zope.interface (4.3.2-1) ...
Setting up alsa-utils (1.1.3-1) ...
Setting up python-mysqldb (1.3.7-1.1) ...
Setting up python-psutil (5.0.1-1) ...
Setting up python-pandas-lib (0.19.2-5.1) ...
Setting up python-isodate (0.5.4-1) ...
Setting up exim4 (4.89-2+deb9u1) ...
Setting up python-sklearn-lib (0.19.0-1~nd90+1) ...
Setting up python-pbr (1.10.0-1) ...
update-alternatives: using /usr/bin/python2-pbr to provide /usr/bin/pbr (pbr) in auto mode
Setting up libbluray1:amd64 (1:0.9.3-3) ...
Setting up mesa-va-drivers:amd64 (13.0.6-1+b2) ...
Setting up glib-networking:amd64 (2.50.0-1+b1) ...
Setting up python-appdirs (1.4.0-3) ...
Setting up python-enum34 (1.1.6-1) ...
Setting up aspell-en (2016.11.20-0-0.1) ...
Setting up python-lxml (3.7.1-1) ...
Setting up python-serial (3.2.1-1) ...
Setting up python-renderpm:amd64 (3.3.0-2) ...
Setting up libfile-listing-perl (6.04-1) ...
Setting up libxcomposite1:amd64 (1:0.4.4-2) ...
Setting up libxcb-shm0:amd64 (1.12-1) ...
Setting up python-funcsigs (1.0.2-3) ...
Setting up libxpm4:amd64 (1:3.5.12-1) ...
Setting up libxt6:amd64 (1:1.1.5-1) ...
Setting up python-libxml2 (2.9.4+dfsg1-2.2) ...
Setting up enchant (1.6.0-11+b1) ...
Setting up python-indexed-gzip (0.3.1.1-1~nd90+1) ...
Setting up libxcb-shape0:amd64 (1.12-1) ...
Setting up libxrender1:amd64 (1:0.9.10-1) ...
Setting up python-citeproc (0.3.0-2) ...
Setting up python-iso8601 (0.1.11-1) ...
Setting up libhttp-message-perl (6.11-1) ...
Setting up g++ (4:6.3.0-4) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up python-statsmodels-lib (0.8.0-1~nd90+1) ...
Setting up libavahi-client3:amd64 (0.6.32-2) ...
Setting up libxcb-keysyms1:amd64 (0.4.0-1+b2) ...
Setting up python-django (1:1.10.7-2) ...
Setting up python-decorator (4.0.11-1) ...
Setting up python-concurrent.futures (3.0.5-3) ...
Setting up libbind9-140:amd64 (1:9.10.3.dfsg.P4-12.3+deb9u1) ...
Setting up python-antlr (2.7.7+dfsg-7) ...
Setting up python-subprocess32 (3.2.7-2) ...
Setting up libinsighttoolkit4.10 (4.10.1-dfsg1-1.1+b1) ...
Setting up python-jsmin (2.2.1-2) ...
Setting up python-github (1.26.0-1) ...
Setting up libxft2:amd64 (2.3.2-1+b2) ...
Setting up python-dbus (1.2.4-1+b1) ...
Remove stale byte-compiled files...
Setting up python-pathlib2 (2.2.0+really2.1.0-1) ...
Setting up libmission-control-plugins0 (1:5.16.3-2.1) ...
Setting up libqt4-dbus:amd64 (4:4.8.7+dfsg-11) ...
Setting up python-pam (0.4.2-13.2) ...
Setting up python-traitlets (4.3.1-1) ...
Setting up python-ipaddress (1.0.17-1) ...
Setting up python-argcomplete (1.8.1-1) ...
Setting up afni-common (16.2.07~dfsg.1-5~nd90+1) ...
Setting up python-queuelib (1.4.2-1) ...
Setting up python-nose (1.3.7-2) ...
Setting up python-pil:amd64 (4.0.0-4) ...
Setting up python-mpmath (0.19-3) ...
Setting up python-patsy (0.4.1+git34-ga5b54c2-1) ...
Setting up libqt4-network:amd64 (4:4.8.7+dfsg-11) ...
Setting up python-webencodings (0.5-2) ...
Setting up git (1:2.11.0-3+nd1~nd90+1) ...
Setting up python-future (0.15.2-4) ...
update-alternatives: using /usr/bin/python2-futurize to provide /usr/bin/futurize (futurize) in auto mode
update-alternatives: using /usr/bin/python2-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode
Setting up isympy-common (1.0-3) ...
Setting up libavahi-gobject0:amd64 (0.6.32-2) ...
Setting up xfonts-base (1:1.0.4+nmu1) ...
Setting up libaudio2:amd64 (1.9.4-5+b1) ...
Setting up fontconfig (2.11.0-6.7+b1) ...
Regenerating fonts cache... done.
Setting up libhttp-negotiate-perl (6.00-2) ...
Setting up libcups2:amd64 (2.2.1-8) ...
Setting up libegl1-mesa:amd64 (13.0.6-1+b2) ...
Setting up python-mvpa2-lib (2.6.1-1~nd90+1) ...
Setting up libxkbfile1:amd64 (1:1.0.9-2) ...
Setting up python-docutils (0.13.1+dfsg-2) ...
update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode
Setting up bind9-host (1:9.10.3.dfsg.P4-12.3+deb9u1) ...
Setting up python-wrapt (1.9.0-2) ...
Setting up gfortran (4:6.3.0-4) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libgstreamer-plugins-base1.0-0:amd64 (1.10.4-1) ...
Setting up python-setuptools (33.1.1-1) ...
Setting up libnetcdf-c++4 (4.2-6) ...
Setting up libxcb-render-util0:amd64 (0.3.9-1) ...
Setting up git-remote-gcrypt (1.0.1-1) ...
Setting up python-urllib3 (1.19.1-1) ...
Setting up python-h5py (2.7.0-1) ...
Setting up libmailtools-perl (2.18-1) ...
Setting up python-numexpr (2.6.2-1~nd90+1) ...
Setting up python-configobj (5.0.6-2) ...
Setting up ants (2.2.0-1~nd90+1) ...
Setting up libhtml-format-perl (2.12-1) ...
Setting up python-networkx (1.11-2) ...
Setting up python-prompt-toolkit (1.0.9-1) ...
Setting up python-chardet (2.3.0-2) ...
Setting up git-annex-standalone (6.20170810+gitgff6f9e203-1~ndall+1) ...
Setting up libxcb-image0:amd64 (0.4.0-1+b2) ...
Setting up python-pycparser (2.17-2) ...
Setting up libxext6:amd64 (2:1.3.3-1+b2) ...
Setting up libxfixes3:amd64 (1:5.0.3-1) ...
Setting up python-scipy (0.18.1-2) ...
Setting up libhttp-cookies-perl (6.01-1) ...
Setting up python-xlwt (0.7.5+debian1-1) ...
Setting up libfabric1 (1.4.0-1) ...
Setting up python-trollius (2.1~b1-4) ...
Setting up libblas-dev (3.7.0-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up python-jinja2 (2.8-1) ...
Setting up python-click (6.6-1) ...
Setting up build-essential (12.3) ...
Setting up python-py (1.4.32-3) ...
Setting up python-httpretty (0.8.14-1) ...
Setting up libatspi2.0-0:amd64 (2.22.0-6) ...
Setting up python-mvpa2 (2.6.1-1~nd90+1) ...
Setting up gifsicle (1.88-3) ...
Setting up python-babel (2.3.4+dfsg.1-2) ...
update-alternatives: using /usr/bin/pybabel-python2 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up libxss1:amd64 (1:1.2.2-1) ...
Setting up libgdk-pixbuf2.0-0:amd64 (2.36.5-2) ...
Setting up python-mdp (3.5-1) ...
Setting up python-rdflib (4.2.1-2) ...
Setting up libsoup2.4-1:amd64 (2.56.0-2) ...
Setting up telepathy-mission-control-5 (1:5.16.3-2.1) ...
Setting up libgd3:amd64 (2.2.4-2) ...
Setting up python-mock (2.0.0-3) ...
Setting up python-sparqlwrapper (1.7.6-3~nd90+1) ...
Setting up libvdpau1:amd64 (1.1.1-6) ...
Setting up gir1.2-gdkpixbuf-2.0:amd64 (2.36.5-2) ...
Setting up python-qrcode (5.3-1) ...
update-alternatives: using /usr/bin/python2-qr to provide /usr/bin/qr (qr) in auto mode
Setting up python-pywt (0.3.0-1+b1) ...
Setting up libhttp-daemon-perl (6.01-1) ...
Setting up libsoup-gnome2.4-1:amd64 (2.56.0-2) ...
Setting up python-pexpect (4.2.1-1) ...
Setting up python-pytest (3.0.6-1) ...
Setting up libqt4-xmlpatterns:amd64 (4:4.8.7+dfsg-11) ...
Setting up python-gitdb (2.0.0-2) ...
Setting up libkmlconvenience1:amd64 (1.3.0-3) ...
Setting up libqtassistantclient4:amd64 (4.6.3-7+b1) ...
Setting up python-cycler (0.10.0-1) ...
Setting up gir1.2-soup-2.4:amd64 (2.56.0-2) ...
Setting up libxmu6:amd64 (2:1.1.2-2) ...
Setting up xauth (1:1.0.9-1+b2) ...
Setting up libgdchart-gd2-noxpm (0.11.5-8+b1) ...
Setting up avahi-daemon (0.6.32-2) ...
invoke-rc.d: could not determine current runlevel
invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block.
invoke-rc.d: could not determine current runlevel
invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block.
Setting up python-dateutil (2.5.3-2) ...
Setting up python-imaging (4.0.0-4) ...
Setting up libcupsimage2:amd64 (2.2.1-8) ...
Setting up fonts-sil-gentiumplus-compact (5.000-2) ...
Setting up python-sklearn (0.19.0-1~nd90+1) ...
Setting up gtk-update-icon-cache (3.22.11-1) ...
Setting up libxcursor1:amd64 (1:1.1.14-1+b4) ...
Setting up python-openpyxl (2.3.0-3) ...
Setting up python-pickleshare (0.7.4-1) ...
Setting up libxxf86dga1:amd64 (2:1.1.4-1+b3) ...
Setting up libkmlregionator1:amd64 (1.3.0-3) ...
Setting up libxm4:amd64 (2.3.4-13) ...
Setting up va-driver-all:amd64 (1.7.3-2) ...
Setting up libpango-1.0-0:amd64 (1.40.5-1) ...
Setting up libwayland-egl1-mesa:amd64 (13.0.6-1+b2) ...
Setting up python-cryptography (1.7.1-3) ...
Setting up libatk-bridge2.0-0:amd64 (2.22.0-2) ...
Setting up python-statsmodels (0.8.0-1~nd90+1) ...
Setting up libhtml-form-perl (6.03-1) ...
Setting up python-telepathy (0.15.19-3) ...
Setting up python-cffi (1.9.1-2) ...
Setting up python-requests (2.12.4-1) ...
Setting up libxv1:amd64 (2:1.0.11-1) ...
Setting up librest-0.7-0:amd64 (0.8.0-2) ...
Setting up libopenmpi2:amd64 (2.0.2-2) ...
Setting up python-nibabel (2.1.0-1) ...
Setting up fonts-sil-gentiumplus (5.000-1) ...
Setting up python-sympy (1.0-3) ...
Setting up python-tables (3.3.0-5) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Setting up python-html5lib (0.999999999-1) ...
Setting up python-git (2.1.3-1~nd90+1) ...
Setting up python-dcmstack (0.6.2+git33-gb43919a.1-1) ...
Setting up libgs9:amd64 (9.20~dfsg-3.2) ...
Setting up telepathy-salut (0.8.1-5.1) ...
Setting up python-prov (1.5.0-1+nd1~nd90+1) ...
Setting up libxrandr2:amd64 (2:1.5.1-1) ...
Setting up libva-x11-1:amd64 (1.7.3-2) ...
Setting up libspectre1:amd64 (0.2.8-1) ...
Setting up python-secretstorage (2.3.1-2) ...
Setting up libxi6:amd64 (2:1.7.9-1) ...
Setting up liblapack-dev (3.7.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libxaw7:amd64 (2:1.0.13-1+b2) ...
Setting up gir1.2-atspi-2.0:amd64 (2.22.0-6) ...
Setting up libcairo2:amd64 (1.14.8-1) ...
Setting up libnss-mdns:amd64 (0.10-8) ...
First installation detected...
Checking NSS setup...
Setting up libnotify4:amd64 (0.7.7-2) ...
Setting up libxinerama1:amd64 (2:1.1.3-1+b3) ...
Setting up libpoppler-glib8:amd64 (0.48.0-2) ...
Setting up libqtgui4:amd64 (4:4.8.7+dfsg-11) ...
Setting up python-keyring (10.1-1) ...
Setting up libhdf5-openmpi-100:amd64 (1.10.0-patch1+docs-3) ...
Setting up qt-at-spi:amd64 (0.4.0-5) ...
Setting up libxdamage1:amd64 (1:1.1.4-2+b3) ...
Setting up python-sphinx (1.4.9-2) ...
Setting up libavutil55:amd64 (7:3.2.5-1) ...
Setting up python-nacl (1.0.1-2) ...
Setting up x11-xkb-utils (7.7+3+b1) ...
Setting up libqt4-designer:amd64 (4:4.8.7+dfsg-11) ...
Setting up python-openssl (16.2.0-1) ...
Setting up python-vcr (1.10.0-1) ...
Setting up python-nilearn (0.2.5~dfsg.1-1~nd90+1) ...
Setting up python-ipython (5.1.0-3) ...
Setting up libtk8.6:amd64 (8.6.6-1+b1) ...
Setting up mesa-vdpau-drivers:amd64 (13.0.6-1+b2) ...
Setting up libqt4-help:amd64 (4:4.8.7+dfsg-11) ...
Setting up libcairo-gobject2:amd64 (1.14.8-1) ...
Setting up python-nipy (0.4.1-1~nd90+1) ...
Setting up libxmhtml1.1:amd64 (1.1.10-2+b1) ...
Setting up python-pandas (0.19.2-5.1) ...
Setting up ipython (5.1.0-3) ...
Setting up python-duecredit (0.6.0-1) ...
Setting up ghostscript (9.20~dfsg-3.2) ...
Setting up xterm (327-2) ...
update-alternatives: using /usr/bin/xterm to provide /usr/bin/x-terminal-emulator (x-terminal-emulator) in auto mode
update-alternatives: using /usr/bin/lxterm to provide /usr/bin/x-terminal-emulator (x-terminal-emulator) in auto mode
Setting up libswresample2:amd64 (7:3.2.5-1) ...
Setting up openmpi-bin (2.0.2-2) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up texlive-binaries (2016.20160513.41080.dfsg-2) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Setting up libxtst6:amd64 (2:1.2.3-1) ...
Setting up libpangoft2-1.0-0:amd64 (1.40.5-1) ...
Setting up libcupsfilters1:amd64 (1.11.6-3) ...
Setting up python-cfflib (2.0.5-2) ...
Setting up python-boto (2.44.0-1) ...
Setting up libgl1-mesa-glx:amd64 (13.0.6-1+b2) ...
Setting up libswscale4:amd64 (7:3.2.5-1) ...
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update-fmtutil has updated the following file(s):
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    /var/lib/texmf/fmtutil.cnf-TEXLIVEDIST
If you want to activate the changes in the above file(s),
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## Installing the NodeSource Node.js v6.x repo...

## Populating apt-get cache...

+ apt-get update
Hit:2 http://neuro.debian.net/debian stretch InRelease
Ign:1 http://cdn-fastly.deb.debian.org/debian stretch InRelease
Hit:3 http://neuro.debian.net/debian data InRelease
Hit:4 http://cdn-fastly.deb.debian.org/debian stretch Release
Reading package lists...

## Installing packages required for setup: apt-transport-https lsb-release...

+ apt-get install -y apt-transport-https lsb-release > /dev/null 2>&1

## Confirming "stretch" is supported...

+ curl -sLf -o /dev/null 'https://deb.nodesource.com/node_6.x/dists/stretch/Release'

## Adding the NodeSource signing key to your keyring...

+ curl -s https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add -
OK

## Creating apt sources list file for the NodeSource Node.js v6.x repo...

+ echo 'deb https://deb.nodesource.com/node_6.x stretch main' > /etc/apt/sources.list.d/nodesource.list
+ echo 'deb-src https://deb.nodesource.com/node_6.x stretch main' >> /etc/apt/sources.list.d/nodesource.list

## Running `apt-get update` for you...

+ apt-get update
Hit:2 http://neuro.debian.net/debian stretch InRelease
Ign:1 http://cdn-fastly.deb.debian.org/debian stretch InRelease
Hit:3 http://neuro.debian.net/debian data InRelease
Hit:4 http://cdn-fastly.deb.debian.org/debian stretch Release
Get:6 https://deb.nodesource.com/node_6.x stretch InRelease [4635 B]
Get:7 https://deb.nodesource.com/node_6.x stretch/main Sources [765 B]
Get:8 https://deb.nodesource.com/node_6.x stretch/main amd64 Packages [960 B]
Fetched 6360 B in 0s (8644 B/s)
Reading package lists...

## Run `apt-get install nodejs` (as root) to install Node.js v6.x and npm

Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  nodejs
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 10.3 MB of archives.
After this operation, 51.4 MB of additional disk space will be used.
Get:1 https://deb.nodesource.com/node_6.x stretch/main amd64 nodejs amd64 6.11.2-1nodesource1~stretch1 [10.3 MB]
Fetched 10.3 MB in 0s (13.6 MB/s)
Selecting previously unselected package nodejs.
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(Reading database ... 181701 files and directories currently installed.)
Preparing to unpack .../nodejs_6.11.2-1nodesource1~stretch1_amd64.deb ...
Unpacking nodejs (6.11.2-1nodesource1~stretch1) ...
Setting up nodejs (6.11.2-1nodesource1~stretch1) ...
Processing triggers for man-db (2.7.6.1-2) ...
/usr/bin/bids-validator -> /usr/lib/node_modules/bids-validator/bin/bids-validator
/usr/lib
`-- bids-validator@0.22.0 
  +-- ajv@4.11.8 
  | +-- co@4.6.0 
  | `-- json-stable-stringify@1.0.1 
  |   `-- jsonify@0.0.0 
  +-- async@2.5.0 
  | `-- lodash@4.17.4 
  +-- bytes@2.5.0 
  +-- cliff@0.1.10 
  | +-- colors@1.0.3 
  | +-- eyes@0.1.8 
  | `-- winston@0.8.3 
  |   +-- async@0.2.10 
  |   +-- colors@0.6.2 
  |   +-- cycle@1.0.3 
  |   +-- isstream@0.1.2 
  |   +-- pkginfo@0.3.1 
  |   `-- stack-trace@0.0.10 
  +-- colors@1.1.2 
  +-- jshint@2.9.5 
  | +-- cli@1.0.1 
  | | `-- glob@7.1.2 
  | |   +-- fs.realpath@1.0.0 
  | |   +-- inflight@1.0.6 
  | |   | `-- wrappy@1.0.2 
  | |   +-- inherits@2.0.3 
  | |   +-- minimatch@3.0.4 
  | |   +-- once@1.4.0 
  | |   `-- path-is-absolute@1.0.1 
  | +-- console-browserify@1.1.0 
  | | `-- date-now@0.1.4 
  | +-- exit@0.1.2 
  | +-- htmlparser2@3.8.3 
  | | +-- domelementtype@1.3.0 
  | | +-- domhandler@2.3.0 
  | | +-- domutils@1.5.1 
  | | | `-- dom-serializer@0.1.0 
  | | |   +-- domelementtype@1.1.3 
  | | |   `-- entities@1.1.1 
  | | +-- entities@1.0.0 
  | | `-- readable-stream@1.1.14 
  | |   +-- core-util-is@1.0.2 
  | |   +-- isarray@0.0.1 
  | |   `-- string_decoder@0.10.31 
  | +-- lodash@3.7.0 
  | +-- shelljs@0.3.0 
  | `-- strip-json-comments@1.0.4 
  +-- minimatch@3.0.3 
  | `-- brace-expansion@1.1.8 
  |   +-- balanced-match@1.0.0 
  |   `-- concat-map@0.0.1 
  +-- nifti-js@1.0.1 
  | `-- yargs@3.32.0 
  |   +-- camelcase@2.1.1 
  |   `-- window-size@0.1.4 
  +-- pako@1.0.5 
  +-- pluralize@3.1.0 
  `-- yargs@6.6.0 
    +-- camelcase@3.0.0 
    +-- cliui@3.2.0 
    | +-- strip-ansi@3.0.1 
    | | `-- ansi-regex@2.1.1 
    | `-- wrap-ansi@2.1.0 
    +-- decamelize@1.2.0 
    +-- get-caller-file@1.0.2 
    +-- os-locale@1.4.0 
    | `-- lcid@1.0.0 
    |   `-- invert-kv@1.0.0 
    +-- read-pkg-up@1.0.1 
    | +-- find-up@1.1.2 
    | | +-- path-exists@2.1.0 
    | | `-- pinkie-promise@2.0.1 
    | |   `-- pinkie@2.0.4 
    | `-- read-pkg@1.1.0 
    |   +-- load-json-file@1.1.0 
    |   | +-- graceful-fs@4.1.11 
    |   | +-- parse-json@2.2.0 
    |   | | `-- error-ex@1.3.1 
    |   | |   `-- is-arrayish@0.2.1 
    |   | +-- pify@2.3.0 
    |   | `-- strip-bom@2.0.0 
    |   |   `-- is-utf8@0.2.1 
    |   +-- normalize-package-data@2.4.0 
    |   | +-- hosted-git-info@2.5.0 
    |   | +-- is-builtin-module@1.0.0 
    |   | | `-- builtin-modules@1.1.1 
    |   | +-- semver@5.4.1 
    |   | `-- validate-npm-package-license@3.0.1 
    |   |   +-- spdx-correct@1.0.2 
    |   |   | `-- spdx-license-ids@1.2.2 
    |   |   `-- spdx-expression-parse@1.0.4 
    |   `-- path-type@1.1.0 
    +-- require-directory@2.1.1 
    +-- require-main-filename@1.0.1 
    +-- set-blocking@2.0.0 
    +-- string-width@1.0.2 
    | +-- code-point-at@1.1.0 
    | `-- is-fullwidth-code-point@1.0.0 
    |   `-- number-is-nan@1.0.1 
    +-- which-module@1.0.0 
    +-- y18n@3.2.1 
    `-- yargs-parser@4.2.1 
      `-- camelcase@3.0.0 

(B
/tmp/tmpfcuqaxvu/image
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python3.5/dist-packages/singularity/build/google.py", line 245, in run_build
    params=params)
  File "/usr/local/lib/python3.5/dist-packages/singularity/build/main.py", line 162, in run_build
    debug=params['debug'])
  File "/usr/local/lib/python3.5/dist-packages/singularity/package.py", line 130, in build_from_spec
    version = get_image_file_hash(image_path)
  File "/usr/local/lib/python3.5/dist-packages/singularity/reproduce.py", line 502, in get_image_file_hash
    with open(image_path, "rb") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpfcuqaxvu/image'
Error in sys.excepthook:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/apport_python_hook.py", line 67, in apport_excepthook
    binary = os.path.realpath(os.path.join(os.getcwd(), sys.argv[0]))
FileNotFoundError: [Errno 2] No such file or directory

Original exception was:
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python3.5/dist-packages/singularity/build/google.py", line 245, in run_build
    params=params)
  File "/usr/local/lib/python3.5/dist-packages/singularity/build/main.py", line 162, in run_build
    debug=params['debug'])
  File "/usr/local/lib/python3.5/dist-packages/singularity/package.py", line 130, in build_from_spec
    version = get_image_file_hash(image_path)
  File "/usr/local/lib/python3.5/dist-packages/singularity/reproduce.py", line 502, in get_image_file_hash
    with open(image_path, "rb") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpfcuqaxvu/image'

It's pretty common to do this - do you think for the next version of the hub it would be preferable to build somewhere other than /tmp? I've had this bug happen to me once before, and it's definitely apt to come up again. It's also good practice to clean up, so I don't want to discourage it. If you are able, please delete / kill this current build.

[yarikoptic]

holy guacamole... in principle nothing should cleanup /tmp that aggressively, silly me just picked up the "way to to things" from elsewhere while installing there bids-validator ;) indeed, building outside of /tmp though would be a good way to avoid such gotchas. Thank you @vsoch . I will stop/fix/push and see how it goes with a new one

[vsoch]

Eggcellent! Let's hope for a good build :)

[vsoch]

and +1 guacamole! :avocado: :avocado: :avocado: :heart: :heart: :heart:

[yarikoptic]

woohoo @vsoch -- it built! and seems to run fine! thanks for all the help

[vsoch]

woooho! No problemo.

[stebo85]

I tried building the minc singularity build based on the docker minc https://hub.docker.com/r/simexp/minc-toolkit/ but unfortunately the graphical applications then do not work and I haven't found a way of fixing this :( register: error while loading shared libraries: libGL.so.1: cannot open shared object file: No such file or directory

Do you have any idea how I could get the build to work on the singularity servers?

[vsoch]

hey @stebo85 - have you tried just bootstrapping that image? If you could provide the steps (singularity definition or commands to reproduce your work thus far) it would be useful to help.

[stebo85]

hey @vsoch. I got it working now :) I built an image based on the deb packages instead of starting from the source code and this works nicely - even with applications that rely on OpenGL. Thank you for your help. Cheers.

[vsoch]

phew that is so good to hear! I've also had more luck taking that approach. I'm going to close the issue.

[yarikoptic]

Well... You might like to add a safeguard that if no output received eg for an hour - kill the build ( similar to how Travis etc do it) and announce it errored