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Conda recipes for the bioconda channel.
https://bioconda.github.io
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Error installing bioconductor-genomeinfodb - ValueError: unsupported format character 'T' (0x54) at index 1973 #41422

Closed lparsons closed 1 year ago

lparsons commented 1 year ago

I am unable to install the latest bioconductor-genomeinfodb (currently version 1.34.9 build r42hdfd78af_0.

This also happens with versions 1.34.8 and 1.34.1.

Version 1.30.1, however, succeeds.

mamba create -n tmp bioconductor-genomeinfodb
Executing transaction: done                                                                                                                                                                                
ERROR conda.core.link:_execute(733): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.                                                             
Rolling back transaction: done                                                                                                                                                                             
class: LinkError                                                                                                                                                                                           
message:                                                                                                                                                                                                   
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0                                                                                                            
location of failed script: /home/lparsons/mambaforge/envs/tmp/bin/.bioconductor-genomeinfodbdata-post-link.sh                                                                                              
==> script messages <==                                                                                                                                                                                    
<None>                                                                                                                                                                                                     
==> script output <==                                                                                                                                                                                      
stdout: /home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz": OK                                                                                                

stderr: ++ dirname -- /home/lparsons/mambaforge/envs/tmp/bin/installBiocDataPackage.sh                                                                                                                     
+ SCRIPT_DIR=/home/lparsons/mambaforge/envs/tmp/bin/../share/bioconductor-data-packages                                                                                                                    
+ json=/home/lparsons/mambaforge/envs/tmp/bin/../share/bioconductor-data-packages/dataURLs.json                                                                                                            
++ yq '."genomeinfodbdata-1.2.9".fn' /home/lparsons/mambaforge/envs/tmp/bin/../share/bioconductor-data-packages/dataURLs.json                                                                              
+ FN='"GenomeInfoDbData_1.2.9.tar.gz"'                                                                                                                                                                     
+ IFS=                                                                                                                                                                                                     
+ read -r value                                                                                                                                                                                            
++ yq '."genomeinfodbdata-1.2.9".urls[]' /home/lparsons/mambaforge/envs/tmp/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-1.2.9".md5' /home/lparsons/mambaforge/envs/tmp/bin/../share/bioconductor-data-packages/dataURLs.json                                                                             
+ MD5='"7cc138cfb74665fdfa8d1c244eac4879"'                                                                                                                                                                 
+ STAGING=/home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9                                                                                                                                  
+ mkdir -p /home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9                                                                                                                                 
+ TARBALL='/home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'                                                                                                
+ SUCCESS=0                                                                                                                                                                                                
+ for URL in ${URLS[@]}                                                                                                                                                                                    
++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
++ tr -d '"'
+ MD5=7cc138cfb74665fdfa8d1c244eac4879
+ curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   412  100   412    0     0   4355      0 --:--:-- --:--:-- --:--:--  4382
100 11.1M  100 11.1M    0     0  15.9M      0 --:--:-- --:--:-- --:--:-- 22.3M
+ [[ 0 == 0 ]]
++ uname -s
+ [[ Linux == \L\i\n\u\x ]]
+ md5sum -c
+ SUCCESS=1
+ break
+ [[ 1 != 1 ]]
+ R CMD INSTALL --library=/home/lparsons/mambaforge/envs/tmp/lib/R/library '/home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'renv/activate.R': No such file or directory
Execution halted

return code: 1

kwargs:
{}

class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /home/lparsons/mambaforge/envs/tmp/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: /home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz": OK

stderr: ++ dirname -- /home/lparsons/mambaforge/envs/tmp/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/home/lparsons/mambaforge/envs/tmp/bin/../share/bioconductor-data-packages
+ json=/home/lparsons/mambaforge/envs/tmp/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /home/lparsons/mambaforge/envs/tmp/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GenomeInfoDbData_1.2.9.tar.gz"'
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".urls[]' /home/lparsons/mambaforge/envs/tmp/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-1.2.9".md5' /home/lparsons/mambaforge/envs/tmp/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
+ STAGING=/home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9
+ mkdir -p /home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9
+ TARBALL='/home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
+ SUCCESS=0
+ for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
++ tr -d '"'
+ MD5=7cc138cfb74665fdfa8d1c244eac4879
+ curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   412  100   412    0     0   4355      0 --:--:-- --:--:-- --:--:--  4382
100 11.1M  100 11.1M    0     0  15.9M      0 --:--:-- --:--:-- --:--:-- 22.3M
+ [[ 0 == 0 ]]
++ uname -s
+ [[ Linux == \L\i\n\u\x ]]
+ md5sum -c
+ SUCCESS=1
+ break
+ [[ 1 != 1 ]]
+ R CMD INSTALL --library=/home/lparsons/mambaforge/envs/tmp/lib/R/library '/home/lparsons/mambaforge/envs/tmp/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'renv/activate.R': No such file or directory
Execution halted

return code: 1

kwargs:
{}

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<                                                                                                                                               

    Traceback (most recent call last):                                                                                                                                                                     
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 934, in exception_converter                                                                                       
        exit_code = _wrapped_main(*args, **kwargs)                                                                                                                                                         
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 892, in _wrapped_main                                                                                             
        result = do_call(parsed_args, p)                                                                                                                                                                   
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 758, in do_call                                                                                                   
        exit_code = create(args, parser)                                                                                                                                                                   
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 632, in create                                                                                                    
        return install(args, parser, "create")                                                                                                                                                             
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 599, in install                                                                                                   
        handle_txn(conda_transaction, prefix, args, newenv)                                                                                                                                                
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/mamba/linking.py", line 44, in handle_txn                                                                                               
        unlink_link_transaction.execute()                                                                                                                                                                  
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/conda/core/link.py", line 284, in execute                                                                                               
        self._execute(tuple(concat(interleave(self.prefix_action_groups.values()))))                                                                                                                       
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/conda/core/link.py", line 747, in _execute                                                                                              
        raise CondaMultiError(tuple(concatv(                                                                                                                                                               
    conda.CondaMultiError: <unprintable CondaMultiError object>                                                                                                                                            

    During handling of the above exception, another exception occurred:                                                                                                                                    

    Traceback (most recent call last):                                                                                                                                                                     
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/conda/exceptions.py", line 1129, in __call__                                                                                            
        return func(*args, **kwargs)                                                                                                                                                                       
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 940, in exception_converter                                                                                       
        print(e, file=sys.stderr)                                                                                                                                                                          
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/conda/__init__.py", line 112, in __str__                                                                                                
        return str('\n').join(str(e) for e in self.errors) + str('\n')                                                                                                                                     
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/conda/__init__.py", line 112, in <genexpr>                                                                                              
        return str('\n').join(str(e) for e in self.errors) + str('\n')                                                                                                                                     
      File "/home/lparsons/mambaforge/lib/python3.10/site-packages/conda/__init__.py", line 68, in __str__                                                                                                 
        return str(self.message % self._kwargs)
    ValueError: unsupported format character 'T' (0x54) at index 1973

`$ /home/lparsons/mambaforge/bin/mamba create -n tmp bioconductor-genomeinfodb`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/home/lparsons/mambaforge/bin/conda
             CONDA_PREFIX=/home/lparsons/mambaforge
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/home/lparsons/mambaforge/bin/python
               CONDA_ROOT=/home/lparsons/mambaforge
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=<not set>
            DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
           MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
                     PATH=/home/lparsons/.plenv/shims:/home/lparsons/.plenv/bin:/home/lparsons/.
                          local/bin:/home/lparsons/tmux_scripts:/home/lparsons/mambaforge/bin:/h
                          ome/lparsons/mambaforge/condabin:/home/lparsons/.nvm/versions/node/v16
                          .3.0/bin:/home/lparsons/.local/bin:/home/lparsons/tmux_scripts:/home/l
                          parsons/.plenv/shims:/home/lparsons/.plenv/bin:/usr/local/sbin:/usr/lo
                          cal/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/sna
                          p/bin:/snap/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
 TMUX_PLUGIN_MANAGER_PATH=/home/lparsons/.tmux/plugins/
               WINDOWPATH=2

     active environment : base
    active env location : /home/lparsons/mambaforge
            shell level : 1
       user config file : /home/lparsons/.condarc
 populated config files : /home/lparsons/mambaforge/.condarc
                          /home/lparsons/.condarc
          conda version : 22.9.0
    conda-build version : not installed
         python version : 3.10.8.final.0
       virtual packages : __cuda=12.0=0
                          __linux=5.19.0=0
                          __glibc=2.35=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/lparsons/mambaforge  (writable)
      conda av data dir : /home/lparsons/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
          package cache : /home/lparsons/mambaforge/pkgs
                          /home/lparsons/.conda/pkgs
       envs directories : /home/lparsons/mambaforge/envs
                          /home/lparsons/.conda/envs
               platform : linux-64
             user-agent : conda/22.9.0 requests/2.28.1 CPython/3.10.8 Linux/5.19.0-43-generic ubuntu/22.04.2 glibc/2.35
                UID:GID : 1001:1001
             netrc file : None
           offline mode : False

An unexpected error has occurred. Conda has prepared the above report.
lparsons commented 1 year ago

It seems this was caused, at least in part, by having an .Rprofile in my home directory when running the mamba command. I believe that got picked up during the tests and caused a failure.