Cannot find CMDSTAN_HOME

[itsdfish]

Hi Rob-

I encountered a strange situation in which CMDSTAN_HOME cannot be found on my system. I am using Ubuntu 16.04 and Julia .7. (@info Stan does not provide the version of Stan). First, I tried adding the path to my bashcr file to no avail. Next, I tried to hard code it into Stan.jl also to no avail. I also tried using the set function, but it did not work either.

I believe it is pointing to the correct location:

dfish@dfish-MS-7850:~/cmdstan-2.17.1$ ls
examples     LICENSE  makefile  README.md           src   test-all.sh
Jenkinsfile  make     Projects  runCmdStanTests.py  stan
dfish@dfish-MS-7850:~/cmdstan-2.17.1$ pwd
/home/dfish/cmdstan-2.17.1

Error:

julia> using Pkg

julia> using Stan
[ Info: Recompiling stale cache file /home/dfish/.julia/compiled/v0.7/Stan/zPI1R.ji for Stan [682df890-35be-576f-97d0-3d8c8b33a550]
WARNING: eval from module Base to Stan:    
Expr(:->, :x, Expr(:block, #= Symbol("/home/dfish/.julia/packages/Documenter/sN5Qn/src/DocChecks.jl"):650 =#, :y = :have_color, #= Symbol("/home/dfish/.julia/packages/Documenter/sN5Qn/src/DocChecks.jl"):650 =#, Expr(:global, :have_color = :x), #= Symbol("/home/dfish/.julia/packages/Documenter/sN5Qn/src/DocChecks.jl"):650 =#, :y))
  ** incremental compilation may be broken for this module **

┌ Warning: `warn()` is deprecated, use `@warn` instead.
│   caller = #warn#781(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::String) at deprecated.jl:1032
└ @ Base ./deprecated.jl:1032
WARNING: Environment variable CMDSTAN_HOME not found. Use set_cmdstan_home!.

julia> CMDSTAN_HOME
""

julia> set_cmdstan_home!("/home/dfish/cmdstan-2.17.1")
"/home/dfish/cmdstan-2.17.1"

julia> CMDSTAN_HOME
"/home/dfish/cmdstan-2.17.1"

julia> using Stan

julia> Pkg.test("Stan")
   Testing Stan
    Status `/tmp/tmppcKWvH/Manifest.toml`
  [9e28174c] BinDeps v0.8.9
  [34da2185] Compat v1.0.1
  [ffbed154] DocStringExtensions v0.4.5
  [e30172f5] Documenter v0.19.3
  [d9be37ee] Homebrew v0.6.4
  [682c06a0] JSON v0.19.0
  [682df890] Stan v3.0.1
  [30578b45] URIParser v0.4.0
  [2a0f44e3] Base64  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Base64`]
  [ade2ca70] Dates  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Dates`]
  [8bb1440f] DelimitedFiles  [`~/julia.7/bin/../share/julia/stdlib/v0.7/DelimitedFiles`]
  [8ba89e20] Distributed  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Distributed`]
  [b77e0a4c] InteractiveUtils  [`~/julia.7/bin/../share/julia/stdlib/v0.7/InteractiveUtils`]
  [76f85450] LibGit2  [`~/julia.7/bin/../share/julia/stdlib/v0.7/LibGit2`]
  [8f399da3] Libdl  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Libdl`]
  [37e2e46d] LinearAlgebra  [`~/julia.7/bin/../share/julia/stdlib/v0.7/LinearAlgebra`]
  [56ddb016] Logging  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Logging`]
  [d6f4376e] Markdown  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Markdown`]
  [a63ad114] Mmap  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Mmap`]
  [44cfe95a] Pkg  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Pkg`]
  [de0858da] Printf  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Printf`]
  [3fa0cd96] REPL  [`~/julia.7/bin/../share/julia/stdlib/v0.7/REPL`]
  [9a3f8284] Random  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Random`]
  [ea8e919c] SHA  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SHA`]
  [9e88b42a] Serialization  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Serialization`]
  [1a1011a3] SharedArrays  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SharedArrays`]
  [6462fe0b] Sockets  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Sockets`]
  [2f01184e] SparseArrays  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SparseArrays`]
  [10745b16] Statistics  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Statistics`]
  [8dfed614] Test  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Test`]
  [cf7118a7] UUIDs  [`~/julia.7/bin/../share/julia/stdlib/v0.7/UUIDs`]
  [4ec0a83e] Unicode  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Unicode`]
┌ Warning: `warn()` is deprecated, use `@warn` instead.
│   caller = #warn#781(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::String) at deprecated.jl:1032
└ @ Base ./deprecated.jl:1032
WARNING: Environment variable CMDSTAN_HOME not found. Use set_cmdstan_home!.
Running tests for Stan-j0.7-v3.0.0:

CMDSTAN_HOME not set or found.
Skipping all tests that depend on CmdStan!

   Testing Stan tests passed 

julia> CMDSTAN_HOME
"/home/dfish/cmdstan-2.17.1"

[goedman]

Hmm, yes pretty late several changes were made in Julia 0.7.0 that are not handled well in Stan.jl. I haven't touched Stan.jl in quite a while. Its on my list ...

Are you using the Mamba components (as Mamba/Gadfly is not yet ported to Julia 0.7.0 anyway)?

If not, you can try to use the new CmdStan.jl I'm developing for Julia 1.0.0. This will look for an environment variable JULIA_CMDSTAN_HOME which in your case should point to "/home/dfish/cmdstan-2.17.1". See the breaking change note in the README.

( Maybe in Julia 0.6.4 you used to define CMDSTAN_HOME in ~/juliarc.jl. In Julia 0.7.0 juliarc.jl is no longer used and replaced by the file ~/.julia/config/startup.jl. )

If done correctly, in your case e.g. in bashrc or in above startup.jl file, versioninfo() in the Julia 0.7.0 REPL should list that environment variable, e.g. on my system JULIA_CMDSTAN_HOME = /Users/rob/Projects/StanSupport/cmdstan.

To install CmdStan in Julia 0.7.0, in the Julia 0.7.0 REPL:

]                            # entering '] return' will get you to the new Pkg manager, Pkg(3)

add CmdStan#master

Hope this helps for now, I will try to take a look at Stan.jl as well. Ultimately it will become an empty shell using CmdStan and the (still to be implemented) features in the StanJulia organization, i.e. StanMamba.jl once Mamba/Gadfly have been ported.

Best, Rob

[goedman]

Chris, you could also try Stan.jl in Julia 0.7.0 by executing Pkg.checkout("Stan") or, better still, going into the Pkg REPL:

]

dev Stan

[goedman]

I think what is happening is that the Pkg.test() feature in Pkg(3) creates a new process to test a package. It appears this new process does not contain the effect of set_cmdstan_home!(...) you just executed. Probably if you include runtests.jl at that point it would work, at least Stan.jl master.

But the question remains why something like export CMDSTAN_HOME=/home/dfish/cmdstan-2.17.1 in you bashrc is not visible after sourcing the bashrc.

Assuming you start julia in a bash shell with a command like clear; julia, just before that point is the environment variable CMDSTAN_HOME visible? Or once Julia is started, just ENV?

I really don't know Ubuntu, so it might take some trial and error to figure this out.

[goedman]

Not sure how familiar you are with the Pkg(3) REPL, but you should be able to:

julia> ]

(v0.7) pkg> test Stan

...

<delete>    # on an empty line gets you back to the julia prompt

julia>

[itsdfish]

Hi Rob-

Thank you for your responses. I tried dev Stan and the new CmdStan, but to no avail. Neither of the environment variables that you mentioned are visible in the REPL:

julia> CMDSTAN_HOME
ERROR: UndefVarError: CMDSTAN_HOME not defined

julia> JULIA_CMDSTAN_HOME
ERROR: UndefVarError: JULIA_CMDSTAN_HOME not defined

It does not appear in the the ENV variable either

julia> print(ENV)
XDG_VTNR=7
XDG_SESSION_ID=c2
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/dfish
CLUTTER_IM_MODULE=xim
SESSION=ubuntu
GPG_AGENT_INFO=/home/dfish/.gnupg/S.gpg-agent:0:1
TERM=xterm-256color
VTE_VERSION=4205
XDG_MENU_PREFIX=gnome-
SHELL=/bin/bash
QT_LINUX_ACCESSIBILITY_ALWAYS_ON=1
WINDOWID=119537670
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1000/1385
GNOME_KEYRING_CONTROL=
GTK_MODULES=gail:atk-bridge:unity-gtk-module
USER=dfish
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
QT_ACCESSIBILITY=1
UNITY_HAS_3D_SUPPORT=true
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
SESSION_MANAGER=local/dfish-MS-7850:@/tmp/.ICE-unix/1626,unix/dfish-MS-7850:/tmp/.ICE-unix/1626
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg
UNITY_DEFAULT_PROFILE=unity
DESKTOP_SESSION=ubuntu
PATH=~/anaconda/bin:/home/dfish/Swift/usr/bin:/home/dfish/bin:/home/dfish/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/dfish/-6445c82d00/bin:/snap/bin
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
XDG_SESSION_TYPE=x11
PWD=/home/dfish/cmdstan-2.17.1
JOB=unity-settings-daemon
XMODIFIERS=@im=ibus
GNOME_KEYRING_PID=
LANG=en_US.UTF-8
GDM_LANG=en_US
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
COMPIZ_CONFIG_PROFILE=ubuntu
IM_CONFIG_PHASE=1
GDMSESSION=ubuntu
SESSIONTYPE=gnome-session
GTK2_MODULES=overlay-scrollbar
SHLVL=1
HOME=/home/dfish
XDG_SEAT=seat0
LANGUAGE=en_US
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
UPSTART_INSTANCE=
UPSTART_EVENTS=xsession started
XDG_SESSION_DESKTOP=ubuntu
LOGNAME=dfish
COMPIZ_BIN_PATH=/usr/bin/
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-HjUvjcxH2L
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/var/lib/snapd/desktop
QT4_IM_MODULE=xim
LESSOPEN=| /usr/bin/lesspipe %s
INSTANCE=
UPSTART_JOB=unity7
XDG_RUNTIME_DIR=/run/user/1000
DISPLAY=:0
XDG_CURRENT_DESKTOP=Unity
GTK_IM_MODULE=ibus
LESSCLOSE=/usr/bin/lesspipe %s %s
XAUTHORITY=/home/dfish/.Xauthority
_=/home/dfish/julia.7/bin/julia
OLDPWD=/home/dfish
OPENBLAS_MAIN_FREE=1

Thanks again for helping me with this.

[goedman]

Hi Chris,

Can you send me your .bashrc and/or .bash_profile? You need to define these environment variables, e.g … export CMDSTAN_HOME=/home/dfish/cmdstan-1.17.1 export JULIA_CMDSTAN_HOME=/home/dfish/cmdstan-1.17.1 ...

After you update say the .bash_profile file you need to ‘run’ this (or logout and login again.

I usually do

. ~/bash_profile

in a terminal just before starting Julia.

If you start Julia by double clicking you will have to logout/login.

Or can you create .julia/config/startup.jl and add to that file:

ENV["CMDSTAN_HOME"]="/home/dfish/cmdstan-1.17.1" ENV["JULIA_CMDSTAN_HOME"]="/home/dfish/cmdstan-1.17.1"

Rob J Goedman goedman@icloud.com

On Aug 8, 2018, at 17:19, fisherc2 notifications@github.com wrote:

Hi Rob-

Thank you for your responses. I tried dev Stan and the new CmdStan, but to no avail. Neither of the environment variables that you mentioned are visible in the REPL:

julia> CMDSTAN_HOME ERROR: UndefVarError: CMDSTAN_HOME not defined

julia> JULIA_CMDSTAN_HOME ERROR: UndefVarError: JULIA_CMDSTAN_HOME not defined

It does not appear in the the ENV variable either

julia> print(ENV) XDG_VTNR=7 XDG_SESSION_ID=c2 XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/dfish CLUTTER_IM_MODULE=xim SESSION=ubuntu GPG_AGENT_INFO=/home/dfish/.gnupg/S.gpg-agent:0:1 TERM=xterm-256color VTE_VERSION=4205 XDG_MENU_PREFIX=gnome- SHELL=/bin/bash QT_LINUX_ACCESSIBILITY_ALWAYS_ON=1 WINDOWID=119537670 UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1000/1385 GNOME_KEYRING_CONTROL= GTK_MODULES=gail:atk-bridge:unity-gtk-module USER=dfish LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.jpg=01;35:.jpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36: QT_ACCESSIBILITY=1 UNITY_HAS_3D_SUPPORT=true XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0 XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0 SSH_AUTH_SOCK=/run/user/1000/keyring/ssh DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path SESSION_MANAGER=local/dfish-MS-7850:@/tmp/.ICE-unix/1626,unix/dfish-MS-7850:/tmp/.ICE-unix/1626 XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg UNITY_DEFAULT_PROFILE=unity DESKTOP_SESSION=ubuntu PATH=~/anaconda/bin:/home/dfish/Swift/usr/bin:/home/dfish/bin:/home/dfish/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/dfish/-6445c82d00/bin:/snap/bin QT_IM_MODULE=ibus QT_QPA_PLATFORMTHEME=appmenu-qt5 XDG_SESSION_TYPE=x11 PWD=/home/dfish/cmdstan-2.17.1 JOB=unity-settings-daemon XMODIFIERS=@im=ibus GNOME_KEYRING_PID= LANG=en_US.UTF-8 GDM_LANG=en_US MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path COMPIZ_CONFIG_PROFILE=ubuntu IM_CONFIG_PHASE=1 GDMSESSION=ubuntu SESSIONTYPE=gnome-session GTK2_MODULES=overlay-scrollbar SHLVL=1 HOME=/home/dfish XDG_SEAT=seat0 LANGUAGE=en_US GNOME_DESKTOP_SESSION_ID=this-is-deprecated UPSTART_INSTANCE= UPSTART_EVENTS=xsession started XDG_SESSION_DESKTOP=ubuntu LOGNAME=dfish COMPIZ_BIN_PATH=/usr/bin/ DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-HjUvjcxH2L XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/var/lib/snapd/desktop QT4_IM_MODULE=xim LESSOPEN=| /usr/bin/lesspipe %s INSTANCE= UPSTART_JOB=unity7 XDG_RUNTIME_DIR=/run/user/1000 DISPLAY=:0 XDG_CURRENT_DESKTOP=Unity GTK_IMMODULE=ibus LESSCLOSE=/usr/bin/lesspipe %s %s XAUTHORITY=/home/dfish/.Xauthority =/home/dfish/julia.7/bin/julia OLDPWD=/home/dfish OPENBLAS_MAIN_FREE=1 Thanks again for helping me with this.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/goedman/Stan.jl/issues/55#issuecomment-411584518, or mute the thread https://github.com/notifications/unsubscribe-auth/AADL6NgUKBOnd9ggUmTS4CK3ljG5c2pVks5uO3INgaJpZM4V0jlN.

[goedman]

Chris, I'm also wondering how this worked previously? Did you define CMDSTAN_HOME in juliarc.jl?

[itsdfish]

Hi Rob-

We have some incremental progress. The bashrc method did not work. However, the startup.jl method worked in some ways. It added the paths to the ENV variable and CmdStan started testing but encountered errors:

using CmdStan

(v0.7) pkg> test CmdStan
   Testing CmdStan
    Status `/tmp/tmpxUV7X5/Manifest.toml`
  [9e28174c] BinDeps v0.8.9
  [593b3428] CmdStan v4.0.0
  [34da2185] Compat v1.0.1
  [ffbed154] DocStringExtensions v0.4.5
  [e30172f5] Documenter v0.19.3
  [d9be37ee] Homebrew v0.6.4
  [682c06a0] JSON v0.19.0
  [30578b45] URIParser v0.4.0
  [2a0f44e3] Base64  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Base64`]
  [ade2ca70] Dates  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Dates`]
  [8bb1440f] DelimitedFiles  [`~/julia.7/bin/../share/julia/stdlib/v0.7/DelimitedFiles`]
  [8ba89e20] Distributed  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Distributed`]
  [b77e0a4c] InteractiveUtils  [`~/julia.7/bin/../share/julia/stdlib/v0.7/InteractiveUtils`]
  [76f85450] LibGit2  [`~/julia.7/bin/../share/julia/stdlib/v0.7/LibGit2`]
  [8f399da3] Libdl  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Libdl`]
  [37e2e46d] LinearAlgebra  [`~/julia.7/bin/../share/julia/stdlib/v0.7/LinearAlgebra`]
  [56ddb016] Logging  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Logging`]
  [d6f4376e] Markdown  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Markdown`]
  [a63ad114] Mmap  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Mmap`]
  [44cfe95a] Pkg  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Pkg`]
  [de0858da] Printf  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Printf`]
  [3fa0cd96] REPL  [`~/julia.7/bin/../share/julia/stdlib/v0.7/REPL`]
  [9a3f8284] Random  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Random`]
  [ea8e919c] SHA  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SHA`]
  [9e88b42a] Serialization  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Serialization`]
  [1a1011a3] SharedArrays  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SharedArrays`]
  [6462fe0b] Sockets  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Sockets`]
  [2f01184e] SparseArrays  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SparseArrays`]
  [10745b16] Statistics  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Statistics`]
  [8dfed614] Test  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Test`]
  [cf7118a7] UUIDs  [`~/julia.7/bin/../share/julia/stdlib/v0.7/UUIDs`]
  [4ec0a83e] Unicode  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Unicode`]
Running tests for CmdStan-j0.7-v1.0.0:

CMDSTAN_HOME set. Try to run tests.

  * test_env.jl *

  * test_utilities.jl *
`echo 2`
`echo 3 4`
`echo 5`

1
2
3
4
5

hello
hello
hello
hello
hello
hello

  * test_cmdtype.jl *
=====> /home/dfish/.julia/packages/CmdStan/zbHOe/test

File /home/dfish/.julia/packages/CmdStan/zbHOe/test/tmp/bernoulli.stan will be updated.

  name =                    "bernoulli"
  nchains =                 4
  num_samples =             1000
  num_warmup =                   1000
  thin =                    1
  monitors =                String[]
  model_file =              "bernoulli.stan"
  data_file =               ""
  output =                  Output()
    file =                    ""
    diagnostics_file =        ""
    refresh =                 100
  method =                  Optimize()
    algorithm =               Lbfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-8
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
      history_size =            5
    iterations =              2000
    save_iterations =         false

  name =                    "bernoulli"
  nchains =                 4
  num_samples =             1000
  num_warmup =                   1000
  thin =                    1
  monitors =                String[]
  model_file =              "bernoulli.stan"
  data_file =               ""
  output =                  Output()
    file =                    ""
    diagnostics_file =        ""
    refresh =                 100
  method =                  Optimize()
    algorithm =               Lbfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-8
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
      history_size =            5
    iterations =              2000
    save_iterations =         false

  method =                  Sample()
    num_samples =             1000
    num_warmup =              1000
    save_warmup =             false
    thin =                    1
    algorithm =               HMC()
      engine =                  NUTS()
        max_depth =               10
      metric =                  CmdStan.diag_e
      stepsize =                1.0
      stepsize_jitter =         1.0
    adapt =                   Adapt()
      gamma =                   0.05
      delta =                   0.8
      kappa =                   0.75
      t0 =                      10.0
      init_buffer =             75
      term_buffer =             50
      window =                  25

  method =                  Sample()
    num_samples =             1000
    num_warmup =              1000
    save_warmup =             false
    thin =                    1
    algorithm =               HMC()
      engine =                  NUTS()
        max_depth =               10
      metric =                  CmdStan.diag_e
      stepsize =                1.0
      stepsize_jitter =         1.0
    adapt =                   Adapt()
      gamma =                   0.05
      delta =                   0.8
      kappa =                   0.75
      t0 =                      10.0
      init_buffer =             75
      term_buffer =             50
      window =                  25

  method =                  Optimize()
    algorithm =               Bfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-9
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
    iterations =              2000
    save_iterations =         true

  method =                  Optimize()
    algorithm =               Bfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-9
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
    iterations =              2000
    save_iterations =         true

  method =                  Diagnose()
    diagnostic =              Gradient()
      epsilon =                 1.0e-6
      error =                   1.0e-7

  method =                  Diagnose()
    diagnostic =              Gradient()
      epsilon =                 1.0e-6
      error =                   1.0e-7

  * test_bernoulli.jl *

=====> /home/dfish/.julia/packages/CmdStan/zbHOe/examples/Bernoulli

File /home/dfish/.julia/packages/CmdStan/zbHOe/examples/Bernoulli/tmp/bernoulli.stan will be updated.

Unreachable reached at 0x7f73d0042ae3

signal (4): Illegal instruction
in expression starting at /home/dfish/.julia/packages/CmdStan/zbHOe/test/test_bernoulli.jl:2
cd at ./file.jl:99
unknown function (ip: 0x7f73d0042b05)
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:324
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:428
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:363 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:686
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:799
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f73dc7d7e8f)
unknown function (ip: 0x6)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:808
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:831
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:841
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:865
include at ./boot.jl:317 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
include at ./client.jl:398
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
macro expansion at /home/dfish/.julia/packages/CmdStan/zbHOe/test/runtests.jl:37 [inlined]
macro expansion at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Test/src/Test.jl:1079 [inlined]
top-level scope at /home/dfish/.julia/packages/CmdStan/zbHOe/test/runtests.jl:30 [inlined]
top-level scope at ./none:0
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:825
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:841
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:865
include at ./boot.jl:317 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
include at ./client.jl:398
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:324
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:428
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:363 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:686
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:799
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f73da3ff9df)
unknown function (ip: 0xffffffffffffffff)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:808
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:831
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:778
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/builtins.c:633
eval at ./boot.jl:319
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
macro expansion at ./logging.jl:317 [inlined]
exec_options at ./client.jl:229
_start at ./client.jl:432
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1538 [inlined]
true_main at /buildworker/worker/package_linux64/build/ui/repl.c:112
main at /buildworker/worker/package_linux64/build/ui/repl.c:233
__libc_start_main at /build/glibc-Cl5G7W/glibc-2.23/csu/../csu/libc-start.c:291
_start at /home/dfish/julia.7/bin/julia (unknown line)
Allocations: 13533591 (Pool: 13531400; Big: 2191); GC: 29
ERROR: Package CmdStan errored during testing

I obtained similar results for Stan:

(v0.7) pkg> test Stan
   Testing Stan
 Resolving package versions...
    Status `/tmp/tmpxLZKkR/Manifest.toml`
  [9e28174c] BinDeps v0.8.9
  [34da2185] Compat v1.0.1
  [ffbed154] DocStringExtensions v0.4.5
  [e30172f5] Documenter v0.19.3
  [d9be37ee] Homebrew v0.6.4
  [682c06a0] JSON v0.19.0
  [682df890] Stan v3.0.1+ [`~/.julia/dev/Stan`]
  [30578b45] URIParser v0.4.0
  [2a0f44e3] Base64  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Base64`]
  [ade2ca70] Dates  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Dates`]
  [8bb1440f] DelimitedFiles  [`~/julia.7/bin/../share/julia/stdlib/v0.7/DelimitedFiles`]
  [8ba89e20] Distributed  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Distributed`]
  [b77e0a4c] InteractiveUtils  [`~/julia.7/bin/../share/julia/stdlib/v0.7/InteractiveUtils`]
  [76f85450] LibGit2  [`~/julia.7/bin/../share/julia/stdlib/v0.7/LibGit2`]
  [8f399da3] Libdl  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Libdl`]
  [37e2e46d] LinearAlgebra  [`~/julia.7/bin/../share/julia/stdlib/v0.7/LinearAlgebra`]
  [56ddb016] Logging  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Logging`]
  [d6f4376e] Markdown  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Markdown`]
  [a63ad114] Mmap  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Mmap`]
  [44cfe95a] Pkg  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Pkg`]
  [de0858da] Printf  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Printf`]
  [3fa0cd96] REPL  [`~/julia.7/bin/../share/julia/stdlib/v0.7/REPL`]
  [9a3f8284] Random  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Random`]
  [ea8e919c] SHA  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SHA`]
  [9e88b42a] Serialization  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Serialization`]
  [1a1011a3] SharedArrays  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SharedArrays`]
  [6462fe0b] Sockets  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Sockets`]
  [2f01184e] SparseArrays  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SparseArrays`]
  [10745b16] Statistics  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Statistics`]
  [8dfed614] Test  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Test`]
  [cf7118a7] UUIDs  [`~/julia.7/bin/../share/julia/stdlib/v0.7/UUIDs`]
  [4ec0a83e] Unicode  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Unicode`]
Running tests for Stan-j0.7-v3.0.0:
CMDSTAN_HOME set. Try to run tests.

  * test_env.jl *

  * test_utilities.jl *
`echo 2`
`echo 3 4`
`echo 5`

1
2
3
4
5

hello
hello
hello
hello
hello
hello

  * test_cmdtype.jl *
WARNING: importing deprecated binding Base.Pkg into Stan.
WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/test/test_cmdtype.jl:5
WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/test/test_cmdtype.jl:5
WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/test/test_cmdtype.jl:5
WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/test/test_cmdtype.jl:5
WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/test/test_cmdtype.jl:5
WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/test/test_cmdtype.jl:5

File /home/dfish/.julia/dev/Stan/test/tmp/bernoulli.stan will be updated.

┌ Warning: `showcompact(x)` is deprecated, use `show(IOContext(stdout, :compact => true), x)` instead.
│   caller = (::getfield(Main, Symbol("##3#4")))() at test_cmdtype.jl:33
└ @ Main ~/.julia/dev/Stan/test/test_cmdtype.jl:33
  name =                    "bernoulli"
  nchains =                 4
  num_samples =             1000
  num_warmup =                   1000
  thin =                    1
  useMamba =                false
  mambaThinning =           1
  monitors =                String[]
  model_file =              "bernoulli.stan"
  data_file =               ""
  output =                  Output()
    file =                    ""
    diagnostics_file =        ""
    refresh =                 100
  method =                  Optimize()
    algorithm =               Lbfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-8
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
      history_size =            5
    iterations =              2000
    save_iterations =         false

  name =                    "bernoulli"
  nchains =                 4
  num_samples =             1000
  num_warmup =                   1000
  thin =                    1
  useMamba =                false
  mambaThinning =           1
  monitors =                String[]
  model_file =              "bernoulli.stan"
  data_file =               ""
  output =                  Output()
    file =                    ""
    diagnostics_file =        ""
    refresh =                 100
  method =                  Optimize()
    algorithm =               Lbfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-8
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
      history_size =            5
    iterations =              2000
    save_iterations =         false

┌ Warning: `showcompact(x)` is deprecated, use `show(IOContext(stdout, :compact => true), x)` instead.
│   caller = (::getfield(Main, Symbol("##3#4")))() at test_cmdtype.jl:42
└ @ Main ~/.julia/dev/Stan/test/test_cmdtype.jl:42
  method =                  Sample()
    num_samples =             1000
    num_warmup =              1000
    save_warmup =             false
    thin =                    1
    algorithm =               HMC()
      engine =                  NUTS()
        max_depth =               10
      metric =                  Stan.diag_e
      stepsize =                1.0
      stepsize_jitter =         1.0
    adapt =                   Adapt()
      gamma =                   0.05
      delta =                   0.8
      kappa =                   0.75
      t0 =                      10.0
      init_buffer =             75
      term_buffer =             50
      window =                  25

  method =                  Sample()
    num_samples =             1000
    num_warmup =              1000
    save_warmup =             false
    thin =                    1
    algorithm =               HMC()
      engine =                  NUTS()
        max_depth =               10
      metric =                  Stan.diag_e
      stepsize =                1.0
      stepsize_jitter =         1.0
    adapt =                   Adapt()
      gamma =                   0.05
      delta =                   0.8
      kappa =                   0.75
      t0 =                      10.0
      init_buffer =             75
      term_buffer =             50
      window =                  25

┌ Warning: `showcompact(x)` is deprecated, use `show(IOContext(stdout, :compact => true), x)` instead.
│   caller = (::getfield(Main, Symbol("##3#4")))() at test_cmdtype.jl:61
└ @ Main ~/.julia/dev/Stan/test/test_cmdtype.jl:61
  method =                  Optimize()
    algorithm =               Bfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-9
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
    iterations =              2000
    save_iterations =         true

  method =                  Optimize()
    algorithm =               Bfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-9
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
    iterations =              2000
    save_iterations =         true

┌ Warning: `showcompact(x)` is deprecated, use `show(IOContext(stdout, :compact => true), x)` instead.
│   caller = (::getfield(Main, Symbol("##3#4")))() at test_cmdtype.jl:71
└ @ Main ~/.julia/dev/Stan/test/test_cmdtype.jl:71
  method =                  Diagnose()
    diagnostic =              Gradient()
      epsilon =                 1.0e-6
      error =                   1.0e-7

  method =                  Diagnose()
    diagnostic =              Gradient()
      epsilon =                 1.0e-6
      error =                   1.0e-7

  * test_bernoulli.jl *

WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.mean is deprecated: it has been moved to the standard library package `Statistics`.
Add `using Statistics` to your imports.
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.mean is deprecated: it has been moved to the standard library package `Statistics`.
Add `using Statistics` to your imports.
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.mean is deprecated: it has been moved to the standard library package `Statistics`.
Add `using Statistics` to your imports.
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.mean is deprecated: it has been moved to the standard library package `Statistics`.
Add `using Statistics` to your imports.
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.mean is deprecated: it has been moved to the standard library package `Statistics`.
Add `using Statistics` to your imports.
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.mean is deprecated: it has been moved to the standard library package `Statistics`.
Add `using Statistics` to your imports.
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.mean is deprecated: it has been moved to the standard library package `Statistics`.
Add `using Statistics` to your imports.
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.mean is deprecated: it has been moved to the standard library package `Statistics`.
Add `using Statistics` to your imports.
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
in #7 at /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl
WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6
WARNING: Base.Pkg is deprecated, run `using Pkg` instead
  likely near /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/bernoulli.jl:6

File /home/dfish/.julia/dev/Stan/Examples/NoMamba/Bernoulli/tmp/bernoulli.stan will be updated.

Unreachable reached at 0x7f337404c3f3

signal (4): Illegal instruction
in expression starting at /home/dfish/.julia/dev/Stan/test/test_bernoulli.jl:2
cd at ./file.jl:99
unknown function (ip: 0x7f337404c415)
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:324
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:428
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:363 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:686
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:799
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f337f9c559f)
unknown function (ip: 0x6)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:808
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:831
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:841
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:865
include at ./boot.jl:317 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
include at ./client.jl:398
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
macro expansion at /home/dfish/.julia/dev/Stan/test/runtests.jl:35 [inlined]
macro expansion at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Test/src/Test.jl:1079 [inlined]
top-level scope at /home/dfish/.julia/dev/Stan/test/runtests.jl:28 [inlined]
top-level scope at ./none:0
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:825
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:841
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:865
include at ./boot.jl:317 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
include at ./client.jl:398
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:324
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:428
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:363 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:686
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:799
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f337d1a793f)
unknown function (ip: 0xffffffffffffffff)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:808
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:831
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:778
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/builtins.c:633
eval at ./boot.jl:319
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
macro expansion at ./logging.jl:317 [inlined]
exec_options at ./client.jl:229
_start at ./client.jl:432
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1538 [inlined]
true_main at /buildworker/worker/package_linux64/build/ui/repl.c:112
main at /buildworker/worker/package_linux64/build/ui/repl.c:233
__libc_start_main at /build/glibc-Cl5G7W/glibc-2.23/csu/../csu/libc-start.c:291
_start at /home/dfish/julia.7/bin/julia (unknown line)
Allocations: 17646961 (Pool: 17644020; Big: 2941); GC: 38
ERROR: Package Stan errored during testing

[itsdfish]

Regarding past methods, I have always had difficulty with the configuration. In early versions, the .bashrc method seemed to work, but at some point it stopped working. At that point I hardcoded the paths in the ENV variable and added it to the top of my script or hardcoded it into the Stan.jl file.

At least the startup.jl method is working. I'm not sure what the Unreachable reached at 0x7f73d0042ae3error is about. I suspect the .7 upgrade will generally be disruptive. Many things appear not to be working properly and are giving deprecation warnings.

[goedman]

Let's try and resolve the unreachable problem next. This is one of my biggest concerns with Julia v0.7.0. I've seen this far too often.

I've made a bunch of updates to Stan.jl late last night and earlier this morning. Do you know how to upgrade a package in .julia/dev? I use git pull in a Terminal in that directory.

The alternative is to just rm Stan and add/dev it again.

julia> ]

(v0.7) pkg> rm Stan

(v0.7) pkg> add Stan.jl#master

(v0.7) pkg> up

(v0.7) pkg> gc

(v0.7) pkg>st

Let me know if this works better. Of course, if you rm Stan and you had made changes they will remain in .julia/dev but in above sequence I now use Stan.jl in packages. That is shown in the st(atus) command. Pkg REPL never updates anything in .julia/dev, a blessing and often confusing. st(atus) is your friend.

[itsdfish]

Unfortunately, the unreachable error is persisting. Here is my output:

(v0.7) pkg> rm Stan
  Updating `~/.julia/environments/v0.7/Project.toml`
  [682df890] - Stan v3.0.1+ [`~/.julia/dev/Stan`]
  Updating `~/.julia/environments/v0.7/Manifest.toml`
  [682df890] - Stan v3.0.1+ [`~/.julia/dev/Stan`]

(v0.7) pkg> add Stan.jl#master
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
   Cloning git-repo `https://github.com/goedman/Stan.jl.git`
  Updating git-repo `https://github.com/goedman/Stan.jl.git`
 Resolving package versions...
 Installed Juno ─────────────── v0.5.2
 Installed Hiccup ───────────── v0.2.2
 Installed TranscodingStreams ─ v0.6.1
 Installed Arpack ───────────── v0.2.2
 Installed Tokenize ─────────── v0.5.2
 Installed Crayons ──────────── v1.0.0
 Installed Revise ───────────── v0.6.4
 Installed Plots ────────────── v0.18.0
 Installed LNR ──────────────── v0.2.0
 Installed GR ───────────────── v0.32.2
  Updating `~/.julia/environments/v0.7/Project.toml`
  [a8cc5b0e] ↑ Crayons v0.5.1 ⇒ v1.0.0
  [e5e0dc1b] ↑ Juno v0.5.1 ⇒ v0.5.2
  [91a5bcdd] ↑ Plots v0.17.4 ⇒ v0.18.0
  [295af30f] ↑ Revise v0.6.3 ⇒ v0.6.4
  [682df890] + Stan v3.5.0 #master (https://github.com/goedman/Stan.jl.git)
  Updating `~/.julia/environments/v0.7/Manifest.toml`
  [7d9fca2a] ↑ Arpack v0.2.1 ⇒ v0.2.2
  [a8cc5b0e] ↑ Crayons v0.5.1 ⇒ v1.0.0
  [28b8d3ca] ↑ GR v0.32.0 ⇒ v0.32.2
  [9fb69e20] ↑ Hiccup v0.2.1 ⇒ v0.2.2
  [e5e0dc1b] ↑ Juno v0.5.1 ⇒ v0.5.2
  [7c4cb9fa] ↑ LNR v0.0.2 ⇒ v0.2.0
  [91a5bcdd] ↑ Plots v0.17.4 ⇒ v0.18.0
  [295af30f] ↑ Revise v0.6.3 ⇒ v0.6.4
  [682df890] + Stan v3.5.0 #master (https://github.com/goedman/Stan.jl.git)
  [0796e94c] ↑ Tokenize v0.5.1 ⇒ v0.5.2
  [3bb67fe8] ↑ TranscodingStreams v0.5.4 ⇒ v0.6.1
  Building Revise → `~/.julia/packages/Revise/vNcfy/deps/build.log`
  Building GR ────→ `~/.julia/packages/GR/crXzk/deps/build.log`
┌ Error: Error building `GR`: 
│ WARNING: Base.Pkg is deprecated, run `using Pkg` instead
│   likely near /home/dfish/.julia/packages/GR/crXzk/deps/build.jl:36
│ WARNING: Base.Pkg is deprecated, run `using Pkg` instead
│   likely near /home/dfish/.julia/packages/GR/crXzk/deps/build.jl:36
│ [ Info: Downloading pre-compiled GR 0.32.0 Ubuntu binary
│ [ Info: Using insecure connection
│ ERROR: LoadError: IOError: could not spawn `curl -g -L -f -o downloads/gr-0.32.0-Ubuntu-x86_64.tar.gz http://gr-framework.org/downloads/gr-0.32.0-Ubuntu-x86_64.tar.gz`: no such file or directory (ENOENT)
│ Stacktrace:
│  [1] _jl_spawn(::String, ::Array{String,1}, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:370
│  [2] (::getfield(Base, Symbol("##499#500")){Cmd})(::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:512
│  [3] setup_stdio(::getfield(Base, Symbol("##499#500")){Cmd}, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:493
│  [4] #_spawn#498(::Nothing, ::Function, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:511
│  [5] _spawn at ./process.jl:507 [inlined]
│  [6] #run#509(::Bool, ::Function, ::Cmd) at ./process.jl:669
│  [7] run at ./process.jl:668 [inlined]
│  [8] download(::String, ::String) at ./download.jl:48
│  [9] top-level scope at logging.jl:313
│  [10] top-level scope at /home/dfish/.julia/packages/GR/crXzk/deps/build.jl:61
│  [11] include at ./boot.jl:317 [inlined]
│  [12] include_relative(::Module, ::String) at ./loading.jl:1038
│  [13] include(::Module, ::String) at ./sysimg.jl:29
│  [14] include(::String) at ./client.jl:398
│  [15] top-level scope at none:0
│ in expression starting at /home/dfish/.julia/packages/GR/crXzk/deps/build.jl:36
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Pkg/src/Operations.jl:1068
  Building Plots ─→ `~/.julia/packages/Plots/mqUvK/deps/build.log`
┌ Error: Error building `Plots`: 
│ [ Info: Cannot find deps/plotly-latest.min.js... downloading latest version.
│ ERROR: LoadError: IOError: could not spawn `curl -g -L -f -o /home/dfish/.julia/packages/Plots/mqUvK/deps/plotly-latest.min.js https://cdn.plot.ly/plotly-latest.min.js`: no such file or directory (ENOENT)
│ Stacktrace:
│  [1] _jl_spawn(::String, ::Array{String,1}, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:370
│  [2] (::getfield(Base, Symbol("##499#500")){Cmd})(::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:512
│  [3] setup_stdio(::getfield(Base, Symbol("##499#500")){Cmd}, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:493
│  [4] #_spawn#498(::Nothing, ::Function, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:511
│  [5] _spawn at ./process.jl:507 [inlined]
│  [6] #run#509(::Bool, ::Function, ::Cmd) at ./process.jl:669
│  [7] run at ./process.jl:668 [inlined]
│  [8] download(::String, ::String) at ./download.jl:48
│  [9] top-level scope at logging.jl:307
│  [10] top-level scope at /home/dfish/.julia/packages/Plots/mqUvK/deps/build.jl:6
│  [11] include at ./boot.jl:317 [inlined]
│  [12] include_relative(::Module, ::String) at ./loading.jl:1038
│  [13] include(::Module, ::String) at ./sysimg.jl:29
│  [14] include(::String) at ./client.jl:398
│  [15] top-level scope at none:0
│ in expression starting at /home/dfish/.julia/packages/Plots/mqUvK/deps/build.jl:5
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Pkg/src/Operations.jl:1068
  Building Arpack → `~/.julia/packages/Arpack/Btbe4/deps/build.log`
┌ Error: Error building `Arpack`: 
│ [ Info: Downloading https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-linux-gnu.tar.gz to /home/dfish/.julia/packages/Arpack/Btbe4/deps/usr/downloads/ArpackBuilder.x86_64-linux-gnu.tar.gz...
│ ERROR: LoadError: Could not download https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-linux-gnu.tar.gz to /home/dfish/.julia/packages/Arpack/Btbe4/deps/usr/downloads/ArpackBuilder.x86_64-linux-gnu.tar.gz
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] macro expansion at ./logging.jl:313 [inlined]
│  [3] #download#89(::Bool, ::Function, ::String, ::String) at /home/dfish/.julia/packages/BinaryProvider/ZbFxn/src/PlatformEngines.jl:443
│  [4] #download at ./none:0 [inlined]
│  [5] #download_verify#90(::Bool, ::Bool, ::Bool, ::Function, ::String, ::String, ::String) at /home/dfish/.julia/packages/BinaryProvider/ZbFxn/src/PlatformEngines.jl:523
│  [6] #download_verify at ./none:0 [inlined]
│  [7] #install#111(::Prefix, ::String, ::Bool, ::Bool, ::Bool, ::Function, ::String, ::String) at /home/dfish/.julia/packages/BinaryProvider/ZbFxn/src/Prefix.jl:348
│  [8] (::getfield(BinaryProvider, Symbol("#kw##install")))(::NamedTuple{(:prefix, :force, :verbose),Tuple{Prefix,Bool,Bool}}, ::typeof(install), ::String, ::String) at ./none:0
│  [9] top-level scope at /home/dfish/.julia/packages/Arpack/Btbe4/deps/build.jl:30
│  [10] include at ./boot.jl:317 [inlined]
│  [11] include_relative(::Module, ::String) at ./loading.jl:1038
│  [12] include(::Module, ::String) at ./sysimg.jl:29
│  [13] include(::String) at ./client.jl:398
│  [14] top-level scope at none:0
│ in expression starting at /home/dfish/.julia/packages/Arpack/Btbe4/deps/build.jl:26
│ [14:29:13] --2018-08-09 14:29:13--  https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-linux-gnu.tar.gz
│ [14:29:13] Resolving github.com (github.com)... 192.30.253.112, 192.30.253.113
│ [14:29:13] Connecting to github.com (github.com)|192.30.253.112|:443... connected.
│ [14:29:13] HTTP request sent, awaiting response... 302 Found
│ [14:29:13] Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/132673190/aa2b862c-659b-11e8-93f3-dcc35685897d?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180809%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180809T182913Z&X-Amz-Expires=300&X-Amz-Signature=39c27f97f44ba10722f03106e21c7f4bcd5937a5c27c490004a978530adeef35&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DArpackBuilder.x86_64-linux-gnu.tar.gz&response-content-type=application%2Foctet-stream [following]
│ [14:29:13] --2018-08-09 14:29:13--  https://github-production-release-asset-2e65be.s3.amazonaws.com/132673190/aa2b862c-659b-11e8-93f3-dcc35685897d?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180809%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180809T182913Z&X-Amz-Expires=300&X-Amz-Signature=39c27f97f44ba10722f03106e21c7f4bcd5937a5c27c490004a978530adeef35&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DArpackBuilder.x86_64-linux-gnu.tar.gz&response-content-type=application%2Foctet-stream
│ [14:29:13] Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.165.147
│ [14:29:13] Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.165.147|:443... connected.
│ [14:29:13] HTTP request sent, awaiting response... 200 OK
│ [14:29:13] Length: 142344 (139K) [application/octet-stream]
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Pkg/src/Operations.jl:1068

(v0.7) pkg> up
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
  Updating git-repo `https://github.com/goedman/Stan.jl.git`
 Resolving package versions...
  Updating `~/.julia/environments/v0.7/Project.toml`
 [no changes]
  Updating `~/.julia/environments/v0.7/Manifest.toml`
 [no changes]

(v0.7) pkg> gc
    Active manifests at:
        `/home/dfish/.julia/environments/v0.7/Manifest.toml`
   Deleted /home/dfish/.julia/packages/Arpack/Kl4q: 196.311 KiB
   Deleted /home/dfish/.julia/packages/Arpack/iUWc: 196.662 KiB
   Deleted /home/dfish/.julia/packages/Arpack/uM2QD: 194.375 KiB
   Deleted /home/dfish/.julia/packages/BinDeps/2wxq: 85.162 KiB
   Deleted /home/dfish/.julia/packages/BinaryProvider/mWAR: 137.957 KiB
   Deleted /home/dfish/.julia/packages/CSV/1VJD: 25.025 MiB
   Deleted /home/dfish/.julia/packages/Calculus/VVY4: 51.658 KiB
   Deleted /home/dfish/.julia/packages/CategoricalArrays/lCVK: 349.586 KiB
   Deleted /home/dfish/.julia/packages/ColorTypes/7oP0: 197.347 KiB
   Deleted /home/dfish/.julia/packages/Compat/BlWu: 190.499 KiB
   Deleted /home/dfish/.julia/packages/Compat/OYxC: 174.409 KiB
   Deleted /home/dfish/.julia/packages/Compat/PrKE: 183.011 KiB
   Deleted /home/dfish/.julia/packages/Compat/ql30: 187.391 KiB
   Deleted /home/dfish/.julia/packages/Crayons/e1SsX: 49.133 KiB
   Deleted /home/dfish/.julia/packages/DataFrames/LwtB: 527.121 KiB
   Deleted /home/dfish/.julia/packages/DataFrames/WM3y: 525.276 KiB
   Deleted /home/dfish/.julia/packages/DataStreams/OGMa: 113.290 KiB
   Deleted /home/dfish/.julia/packages/DataStructures/Zet9: 402.748 KiB
   Deleted /home/dfish/.julia/packages/DataStructures/eUHI: 397.556 KiB
   Deleted /home/dfish/.julia/packages/DataStructures/vvd8: 398.222 KiB
   Deleted /home/dfish/.julia/packages/Distributions/dwhW: 872.371 KiB
   Deleted /home/dfish/.julia/packages/Distributions/lJq5: 866.586 KiB
   Deleted /home/dfish/.julia/packages/Distributions/zK5A: 871.394 KiB
   Deleted /home/dfish/.julia/packages/FixedPointNumbers/OSxF: 39.282 KiB
   Deleted /home/dfish/.julia/packages/GR/PZ9b: 19.374 MiB
   Deleted /home/dfish/.julia/packages/GR/u3bF: 19.378 MiB
   Deleted /home/dfish/.julia/packages/Hiccup/Tweiq: 7.398 KiB
   Deleted /home/dfish/.julia/packages/Iterators/hSc9: 93.153 KiB
   Deleted /home/dfish/.julia/packages/JSON/BopY: 80.102 KiB
   Deleted /home/dfish/.julia/packages/Juno/nMYPI: 12.008 KiB
   Deleted /home/dfish/.julia/packages/LNR/k53vj: 5.182 KiB
   Deleted /home/dfish/.julia/packages/Literate/kF6HC: 76.574 KiB
   Deleted /home/dfish/.julia/packages/Missings/jFaS: 38.315 KiB
   Deleted /home/dfish/.julia/packages/NaNMath/yjdm: 11.415 KiB
   Deleted /home/dfish/.julia/packages/NamedTuples/MIrn: 31.694 KiB
   Deleted /home/dfish/.julia/packages/OptimTestProblems/pwGuQ: 47.379 KiB
   Deleted /home/dfish/.julia/packages/PDMats/PxDD: 45.863 KiB
   Deleted /home/dfish/.julia/packages/Parameters/O9cu: 63.229 KiB
   Deleted /home/dfish/.julia/packages/Parameters/cKWy: 53.185 KiB
   Deleted /home/dfish/.julia/packages/Plots/V3tQ: 721.327 KiB
   Deleted /home/dfish/.julia/packages/QuadGK/Pnbq: 22.390 KiB
   Deleted /home/dfish/.julia/packages/RecursiveArrayTools/iHROO: 37.016 KiB
   Deleted /home/dfish/.julia/packages/Reexport/XnNe: 5.097 KiB
   Deleted /home/dfish/.julia/packages/Revise/1bMIH: 122.455 KiB
   Deleted /home/dfish/.julia/packages/Revise/eToz: 119.610 KiB
   Deleted /home/dfish/.julia/packages/Revise/iORQ: 77.686 KiB
   Deleted /home/dfish/.julia/packages/Revise/tGBM: 75.961 KiB
   Deleted /home/dfish/.julia/packages/Rmath/ENY5: 1.548 MiB
   Deleted /home/dfish/.julia/packages/Rmath/ewAF: 159.350 KiB
   Deleted /home/dfish/.julia/packages/SortingAlgorithms/fA7W: 23.446 KiB
   Deleted /home/dfish/.julia/packages/SortingAlgorithms/ybNh: 23.349 KiB
   Deleted /home/dfish/.julia/packages/SpecialFunctions/585p: 12.840 MiB
   Deleted /home/dfish/.julia/packages/SpecialFunctions/kvjJ: 365.749 KiB
   Deleted /home/dfish/.julia/packages/Stan/vXYqK: 4.113 MiB
   Deleted /home/dfish/.julia/packages/StaticArrays/MuoW: 832.264 KiB
   Deleted /home/dfish/.julia/packages/StatsBase/PueG: 374.196 KiB
   Deleted /home/dfish/.julia/packages/StatsBase/xZVL: 371.670 KiB
   Deleted /home/dfish/.julia/packages/StatsFuns/RWL6: 72.355 KiB
   Deleted /home/dfish/.julia/packages/Suppressor/qdsyO: 16.545 KiB
   Deleted /home/dfish/.julia/packages/Tokenize/rfs3t: 141.411 KiB
   Deleted /home/dfish/.julia/packages/TranscodingStreams/MxFC: 179.385 KiB
   Deleted /home/dfish/.julia/packages/TranscodingStreams/xqPx: 179.467 KiB
   Deleted /home/dfish/.julia/packages/URIParser/2oTQ: 24.151 KiB
   Deleted /home/dfish/.julia/packages/WeakRefStrings/YrK6: 27.328 KiB
   Deleted 64 package installations : 93.748 MiB

(v0.7) pkg> st
    Status `~/.julia/environments/v0.7/Project.toml`
  [c52e3926] Atom v0.7.2
  [6e4b80f9] BenchmarkTools v0.3.2
  [336ed68f] CSV v0.3.0
  [593b3428] CmdStan v4.0.0
  [a8cc5b0e] Crayons v1.0.0
  [a93c6f00] DataFrames v0.13.0
  [aaf54ef3] DistributedArrays v0.5.0
  [31c24e10] Distributions v0.16.2
  [c8e1da08] IterTools v1.0.0
  [e5e0dc1b] Juno v0.5.2
  [5fb14364] OhMyREPL v0.3.0
  [429524aa] Optim v0.15.3
  [d96e819e] Parameters v0.9.2
  [91a5bcdd] Plots v0.18.0
  [92933f4c] ProgressMeter v0.5.6
  [295af30f] Revise v0.6.4
  [682df890] Stan v3.5.0 #master (https://github.com/goedman/Stan.jl.git)
  [9a3f8284] Random 
  [10745b16] Statistics 

julia> using Pkg

julia> using Stan
[ Info: Recompiling stale cache file /home/dfish/.julia/compiled/v0.7/Stan/zPI1R.ji for Stan [682df890-35be-576f-97d0-3d8c8b33a550]
WARNING: eval from module Base to Stan:    
Expr(:->, :x, Expr(:block, #= Symbol("/home/dfish/.julia/packages/Documenter/sN5Qn/src/DocChecks.jl"):650 =#, :y = :have_color, #= Symbol("/home/dfish/.julia/packages/Documenter/sN5Qn/src/DocChecks.jl"):650 =#, Expr(:global, :have_color = :x), #= Symbol("/home/dfish/.julia/packages/Documenter/sN5Qn/src/DocChecks.jl"):650 =#, :y))
  ** incremental compilation may be broken for this module **

(v0.7) pkg> test Stan
   Testing Stan
    Status `/tmp/tmpDYIyUu/Manifest.toml`
  [9e28174c] BinDeps v0.8.9
  [34da2185] Compat v1.0.1
  [ffbed154] DocStringExtensions v0.4.5
  [e30172f5] Documenter v0.19.3
  [d9be37ee] Homebrew v0.6.4
  [682c06a0] JSON v0.19.0
  [682df890] Stan v3.5.0 #master (https://github.com/goedman/Stan.jl.git)
  [30578b45] URIParser v0.4.0
  [2a0f44e3] Base64  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Base64`]
  [ade2ca70] Dates  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Dates`]
  [8bb1440f] DelimitedFiles  [`~/julia.7/bin/../share/julia/stdlib/v0.7/DelimitedFiles`]
  [8ba89e20] Distributed  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Distributed`]
  [b77e0a4c] InteractiveUtils  [`~/julia.7/bin/../share/julia/stdlib/v0.7/InteractiveUtils`]
  [76f85450] LibGit2  [`~/julia.7/bin/../share/julia/stdlib/v0.7/LibGit2`]
  [8f399da3] Libdl  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Libdl`]
  [37e2e46d] LinearAlgebra  [`~/julia.7/bin/../share/julia/stdlib/v0.7/LinearAlgebra`]
  [56ddb016] Logging  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Logging`]
  [d6f4376e] Markdown  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Markdown`]
  [a63ad114] Mmap  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Mmap`]
  [44cfe95a] Pkg  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Pkg`]
  [de0858da] Printf  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Printf`]
  [3fa0cd96] REPL  [`~/julia.7/bin/../share/julia/stdlib/v0.7/REPL`]
  [9a3f8284] Random  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Random`]
  [ea8e919c] SHA  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SHA`]
  [9e88b42a] Serialization  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Serialization`]
  [1a1011a3] SharedArrays  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SharedArrays`]
  [6462fe0b] Sockets  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Sockets`]
  [2f01184e] SparseArrays  [`~/julia.7/bin/../share/julia/stdlib/v0.7/SparseArrays`]
  [10745b16] Statistics  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Statistics`]
  [8dfed614] Test  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Test`]
  [cf7118a7] UUIDs  [`~/julia.7/bin/../share/julia/stdlib/v0.7/UUIDs`]
  [4ec0a83e] Unicode  [`~/julia.7/bin/../share/julia/stdlib/v0.7/Unicode`]
Running tests for Stan-j0.7-v3.5.0:
CMDSTAN_HOME set. Try to run tests.

  * test_env.jl *

  * test_utilities.jl *
`echo 2`
`echo 3 4`
`echo 5`

1
2
3
4
5

hello
hello
hello
hello
hello
hello

  * test_cmdtype.jl *

File /home/dfish/.julia/packages/Stan/a6xnA/test/tmp/bernoulli.stan will be updated.

  name =                    "bernoulli"
  nchains =                 4
  num_samples =             1000
  num_warmup =                   1000
  thin =                    1
  useMamba =                false
  mambaThinning =           1
  monitors =                String[]
  model_file =              "bernoulli.stan"
  data_file =               ""
  output =                  Output()
    file =                    ""
    diagnostics_file =        ""
    refresh =                 100
  method =                  Optimize()
    algorithm =               Lbfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-8
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
      history_size =            5
    iterations =              2000
    save_iterations =         false

  name =                    "bernoulli"
  nchains =                 4
  num_samples =             1000
  num_warmup =                   1000
  thin =                    1
  useMamba =                false
  mambaThinning =           1
  monitors =                String[]
  model_file =              "bernoulli.stan"
  data_file =               ""
  output =                  Output()
    file =                    ""
    diagnostics_file =        ""
    refresh =                 100
  method =                  Optimize()
    algorithm =               Lbfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-8
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
      history_size =            5
    iterations =              2000
    save_iterations =         false

  method =                  Sample()
    num_samples =             1000
    num_warmup =              1000
    save_warmup =             false
    thin =                    1
    algorithm =               HMC()
      engine =                  NUTS()
        max_depth =               10
      metric =                  Stan.diag_e
      stepsize =                1.0
      stepsize_jitter =         1.0
    adapt =                   Adapt()
      gamma =                   0.05
      delta =                   0.8
      kappa =                   0.75
      t0 =                      10.0
      init_buffer =             75
      term_buffer =             50
      window =                  25

  method =                  Sample()
    num_samples =             1000
    num_warmup =              1000
    save_warmup =             false
    thin =                    1
    algorithm =               HMC()
      engine =                  NUTS()
        max_depth =               10
      metric =                  Stan.diag_e
      stepsize =                1.0
      stepsize_jitter =         1.0
    adapt =                   Adapt()
      gamma =                   0.05
      delta =                   0.8
      kappa =                   0.75
      t0 =                      10.0
      init_buffer =             75
      term_buffer =             50
      window =                  25

  method =                  Optimize()
    algorithm =               Bfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-9
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
    iterations =              2000
    save_iterations =         true

  method =                  Optimize()
    algorithm =               Bfgs()
      init_alpha =              0.001
      tol_obj =                 1.0e-9
      tol_grad =                1.0e-8
      tol_param =               1.0e-8
    iterations =              2000
    save_iterations =         true

  method =                  Diagnose()
    diagnostic =              Gradient()
      epsilon =                 1.0e-6
      error =                   1.0e-7

  method =                  Diagnose()
    diagnostic =              Gradient()
      epsilon =                 1.0e-6
      error =                   1.0e-7

  * test_bernoulli.jl *

File /home/dfish/.julia/packages/Stan/a6xnA/Examples/NoMamba/Bernoulli/tmp/bernoulli.stan will be updated.

Unreachable reached at 0x7f37f0064b93

signal (4): Illegal instruction
in expression starting at /home/dfish/.julia/packages/Stan/a6xnA/test/test_bernoulli.jl:2
cd at ./file.jl:99
unknown function (ip: 0x7f37f0064bb5)
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:324
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:428
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:363 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:686
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:799
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f37fbbfe67f)
unknown function (ip: 0x6)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:808
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:831
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:841
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:865
include at ./boot.jl:317 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
include at ./client.jl:398
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
macro expansion at /home/dfish/.julia/packages/Stan/a6xnA/test/runtests.jl:35 [inlined]
macro expansion at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Test/src/Test.jl:1079 [inlined]
top-level scope at /home/dfish/.julia/packages/Stan/a6xnA/test/runtests.jl:28 [inlined]
top-level scope at ./none:0
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:825
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:841
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:865
include at ./boot.jl:317 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
include at ./client.jl:398
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:324
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:428
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:363 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:686
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:799
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f37fa4239df)
unknown function (ip: 0xffffffffffffffff)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:808
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:831
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:778
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/builtins.c:633
eval at ./boot.jl:319
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
macro expansion at ./logging.jl:317 [inlined]
exec_options at ./client.jl:229
_start at ./client.jl:432
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182
jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1538 [inlined]
true_main at /buildworker/worker/package_linux64/build/ui/repl.c:112
main at /buildworker/worker/package_linux64/build/ui/repl.c:233
__libc_start_main at /build/glibc-Cl5G7W/glibc-2.23/csu/../csu/libc-start.c:291
_start at /home/dfish/julia.7/bin/julia (unknown line)
Allocations: 16101658 (Pool: 16098970; Big: 2688); GC: 35
ERROR: Package Stan errored during testing

(v0.7) pkg> 

[goedman]

This is a directory problem. It is trying to:

ProjDir = joinpath(dirname(@FILE), "..", "examples", "Bernoulli") cd(ProjDir) do ...

but it shows this /a6xnA/ level in the path: in expression starting at /home/dfish/.julia/packages/Stan/a6xnA/test/test_bernoulli.jl:2 cd at ./file.jl:99

Can you send me your output of versioninfo()? Rob J Goedman goedman@icloud.com

On Aug 9, 2018, at 12:32, fisherc2 notifications@github.com wrote:

Unfortunately, the unreachable error is persisting. Here is my output:

(v0.7) pkg> rm Stan Updating ~/.julia/environments/v0.7/Project.toml [682df890] - Stan v3.0.1+ [~/.julia/dev/Stan] Updating ~/.julia/environments/v0.7/Manifest.toml [682df890] - Stan v3.0.1+ [~/.julia/dev/Stan]

(v0.7) pkg> add Stan.jl#master Updating registry at ~/.julia/registries/General Updating git-repo https://github.com/JuliaRegistries/General.git Cloning git-repo https://github.com/goedman/Stan.jl.git Updating git-repo https://github.com/goedman/Stan.jl.git Resolving package versions... Installed Juno ─────────────── v0.5.2 Installed Hiccup ───────────── v0.2.2 Installed TranscodingStreams ─ v0.6.1 Installed Arpack ───────────── v0.2.2 Installed Tokenize ─────────── v0.5.2 Installed Crayons ──────────── v1.0.0 Installed Revise ───────────── v0.6.4 Installed Plots ────────────── v0.18.0 Installed LNR ──────────────── v0.2.0 Installed GR ───────────────── v0.32.2 Updating ~/.julia/environments/v0.7/Project.toml [a8cc5b0e] ↑ Crayons v0.5.1 ⇒ v1.0.0 [e5e0dc1b] ↑ Juno v0.5.1 ⇒ v0.5.2 [91a5bcdd] ↑ Plots v0.17.4 ⇒ v0.18.0 [295af30f] ↑ Revise v0.6.3 ⇒ v0.6.4 [682df890] + Stan v3.5.0 #master (https://github.com/goedman/Stan.jl.git) Updating ~/.julia/environments/v0.7/Manifest.toml [7d9fca2a] ↑ Arpack v0.2.1 ⇒ v0.2.2 [a8cc5b0e] ↑ Crayons v0.5.1 ⇒ v1.0.0 [28b8d3ca] ↑ GR v0.32.0 ⇒ v0.32.2 [9fb69e20] ↑ Hiccup v0.2.1 ⇒ v0.2.2 [e5e0dc1b] ↑ Juno v0.5.1 ⇒ v0.5.2 [7c4cb9fa] ↑ LNR v0.0.2 ⇒ v0.2.0 [91a5bcdd] ↑ Plots v0.17.4 ⇒ v0.18.0 [295af30f] ↑ Revise v0.6.3 ⇒ v0.6.4 [682df890] + Stan v3.5.0 #master (https://github.com/goedman/Stan.jl.git) [0796e94c] ↑ Tokenize v0.5.1 ⇒ v0.5.2 [3bb67fe8] ↑ TranscodingStreams v0.5.4 ⇒ v0.6.1 Building Revise → ~/.julia/packages/Revise/vNcfy/deps/build.log Building GR ────→ ~/.julia/packages/GR/crXzk/deps/build.log ┌ Error: Error building GR: │ WARNING: Base.Pkg is deprecated, run using Pkg instead │ likely near /home/dfish/.julia/packages/GR/crXzk/deps/build.jl:36 │ WARNING: Base.Pkg is deprecated, run using Pkg instead │ likely near /home/dfish/.julia/packages/GR/crXzk/deps/build.jl:36 │ [ Info: Downloading pre-compiled GR 0.32.0 Ubuntu binary │ [ Info: Using insecure connection │ ERROR: LoadError: IOError: could not spawn curl -g -L -f -o downloads/gr-0.32.0-Ubuntu-x86_64.tar.gz http://gr-framework.org/downloads/gr-0.32.0-Ubuntu-x86_64.tar.gz: no such file or directory (ENOENT) │ Stacktrace: │ [1] _jl_spawn(::String, ::Array{String,1}, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:370 │ [2] (::getfield(Base, Symbol("##499#500")){Cmd})(::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:512 │ [3] setup_stdio(::getfield(Base, Symbol("##499#500")){Cmd}, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:493 │ [4] #_spawn#498(::Nothing, ::Function, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:511 │ [5] _spawn at ./process.jl:507 [inlined] │ [6] #run#509(::Bool, ::Function, ::Cmd) at ./process.jl:669 │ [7] run at ./process.jl:668 [inlined] │ [8] download(::String, ::String) at ./download.jl:48 │ [9] top-level scope at logging.jl:313 │ [10] top-level scope at /home/dfish/.julia/packages/GR/crXzk/deps/build.jl:61 │ [11] include at ./boot.jl:317 [inlined] │ [12] include_relative(::Module, ::String) at ./loading.jl:1038 │ [13] include(::Module, ::String) at ./sysimg.jl:29 │ [14] include(::String) at ./client.jl:398 │ [15] top-level scope at none:0 │ in expression starting at /home/dfish/.julia/packages/GR/crXzk/deps/build.jl:36 └ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Pkg/src/Operations.jl:1068 Building Plots ─→ ~/.julia/packages/Plots/mqUvK/deps/build.log ┌ Error: Error building Plots: │ [ Info: Cannot find deps/plotly-latest.min.js... downloading latest version. │ ERROR: LoadError: IOError: could not spawn curl -g -L -f -o /home/dfish/.julia/packages/Plots/mqUvK/deps/plotly-latest.min.js https://cdn.plot.ly/plotly-latest.min.js: no such file or directory (ENOENT) │ Stacktrace: │ [1] _jl_spawn(::String, ::Array{String,1}, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:370 │ [2] (::getfield(Base, Symbol("##499#500")){Cmd})(::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:512 │ [3] setup_stdio(::getfield(Base, Symbol("##499#500")){Cmd}, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:493 │ [4] #_spawn#498(::Nothing, ::Function, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) at ./process.jl:511 │ [5] _spawn at ./process.jl:507 [inlined] │ [6] #run#509(::Bool, ::Function, ::Cmd) at ./process.jl:669 │ [7] run at ./process.jl:668 [inlined] │ [8] download(::String, ::String) at ./download.jl:48 │ [9] top-level scope at logging.jl:307 │ [10] top-level scope at /home/dfish/.julia/packages/Plots/mqUvK/deps/build.jl:6 │ [11] include at ./boot.jl:317 [inlined] │ [12] include_relative(::Module, ::String) at ./loading.jl:1038 │ [13] include(::Module, ::String) at ./sysimg.jl:29 │ [14] include(::String) at ./client.jl:398 │ [15] top-level scope at none:0 │ in expression starting at /home/dfish/.julia/packages/Plots/mqUvK/deps/build.jl:5 └ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Pkg/src/Operations.jl:1068 Building Arpack → ~/.julia/packages/Arpack/Btbe4/deps/build.log ┌ Error: Error building Arpack: │ [ Info: Downloading https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-linux-gnu.tar.gz to /home/dfish/.julia/packages/Arpack/Btbe4/deps/usr/downloads/ArpackBuilder.x86_64-linux-gnu.tar.gz... │ ERROR: LoadError: Could not download https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-linux-gnu.tar.gz to /home/dfish/.julia/packages/Arpack/Btbe4/deps/usr/downloads/ArpackBuilder.x86_64-linux-gnu.tar.gz │ Stacktrace: │ [1] error(::String) at ./error.jl:33 │ [2] macro expansion at ./logging.jl:313 [inlined] │ [3] #download#89(::Bool, ::Function, ::String, ::String) at /home/dfish/.julia/packages/BinaryProvider/ZbFxn/src/PlatformEngines.jl:443 │ [4] #download at ./none:0 [inlined] │ [5] #download_verify#90(::Bool, ::Bool, ::Bool, ::Function, ::String, ::String, ::String) at /home/dfish/.julia/packages/BinaryProvider/ZbFxn/src/PlatformEngines.jl:523 │ [6] #download_verify at ./none:0 [inlined] │ [7] #install#111(::Prefix, ::String, ::Bool, ::Bool, ::Bool, ::Function, ::String, ::String) at /home/dfish/.julia/packages/BinaryProvider/ZbFxn/src/Prefix.jl:348 │ [8] (::getfield(BinaryProvider, Symbol("#kw##install")))(::NamedTuple{(:prefix, :force, :verbose),Tuple{Prefix,Bool,Bool}}, ::typeof(install), ::String, ::String) at ./none:0 │ [9] top-level scope at /home/dfish/.julia/packages/Arpack/Btbe4/deps/build.jl:30 │ [10] include at ./boot.jl:317 [inlined] │ [11] include_relative(::Module, ::String) at ./loading.jl:1038 │ [12] include(::Module, ::String) at ./sysimg.jl:29 │ [13] include(::String) at ./client.jl:398 │ [14] top-level scope at none:0 │ in expression starting at /home/dfish/.julia/packages/Arpack/Btbe4/deps/build.jl:26 │ [14:29:13] --2018-08-09 14:29:13-- https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-linux-gnu.tar.gz │ [14:29:13] Resolving github.com (github.com)... 192.30.253.112, 192.30.253.113 │ [14:29:13] Connecting to github.com (github.com)|192.30.253.112|:443... connected. │ [14:29:13] HTTP request sent, awaiting response... 302 Found │ [14:29:13] Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/132673190/aa2b862c-659b-11e8-93f3-dcc35685897d?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180809%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180809T182913Z&X-Amz-Expires=300&X-Amz-Signature=39c27f97f44ba10722f03106e21c7f4bcd5937a5c27c490004a978530adeef35&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DArpackBuilder.x86_64-linux-gnu.tar.gz&response-content-type=application%2Foctet-stream [following] │ [14:29:13] --2018-08-09 14:29:13-- https://github-production-release-asset-2e65be.s3.amazonaws.com/132673190/aa2b862c-659b-11e8-93f3-dcc35685897d?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180809%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180809T182913Z&X-Amz-Expires=300&X-Amz-Signature=39c27f97f44ba10722f03106e21c7f4bcd5937a5c27c490004a978530adeef35&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DArpackBuilder.x86_64-linux-gnu.tar.gz&response-content-type=application%2Foctet-stream │ [14:29:13] Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.165.147 │ [14:29:13] Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.165.147|:443... connected. │ [14:29:13] HTTP request sent, awaiting response... 200 OK │ [14:29:13] Length: 142344 (139K) [application/octet-stream] └ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Pkg/src/Operations.jl:1068

(v0.7) pkg> up Updating registry at ~/.julia/registries/General Updating git-repo https://github.com/JuliaRegistries/General.git Updating git-repo https://github.com/goedman/Stan.jl.git Resolving package versions... Updating ~/.julia/environments/v0.7/Project.toml [no changes] Updating ~/.julia/environments/v0.7/Manifest.toml [no changes]

(v0.7) pkg> gc Active manifests at: /home/dfish/.julia/environments/v0.7/Manifest.toml Deleted /home/dfish/.julia/packages/Arpack/Kl4q: 196.311 KiB Deleted /home/dfish/.julia/packages/Arpack/iUWc: 196.662 KiB Deleted /home/dfish/.julia/packages/Arpack/uM2QD: 194.375 KiB Deleted /home/dfish/.julia/packages/BinDeps/2wxq: 85.162 KiB Deleted /home/dfish/.julia/packages/BinaryProvider/mWAR: 137.957 KiB Deleted /home/dfish/.julia/packages/CSV/1VJD: 25.025 MiB Deleted /home/dfish/.julia/packages/Calculus/VVY4: 51.658 KiB Deleted /home/dfish/.julia/packages/CategoricalArrays/lCVK: 349.586 KiB Deleted /home/dfish/.julia/packages/ColorTypes/7oP0: 197.347 KiB Deleted /home/dfish/.julia/packages/Compat/BlWu: 190.499 KiB Deleted /home/dfish/.julia/packages/Compat/OYxC: 174.409 KiB Deleted /home/dfish/.julia/packages/Compat/PrKE: 183.011 KiB Deleted /home/dfish/.julia/packages/Compat/ql30: 187.391 KiB Deleted /home/dfish/.julia/packages/Crayons/e1SsX: 49.133 KiB Deleted /home/dfish/.julia/packages/DataFrames/LwtB: 527.121 KiB Deleted /home/dfish/.julia/packages/DataFrames/WM3y: 525.276 KiB Deleted /home/dfish/.julia/packages/DataStreams/OGMa: 113.290 KiB Deleted /home/dfish/.julia/packages/DataStructures/Zet9: 402.748 KiB Deleted /home/dfish/.julia/packages/DataStructures/eUHI: 397.556 KiB Deleted /home/dfish/.julia/packages/DataStructures/vvd8: 398.222 KiB Deleted /home/dfish/.julia/packages/Distributions/dwhW: 872.371 KiB Deleted /home/dfish/.julia/packages/Distributions/lJq5: 866.586 KiB Deleted /home/dfish/.julia/packages/Distributions/zK5A: 871.394 KiB Deleted /home/dfish/.julia/packages/FixedPointNumbers/OSxF: 39.282 KiB Deleted /home/dfish/.julia/packages/GR/PZ9b: 19.374 MiB Deleted /home/dfish/.julia/packages/GR/u3bF: 19.378 MiB Deleted /home/dfish/.julia/packages/Hiccup/Tweiq: 7.398 KiB Deleted /home/dfish/.julia/packages/Iterators/hSc9: 93.153 KiB Deleted /home/dfish/.julia/packages/JSON/BopY: 80.102 KiB Deleted /home/dfish/.julia/packages/Juno/nMYPI: 12.008 KiB Deleted /home/dfish/.julia/packages/LNR/k53vj: 5.182 KiB Deleted /home/dfish/.julia/packages/Literate/kF6HC: 76.574 KiB Deleted /home/dfish/.julia/packages/Missings/jFaS: 38.315 KiB Deleted /home/dfish/.julia/packages/NaNMath/yjdm: 11.415 KiB Deleted /home/dfish/.julia/packages/NamedTuples/MIrn: 31.694 KiB Deleted /home/dfish/.julia/packages/OptimTestProblems/pwGuQ: 47.379 KiB Deleted /home/dfish/.julia/packages/PDMats/PxDD: 45.863 KiB Deleted /home/dfish/.julia/packages/Parameters/O9cu: 63.229 KiB Deleted /home/dfish/.julia/packages/Parameters/cKWy: 53.185 KiB Deleted /home/dfish/.julia/packages/Plots/V3tQ: 721.327 KiB Deleted /home/dfish/.julia/packages/QuadGK/Pnbq: 22.390 KiB Deleted /home/dfish/.julia/packages/RecursiveArrayTools/iHROO: 37.016 KiB Deleted /home/dfish/.julia/packages/Reexport/XnNe: 5.097 KiB Deleted /home/dfish/.julia/packages/Revise/1bMIH: 122.455 KiB Deleted /home/dfish/.julia/packages/Revise/eToz: 119.610 KiB Deleted /home/dfish/.julia/packages/Revise/iORQ: 77.686 KiB Deleted /home/dfish/.julia/packages/Revise/tGBM: 75.961 KiB Deleted /home/dfish/.julia/packages/Rmath/ENY5: 1.548 MiB Deleted /home/dfish/.julia/packages/Rmath/ewAF: 159.350 KiB Deleted /home/dfish/.julia/packages/SortingAlgorithms/fA7W: 23.446 KiB Deleted /home/dfish/.julia/packages/SortingAlgorithms/ybNh: 23.349 KiB Deleted /home/dfish/.julia/packages/SpecialFunctions/585p: 12.840 MiB Deleted /home/dfish/.julia/packages/SpecialFunctions/kvjJ: 365.749 KiB Deleted /home/dfish/.julia/packages/Stan/vXYqK: 4.113 MiB Deleted /home/dfish/.julia/packages/StaticArrays/MuoW: 832.264 KiB Deleted /home/dfish/.julia/packages/StatsBase/PueG: 374.196 KiB Deleted /home/dfish/.julia/packages/StatsBase/xZVL: 371.670 KiB Deleted /home/dfish/.julia/packages/StatsFuns/RWL6: 72.355 KiB Deleted /home/dfish/.julia/packages/Suppressor/qdsyO: 16.545 KiB Deleted /home/dfish/.julia/packages/Tokenize/rfs3t: 141.411 KiB Deleted /home/dfish/.julia/packages/TranscodingStreams/MxFC: 179.385 KiB Deleted /home/dfish/.julia/packages/TranscodingStreams/xqPx: 179.467 KiB Deleted /home/dfish/.julia/packages/URIParser/2oTQ: 24.151 KiB Deleted /home/dfish/.julia/packages/WeakRefStrings/YrK6: 27.328 KiB Deleted 64 package installations : 93.748 MiB

(v0.7) pkg> st Status ~/.julia/environments/v0.7/Project.toml [c52e3926] Atom v0.7.2 [6e4b80f9] BenchmarkTools v0.3.2 [336ed68f] CSV v0.3.0 [593b3428] CmdStan v4.0.0 [a8cc5b0e] Crayons v1.0.0 [a93c6f00] DataFrames v0.13.0 [aaf54ef3] DistributedArrays v0.5.0 [31c24e10] Distributions v0.16.2 [c8e1da08] IterTools v1.0.0 [e5e0dc1b] Juno v0.5.2 [5fb14364] OhMyREPL v0.3.0 [429524aa] Optim v0.15.3 [d96e819e] Parameters v0.9.2 [91a5bcdd] Plots v0.18.0 [92933f4c] ProgressMeter v0.5.6 [295af30f] Revise v0.6.4 [682df890] Stan v3.5.0 #master (https://github.com/goedman/Stan.jl.git) [9a3f8284] Random [10745b16] Statistics

julia> using Pkg

julia> using Stan [ Info: Recompiling stale cache file /home/dfish/.julia/compiled/v0.7/Stan/zPI1R.ji for Stan [682df890-35be-576f-97d0-3d8c8b33a550] WARNING: eval from module Base to Stan:
Expr(:->, :x, Expr(:block, #= Symbol("/home/dfish/.julia/packages/Documenter/sN5Qn/src/DocChecks.jl"):650 =#, :y = :have_color, #= Symbol("/home/dfish/.julia/packages/Documenter/sN5Qn/src/DocChecks.jl"):650 =#, Expr(:global, :have_color = :x), #= Symbol("/home/dfish/.julia/packages/Documenter/sN5Qn/src/DocChecks.jl"):650 =#, :y)) incremental compilation may be broken for this module

(v0.7) pkg> test Stan Testing Stan Status /tmp/tmpDYIyUu/Manifest.toml [9e28174c] BinDeps v0.8.9 [34da2185] Compat v1.0.1 [ffbed154] DocStringExtensions v0.4.5 [e30172f5] Documenter v0.19.3 [d9be37ee] Homebrew v0.6.4 [682c06a0] JSON v0.19.0 [682df890] Stan v3.5.0 #master (https://github.com/goedman/Stan.jl.git) [30578b45] URIParser v0.4.0 [2a0f44e3] Base64 [~/julia.7/bin/../share/julia/stdlib/v0.7/Base64] [ade2ca70] Dates [~/julia.7/bin/../share/julia/stdlib/v0.7/Dates] [8bb1440f] DelimitedFiles [~/julia.7/bin/../share/julia/stdlib/v0.7/DelimitedFiles] [8ba89e20] Distributed [~/julia.7/bin/../share/julia/stdlib/v0.7/Distributed] [b77e0a4c] InteractiveUtils [~/julia.7/bin/../share/julia/stdlib/v0.7/InteractiveUtils] [76f85450] LibGit2 [~/julia.7/bin/../share/julia/stdlib/v0.7/LibGit2] [8f399da3] Libdl [~/julia.7/bin/../share/julia/stdlib/v0.7/Libdl] [37e2e46d] LinearAlgebra [~/julia.7/bin/../share/julia/stdlib/v0.7/LinearAlgebra] [56ddb016] Logging [~/julia.7/bin/../share/julia/stdlib/v0.7/Logging] [d6f4376e] Markdown [~/julia.7/bin/../share/julia/stdlib/v0.7/Markdown] [a63ad114] Mmap [~/julia.7/bin/../share/julia/stdlib/v0.7/Mmap] [44cfe95a] Pkg [~/julia.7/bin/../share/julia/stdlib/v0.7/Pkg] [de0858da] Printf [~/julia.7/bin/../share/julia/stdlib/v0.7/Printf] [3fa0cd96] REPL [~/julia.7/bin/../share/julia/stdlib/v0.7/REPL] [9a3f8284] Random [~/julia.7/bin/../share/julia/stdlib/v0.7/Random] [ea8e919c] SHA [~/julia.7/bin/../share/julia/stdlib/v0.7/SHA] [9e88b42a] Serialization [~/julia.7/bin/../share/julia/stdlib/v0.7/Serialization] [1a1011a3] SharedArrays [~/julia.7/bin/../share/julia/stdlib/v0.7/SharedArrays] [6462fe0b] Sockets [~/julia.7/bin/../share/julia/stdlib/v0.7/Sockets] [2f01184e] SparseArrays [~/julia.7/bin/../share/julia/stdlib/v0.7/SparseArrays] [10745b16] Statistics [~/julia.7/bin/../share/julia/stdlib/v0.7/Statistics] [8dfed614] Test [~/julia.7/bin/../share/julia/stdlib/v0.7/Test] [cf7118a7] UUIDs [~/julia.7/bin/../share/julia/stdlib/v0.7/UUIDs] [4ec0a83e] Unicode [~/julia.7/bin/../share/julia/stdlib/v0.7/Unicode] Running tests for Stan-j0.7-v3.5.0: CMDSTAN_HOME set. Try to run tests.

• test_env.jl *

• test_utilities.jl * echo 2 echo 3 4 echo 5

1 2 3 4 5

hello hello hello hello hello hello

• test_cmdtype.jl *

File /home/dfish/.julia/packages/Stan/a6xnA/test/tmp/bernoulli.stan will be updated.

name = "bernoulli" nchains = 4 num_samples = 1000 num_warmup = 1000 thin = 1 useMamba = false mambaThinning = 1 monitors = String[] model_file = "bernoulli.stan" data_file = "" output = Output() file = "" diagnostics_file = "" refresh = 100 method = Optimize() algorithm = Lbfgs() init_alpha = 0.001 tol_obj = 1.0e-8 tol_grad = 1.0e-8 tol_param = 1.0e-8 history_size = 5 iterations = 2000 save_iterations = false

name = "bernoulli" nchains = 4 num_samples = 1000 num_warmup = 1000 thin = 1 useMamba = false mambaThinning = 1 monitors = String[] model_file = "bernoulli.stan" data_file = "" output = Output() file = "" diagnostics_file = "" refresh = 100 method = Optimize() algorithm = Lbfgs() init_alpha = 0.001 tol_obj = 1.0e-8 tol_grad = 1.0e-8 tol_param = 1.0e-8 history_size = 5 iterations = 2000 save_iterations = false

method = Sample() num_samples = 1000 num_warmup = 1000 save_warmup = false thin = 1 algorithm = HMC() engine = NUTS() max_depth = 10 metric = Stan.diag_e stepsize = 1.0 stepsize_jitter = 1.0 adapt = Adapt() gamma = 0.05 delta = 0.8 kappa = 0.75 t0 = 10.0 init_buffer = 75 term_buffer = 50 window = 25

method = Sample() num_samples = 1000 num_warmup = 1000 save_warmup = false thin = 1 algorithm = HMC() engine = NUTS() max_depth = 10 metric = Stan.diag_e stepsize = 1.0 stepsize_jitter = 1.0 adapt = Adapt() gamma = 0.05 delta = 0.8 kappa = 0.75 t0 = 10.0 init_buffer = 75 term_buffer = 50 window = 25

method = Optimize() algorithm = Bfgs() init_alpha = 0.001 tol_obj = 1.0e-9 tol_grad = 1.0e-8 tol_param = 1.0e-8 iterations = 2000 save_iterations = true

method = Optimize() algorithm = Bfgs() init_alpha = 0.001 tol_obj = 1.0e-9 tol_grad = 1.0e-8 tol_param = 1.0e-8 iterations = 2000 save_iterations = true

method = Diagnose() diagnostic = Gradient() epsilon = 1.0e-6 error = 1.0e-7

method = Diagnose() diagnostic = Gradient() epsilon = 1.0e-6 error = 1.0e-7

• test_bernoulli.jl *

File /home/dfish/.julia/packages/Stan/a6xnA/Examples/NoMamba/Bernoulli/tmp/bernoulli.stan will be updated.

Unreachable reached at 0x7f37f0064b93

signal (4): Illegal instruction in expression starting at /home/dfish/.julia/packages/Stan/a6xnA/test/test_bernoulli.jl:2 cd at ./file.jl:99 unknown function (ip: 0x7f37f0064bb5) jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829 jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182 do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:324 eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:428 eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:363 [inlined] eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:686 jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:799 unknown function (ip: 0xfffffffffffffffe) unknown function (ip: 0x7f37fbbfe67f) unknown function (ip: 0x6) jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:808 jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:831 jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:841 jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:865 include at ./boot.jl:317 [inlined] include_relative at ./loading.jl:1038 include at ./sysimg.jl:29 jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182 include at ./client.jl:398 jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182 macro expansion at /home/dfish/.julia/packages/Stan/a6xnA/test/runtests.jl:35 [inlined] macro expansion at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v0.7/Test/src/Test.jl:1079 [inlined] top-level scope at /home/dfish/.julia/packages/Stan/a6xnA/test/runtests.jl:28 [inlined] top-level scope at ./none:0 jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829 jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:825 jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:841 jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:865 include at ./boot.jl:317 [inlined] include_relative at ./loading.jl:1038 include at ./sysimg.jl:29 jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182 include at ./client.jl:398 jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1829 jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182 do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:324 eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:428 eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:363 [inlined] eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:686 jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:799 unknown function (ip: 0xfffffffffffffffe) unknown function (ip: 0x7f37fa4239df) unknown function (ip: 0xffffffffffffffff) jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:808 jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:831 jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:778 jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/builtins.c:633 eval at ./boot.jl:319 jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182 macro expansion at ./logging.jl:317 [inlined] exec_options at ./client.jl:229 _start at ./client.jl:432 jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2182 jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1538 [inlined] true_main at /buildworker/worker/package_linux64/build/ui/repl.c:112 main at /buildworker/worker/package_linux64/build/ui/repl.c:233 __libc_start_main at /build/glibc-Cl5G7W/glibc-2.23/csu/../csu/libc-start.c:291 _start at /home/dfish/julia.7/bin/julia (unknown line) Allocations: 16101658 (Pool: 16098970; Big: 2688); GC: 35 ERROR: Package Stan errored during testing

(v0.7) pkg>

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[itsdfish]

Hmm. Odd. Here is my version info:

julia> versioninfo()
Julia Version 0.7.0
Commit a4cb80f3ed (2018-08-08 06:46 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4790K CPU @ 4.00GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, haswell)
Environment:
  JULIA_CMDSTAN_HOME = /home/dfish/cmdstan-1.17.1

[goedman]

I’ll dig a bit deeper this afternoon (in about 2 hours or so).

Rob J Goedman goedman@icloud.com

On Aug 9, 2018, at 12:51, fisherc2 notifications@github.com wrote:

Hmm. Odd. Here is my version info:

julia> versioninfo() Julia Version 0.7.0 Commit a4cb80f3ed (2018-08-08 06:46 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) CPU: Intel(R) Core(TM) i7-4790K CPU @ 4.00GHz WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-6.0.0 (ORCJIT, haswell) Environment: JULIA_CMDSTAN_HOME = /home/dfish/cmdstan-1.17.1

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/goedman/Stan.jl/issues/55#issuecomment-411859765, or mute the thread https://github.com/notifications/unsubscribe-auth/AADL6KK3cZ9p2XTaxKGZWpaydeeG5VNdks5uPIS_gaJpZM4V0jlN.

[itsdfish]

Rob-

Out of desperation, I removed Julia and the packages and started over with a clean install. I added the ENV variable to the startup.jl file and it seems to be working. I have no idea what the problem was, but sometimes a clean install does the trick.

Test Summary: | Pass  Total
Stan.jl       |   12     12

   Testing Stan tests passed 

[goedman]

Aah, missed your earlier email. That would have been my next suggestion, Pkg3 is sensitive to problems in directory trees.

Sent from Rob Goedman's iPad Pro

On Aug 9, 2018, at 1:59 PM, fisherc2 notifications@github.com wrote:

Rob-

Out of desperation, I removed Julia and the packages and started over with a clean install. I added the ENV variable to the startup.jl file and it seems to be working. I have no idea what the problem was, but sometimes a clean install does the trick.

Test Summary: | Pass Total Stan.jl | 12 12

Testing Stan tests passed

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