bioconda-utils icon indicating copy to clipboard operation
bioconda-utils copied to clipboard

Published 20 hours ago • verified publisher icon bioconda

bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0 problems with installation

Open francescasci91 opened this issue 1 year ago • 7 comments

Hi, I'm trying to install genomeinfodbdata-1.2.9 but an error occurs during the installation: In particualar this is the report:

message: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0 location of failed script: /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/.bioconductor-genomeinfodbdata-post-link.sh ==> script messages <== <None> ==> script output <== stdout: /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz": OK ERROR: sub-architecture 'R' is not installed ERROR: sub-architecture 'R.c~' is not installed

stderr: ++ dirname -- /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/installBiocDataPackage.sh

  • SCRIPT_DIR=/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages
  • json=/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages/dataURLs.json ++ yq '."genomeinfodbdata-1.2.9".fn' /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages/dataURLs.json
  • FN='"GenomeInfoDbData_1.2.9.tar.gz"'
  • IFS=
  • read -r value ++ yq '."genomeinfodbdata-1.2.9".urls[]' /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages/dataURLs.json
  • URLS+=($value)
  • IFS=
  • read -r value
  • URLS+=($value)
  • IFS=
  • read -r value
  • URLS+=($value)
  • IFS=
  • read -r value ++ yq '."genomeinfodbdata-1.2.9".md5' /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages/dataURLs.json
  • MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
  • STAGING=/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9
  • mkdir -p /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9
  • TARBALL='/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
  • SUCCESS=0
  • for URL in '${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 11.1M 100 11.1M 0 0 7708k 0 0:00:01 0:00:01 --:--:-- 7705k
  • [[ 0 == 0 ]] ++ uname -s
  • [[ Linux == \L\i\n\u\x ]]
  • md5sum -c
  • SUCCESS=1
  • break
  • [[ 1 != 1 ]]
  • R CMD INSTALL --library=/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/lib/R/library '/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
  • installing source package ‘GenomeInfoDbData’ ... ** using staged installation ** data ** inst ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location *** arch - R *** arch - R.c~ ERROR: loading failed for ‘R’, ‘R.c~’
  • removing ‘/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/lib/R/library/GenomeInfoDbData’
  • restoring previous ‘/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/lib/R/library/GenomeInfoDbData’

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: /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/.bioconductor-genomeinfodbdata-post-link.sh ==> script messages <== <None> ==> script output <== stdout: /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz": OK ERROR: sub-architecture 'R' is not installed ERROR: sub-architecture 'R.c~' is not installed

stderr: ++ dirname -- /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/installBiocDataPackage.sh

  • SCRIPT_DIR=/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages
  • json=/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages/dataURLs.json ++ yq '."genomeinfodbdata-1.2.9".fn' /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages/dataURLs.json
  • FN='"GenomeInfoDbData_1.2.9.tar.gz"'
  • IFS=
  • read -r value ++ yq '."genomeinfodbdata-1.2.9".urls[]' /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages/dataURLs.json
  • URLS+=($value)
  • IFS=
  • read -r value
  • URLS+=($value)
  • IFS=
  • read -r value
  • URLS+=($value)
  • IFS=
  • read -r value ++ yq '."genomeinfodbdata-1.2.9".md5' /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/bin/../share/bioconductor-data-packages/dataURLs.json
  • MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
  • STAGING=/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9
  • mkdir -p /hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9
  • TARBALL='/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
  • SUCCESS=0
  • for URL in '${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 11.1M 100 11.1M 0 0 7708k 0 0:00:01 0:00:01 --:--:-- 7705k
  • [[ 0 == 0 ]] ++ uname -s
  • [[ Linux == \L\i\n\u\x ]]
  • md5sum -c
  • SUCCESS=1
  • break
  • [[ 1 != 1 ]]
  • R CMD INSTALL --library=/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/lib/R/library '/hpcnfs/home/ieo5212/miniconda3/envs/R_single_cell1/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
  • installing source package ‘GenomeInfoDbData’ ... ** using staged installation ** data ** inst ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location *** arch - R *** arch - R.c~ ERROR: loading failed for ‘R’, ‘R.c~’

return code: 1

ValueError: unsupported format character 'T' (0x54) at index 2255

Thanks Francesca

francescasci91 avatar Nov 15 '22 11:11 francescasci91