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

Question

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

francescasci91 opened this issue 2 years 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 <==

==> 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
Francesca

Answer 1 · 2022-11-28T09:21:31.000Z

On what platform do you see this? I can't reproduce it on Linux.

Answer 2 · 2023-01-07T13:48:01.000Z

I just got the exact same error while trying to install genomeinfodbdata-1.2.9 as a dependency of seqinr on linux-64. I used the following command: conda install -c bioconda r-seqinr. Any help would be appreciated!

Answer 3 · 2023-01-07T14:59:13.000Z

@francescasci91, @charlottewright are you installing into an environment that has a lot of other things in it?

On both Linux and macOS I'm able to create fresh environments no problem, e.g.

conda create -n test1 bioconductor-genomeinfodb=1.2.9

and

conda create -n test2 r-seqinr

(using the setup information from https://bioconda.github.io/ with the correct order of channels, so -c bioconda is not used)

Answer 4 · 2023-06-03T04:43:44.000Z

Ran into the same error. Installed a different package with mamba, which updated a long list of R related packages. After that it worked.

Answer 5 · 2024-02-11T00:07:45.000Z

Ran into the same error. Installed a different package with mamba, which updated a long list of R related packages. After that it worked.

Hi, I am stuck in the same error too, macOS, M1 chip, I have been trying to uninstall and reinstall many times but this step always not work and showed like this:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(945): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.
Rolling back transaction: done

LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout:
stderr: /Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/tab-qiime: /Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/qiime: /Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/python: bad interpreter: Bad CPU type in executable
++ dirname -- /Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/installBiocDataPackage.sh

SCRIPT_DIR=/Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/../share/bioconductor-data-packages
json=/Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/../share/bioconductor-data-packages/dataURLs.json
/Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/installBiocDataPackage.sh: /Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/yq: /Users/nakajimalab/anaconda3/envs/qiime2-2023.7/bin/python3.8: bad interpreter: Bad CPU type in executable
FN=

return code: 126

Could you please provide more details for your solution and any advices? Really appreciate that!

Answer 6 · 2024-02-11T00:22:43.000Z

@zombiebride226 , pretty sure I'm not the best person to give advice, but in my case it was an old conda environment that didn't play nice with newer packages anymore.

I would probably start from scratch (like conda env export --from-history > env.yml , then delete and re-install everything still needed).

Answer 7 · 2024-02-11T01:07:45.000Z

@zombiebride226 , pretty sure I'm not the best person to give advice, but in my case it was an old conda environment that didn't play nice with newer packages anymore.

I would probably start from scratch (like conda env export --from-history > env.yml , then delete and re-install everything still needed).

thank you for your reply! I see your situation and solution, I will try your method too.