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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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Conda install error #128

Closed Glfrey closed 4 days ago

Glfrey commented 1 month ago

Hi all,

Installing version 4.0.0 via conda triggers the following error:

Preparing transaction: done                                                                                                             
Verifying transaction: done                                                                                                             
Executing transaction: done                                                                                                             
ERROR conda.core.link:_execute(950): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1'.                                                                                                                                 
Rolling back transaction: done                                                                                                          
class: LinkError                                                                                                                        
message:                                                                                                                                
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1                                        
location of failed script: /opt/software/EarlGrey/bin/.bioconductor-genomeinfodbdata-post-link.sh                                       
==> script messages <==                                                                                                                 
<None>                                                                                                                                  
==> script output <==                                                                                                                   
stdout: /opt/software/EarlGrey/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz": OK                                       

stderr: ++ dirname -- /opt/software/EarlGrey/bin/installBiocDataPackage.sh                                                              
+ SCRIPT_DIR=/opt/software/EarlGrey/bin/../share/bioconductor-data-packages                                                             
+ json=/opt/software/EarlGrey/bin/../share/bioconductor-data-packages/dataURLs.json                                                     
++ yq '."genomeinfodbdata-1.2.11".fn' /opt/software/EarlGrey/bin/../share/bioconductor-data-packages/dataURLs.json                      
+ FN='"GenomeInfoDbData_1.2.11.tar.gz"'                                                                                                 
+ IFS=                                                                                                                                  
+ read -r value                                                                                                                         
++ yq '."genomeinfodbdata-1.2.11".urls[]' /opt/software/EarlGrey/bin/../share/bioconductor-data-packages/dataURLs.json                  
+ URLS+=($value)                                                                                                                        
+ IFS=                                                                                                                                  
+ read -r value                                                                                                                         
+ URLS+=($value)                                                                                                                        
+ IFS=                                                                                                                                  
+ read -r value                                                                                                                         
+ URLS+=($value)                                                                                                                        
+ IFS=                                                                                                                                  
+ read -r value                                                                                                                         
++ yq '."genomeinfodbdata-1.2.11".md5' /opt/software/EarlGrey/bin/../share/bioconductor-data-packages/dataURLs.json                     
+ MD5='"2a4cbfc2031992fed3c9445f450890a2"'                                                                                              
+ STAGING=/opt/software/EarlGrey/share/genomeinfodbdata-1.2.11                                                                          
+ mkdir -p /opt/software/EarlGrey/share/genomeinfodbdata-1.2.11                                                                         
+ TARBALL='/opt/software/EarlGrey/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz"'
+ SUCCESS=0
+ for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
++ echo '"2a4cbfc2031992fed3c9445f450890a2"'
++ tr -d '"'
+ MD5=2a4cbfc2031992fed3c9445f450890a2
+ curl -L https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   416  100   416    0     0   1598      0 --:--:-- --:--:-- --:--:--  1600

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 11.7M  100 11.7M    0     0  7967k      0  0:00:01  0:00:01 --:--:-- 13.2M
+ [[ 0 == 0 ]]
++ uname -s
+ [[ Linux == \L\i\n\u\x ]]
+ md5sum -c
+ SUCCESS=1
+ break
+ [[ 1 != 1 ]]
+ R CMD INSTALL --library=/opt/software/EarlGrey/lib/R/library '/opt/software/EarlGrey/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz"'
During startup - Warning messages:
1: package ‘utils’ in options("defaultPackages") was not found 
2: package ‘stats’ in options("defaultPackages") was not found 
Error: .onLoad failed in loadNamespace() for 'utils', details:
  call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
  error: error in running command

return code: 1

kwargs:
{}

Traceback (most recent call last):
  File "/opt/software/conda/lib/python3.12/site-packages/conda/exception_handler.py", line 18, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/cli/main.py", line 84, in main_subshell
    exit_code = do_call(args, parser)
                ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/cli/conda_argparse.py", line 200, in do_call
    result = getattr(module, func_name)(args, parser)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/notices/core.py", line 132, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/cli/main_create.py", line 137, in execute
    return install(args, parser, "create")
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/cli/install.py", line 455, in install
    handle_txn(unlink_link_transaction, prefix, args, newenv)
  File "/opt/software/conda/lib/python3.12/site-packages/conda/cli/install.py", line 526, in handle_txn
    unlink_link_transaction.execute()
  File "/opt/software/conda/lib/python3.12/site-packages/conda/core/link.py", line 354, in execute
    self._execute(
  File "/opt/software/conda/lib/python3.12/site-packages/conda/core/link.py", line 970, in _execute
    raise CondaMultiError(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1
location of failed script: /opt/software/EarlGrey/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: /opt/software/EarlGrey/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz": OK

stderr: ++ dirname -- /opt/software/EarlGrey/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/opt/software/EarlGrey/bin/../share/bioconductor-data-packages
+ json=/opt/software/EarlGrey/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.11".fn' /opt/software/EarlGrey/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GenomeInfoDbData_1.2.11.tar.gz"'
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.11".urls[]' /opt/software/EarlGrey/bin/../share/bioconductor-data-packages/dataURLs.json
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.11".md5' /opt/software/EarlGrey/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"2a4cbfc2031992fed3c9445f450890a2"'
+ STAGING=/opt/software/EarlGrey/share/genomeinfodbdata-1.2.11
+ mkdir -p /opt/software/EarlGrey/share/genomeinfodbdata-1.2.11
+ TARBALL='/opt/software/EarlGrey/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz"'
+ SUCCESS=0
+ for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
++ echo '"2a4cbfc2031992fed3c9445f450890a2"'
++ tr -d '"'
+ MD5=2a4cbfc2031992fed3c9445f450890a2
+ curl -L https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   416  100   416    0     0   1598      0 --:--:-- --:--:-- --:--:--  1600

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 11.7M  100 11.7M    0     0  7967k      0  0:00:01  0:00:01 --:--:-- 13.2M
+ [[ 0 == 0 ]]
++ uname -s
+ [[ Linux == \L\i\n\u\x ]]
+ md5sum -c
+ SUCCESS=1
+ break
+ [[ 1 != 1 ]]
+ R CMD INSTALL --library=/opt/software/EarlGrey/lib/R/library '/opt/software/EarlGrey/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz"'
During startup - Warning messages:
1: package ‘utils’ in options("defaultPackages") was not found 
2: package ‘stats’ in options("defaultPackages") was not found 
Error: .onLoad failed in loadNamespace() for 'utils', details:
  call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
  error: error in running command

return code: 1

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/software/conda/bin/conda", line 13, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/cli/main.py", line 128, in main
    return conda_exception_handler(main, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/exception_handler.py", line 388, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/exception_handler.py", line 21, in __call__
    return self.handle_exception(exc_val, exc_tb)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/exception_handler.py", line 62, in handle_exception
    return self.handle_application_exception(exc_val, exc_tb)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/exception_handler.py", line 78, in handle_application_exception
    self._print_conda_exception(exc_val, exc_tb)
  File "/opt/software/conda/lib/python3.12/site-packages/conda/exception_handler.py", line 84, in _print_conda_exception
    print_conda_exception(exc_val, exc_tb)
  File "/opt/software/conda/lib/python3.12/site-packages/conda/exceptions.py", line 1262, in print_conda_exception
    stderrlog.error("\n%r\n", exc_val)
  File "/opt/software/conda/lib/python3.12/logging/__init__.py", line 1568, in error
    self._log(ERROR, msg, args, **kwargs)
  File "/opt/software/conda/lib/python3.12/logging/__init__.py", line 1684, in _log
    self.handle(record)
  File "/opt/software/conda/lib/python3.12/logging/__init__.py", line 1695, in handle
    maybe_record = self.filter(record)
                   ^^^^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/logging/__init__.py", line 858, in filter
    result = f.filter(record)
             ^^^^^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/gateways/logging.py", line 67, in filter
    record.msg = record.msg % new_args
                 ~~~~~~~~~~~^~~~~~~~~~
  File "/opt/software/conda/lib/python3.12/site-packages/conda/__init__.py", line 125, in __repr__
    errs.append(e.__repr__())
                ^^^^^^^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/__init__.py", line 79, in __repr__
    return f"{self.__class__.__name__}: {self}"
                                        ^^^^^^
  File "/opt/software/conda/lib/python3.12/site-packages/conda/__init__.py", line 83, in __str__
    return str(self.message % self._kwargs)
               ~~~~~~~~~~~~~^~~~~~~~~~~~~~
ValueError: unsupported format character 'T' (0x54) at index 1855
FATAL:   While performing build: while running engine: exit status 1

I'm not familiar with this error at all, but it looks like an error with one of the dependencies? I'd be grateful for any of your insight.

Thank you!

TobyBaril commented 3 weeks ago

Hi,

This looks like an issue with Bioconductor. I haven't been able to reproduce this issue - is there anything unusual about your system (permissions, OS, etc?). Sometimes these post-script issues can trigger if the user does not have write/execute permissions for the conda install directory, which can happen on shared systems/servers.

TobyBaril commented 4 days ago

closing due to lack of activity

Yutang-ETH commented 12 hours ago

Hi @TobyBaril ,

I got the the same error while installing v4.4.4 via conda. Looks like there is something wrong with conda installation of genomeinfodbdata-1.2.11. Google led me to this thread, https://github.com/bioconda/bioconda-recipes/issues/31349; looks like this is an unsolved issue.

By the way, I tried mamba first, which was much quicker than conda. However, it got stuck when downloading the Dfam dataset. This is because at ETH Zurich (at least our department D-usys), we need the proxy to access the external resources. Unfortunately, mamba doesn't work with proxy. Only conda dose. https://github.com/mamba-org/mamba/issues/2438

If you could spend a little time looking into this issue, I would appreciate that very much. Otherwise, the last solution for me would be using the singularity container.

Thank you very much, and look forward to your reply. Yutang

Information of our machine below: -bash-4.4$ cat /etc/os-release NAME="Rocky Linux" VERSION="8.10 (Green Obsidian)" ID="rocky" ID_LIKE="rhel centos fedora" VERSION_ID="8.10" PLATFORM_ID="platform:el8" PRETTY_NAME="Rocky Linux 8.10 (Green Obsidian)" ANSI_COLOR="0;32" LOGO="fedora-logo-icon" CPE_NAME="cpe:/o:rocky:rocky:8:GA" HOME_URL="https://rockylinux.org/" BUG_REPORT_URL="https://bugs.rockylinux.org/" SUPPORT_END="2029-05-31" ROCKY_SUPPORT_PRODUCT="Rocky-Linux-8" ROCKY_SUPPORT_PRODUCT_VERSION="8.10" REDHAT_SUPPORT_PRODUCT="Rocky Linux" REDHAT_SUPPORT_PRODUCT_VERSION="8.10"

-bash-4.4$ uname -a Linux g-wst-mpb-calc 4.18.0-553.16.1.el8_10.x86_64 #1 SMP Thu Aug 8 17:47:08 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux