bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0 problems

[Quianter]

hi MGI: Hi, I'm trying to install DNBC4tools2.1.1 in my linux account, but an error occurs during conda environment create: 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 <==

==> 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 <==

==> 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

[lishuangshuang0616]

Can you check the R version of R_single_cell1? Is this environment a newly created environment, created using conda create dnbc4toos.yaml?

Try: conda clean --all -y remove the mirrors in ~/.condarc

[Quianter]

Can you check the R version of R_single_cell1? Is this environment a newly created environment, created using conda create dnbc4toos.yaml?

Try: conda clean --all -y remove the mirrors in ~/.condarc

it is a newly created conda environment based on dnbc4toos.yaml, the intresting thing is the same conda install pipeline can complete in my another cluster server successfully. So, does it need a specific version compiler in my base environment, like gcc or cmake?

[lishuangshuang0616]

Can it be installed successfully? @Quianter

[Quianter]

Can it be installed successfully? @Quianter

Thanks, I had done it yesterday with creating new conda env after conda reinstall.