Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

go.db fails to install #53096

Closed
ND91 opened this issue Jan 8, 2025 · 2 comments
Closed

go.db fails to install #53096

ND91 opened this issue Jan 8, 2025 · 2 comments

Comments

@ND91
Copy link

ND91 commented Jan 8, 2025

I'm unable to install bioconductor-go.db 3.20.0 when running mamba install bioconda::bioconductor-go.db . See output at the bottom of this post.

The problem appears to be a post-link error. I checked the FAQs and tried to increase the build from _0 to _1 (https://bioconda.github.io/faqs.html#why-are-bioconductor-data-packages-failing-to-install).

mamba install bioconda::bioconductor-go.db=3.20.0=r44hdfd78af_1

However, that fails as well.

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
Transaction

  Prefix: /net/beegfs/scratch/aliyim/local/mambaforge/envs/test

  Updating specs:

   - bioconda::bioconductor-go.db


  Package                               Version  Build                Channel                    Size
───────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                           0.1  conda_forge          conda-forge/linux-64     Cached
  + _openmp_mutex                           4.5  2_gnu                conda-forge/linux-64     Cached
  + _r-mutex                              1.0.1  anacondar_1          conda-forge/noarch       Cached
  + argcomplete                           3.5.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + binutils_impl_linux-64                 2.43  h4bf12b8_2           conda-forge/linux-64     Cached
  + bioconductor-annotationdbi           1.68.0  r44hdfd78af_0        bioconda/noarch          Cached
  + bioconductor-biobase                 2.66.0  r44h3df3fcb_0        bioconda/linux-64        Cached
  + bioconductor-biocgenerics            0.52.0  r44hdfd78af_0        bioconda/noarch          Cached
  + bioconductor-biostrings              2.74.0  r44h3df3fcb_0        bioconda/linux-64        Cached
  + bioconductor-data-packages       20250105.1  hdfd78af_0           bioconda/noarch          Cached
  + bioconductor-genomeinfodb            1.42.0  r44hdfd78af_0        bioconda/noarch          Cached
  + bioconductor-genomeinfodbdata        1.2.13  r44hdfd78af_0        bioconda/noarch          Cached
  + bioconductor-go.db                   3.20.0  r44hdfd78af_0        bioconda/noarch          Cached
  + bioconductor-iranges                 2.40.0  r44h3df3fcb_0        bioconda/linux-64        Cached
  + bioconductor-keggrest                1.46.0  r44hdfd78af_0        bioconda/noarch          Cached
  + bioconductor-s4vectors               0.44.0  r44h3df3fcb_0        bioconda/linux-64        Cached
  + bioconductor-ucsc.utils               1.2.0  r44hdfd78af_0        bioconda/noarch          Cached
  + bioconductor-xvector                 0.46.0  r44h15a9599_0        bioconda/linux-64        Cached
  + bioconductor-zlibbioc                1.52.0  r44h3df3fcb_0        bioconda/linux-64        Cached
  + bwidget                              1.10.1  ha770c72_0           conda-forge/linux-64     Cached
  + bzip2                                 1.0.8  h4bc722e_7           conda-forge/linux-64     Cached
  + c-ares                               1.34.4  hb9d3cd8_0           conda-forge/linux-64     Cached
  + ca-certificates                  2024.12.14  hbcca054_0           conda-forge/linux-64     Cached
  + cairo                                1.18.2  h3394656_1           conda-forge/linux-64     Cached
  + curl                                 8.11.1  h332b0f4_0           conda-forge/linux-64     Cached
  + font-ttf-dejavu-sans-mono              2.37  hab24e00_0           conda-forge/noarch       Cached
  + font-ttf-inconsolata                  3.000  h77eed37_0           conda-forge/noarch       Cached
  + font-ttf-source-code-pro              2.038  h77eed37_0           conda-forge/noarch       Cached
  + font-ttf-ubuntu                        0.83  h77eed37_3           conda-forge/noarch       Cached
  + fontconfig                           2.15.0  h7e30c49_1           conda-forge/linux-64     Cached
  + fonts-conda-ecosystem                     1  0                    conda-forge/noarch       Cached
  + fonts-conda-forge                         1  0                    conda-forge/noarch       Cached
  + freetype                             2.12.1  h267a509_2           conda-forge/linux-64     Cached
  + fribidi                              1.0.10  h36c2ea0_0           conda-forge/linux-64     Cached
  + gcc_impl_linux-64                    14.2.0  h6b349bd_1           conda-forge/linux-64     Cached
  + gfortran_impl_linux-64               14.2.0  hc73f493_1           conda-forge/linux-64     Cached
  + graphite2                            1.3.13  h59595ed_1003        conda-forge/linux-64     Cached
  + gsl                                     2.7  he838d99_0           conda-forge/linux-64     Cached
  + gxx_impl_linux-64                    14.2.0  h2c03514_1           conda-forge/linux-64     Cached
  + harfbuzz                             10.1.0  h0b3b770_0           conda-forge/linux-64     Cached
  + icu                                    75.1  he02047a_0           conda-forge/linux-64     Cached
  + jq                                    1.7.1  hd590300_0           conda-forge/linux-64     Cached
  + kernel-headers_linux-64              3.10.0  he073ed8_18          conda-forge/noarch       Cached
  + keyutils                              1.6.1  h166bdaf_0           conda-forge/linux-64     Cached
  + krb5                                 1.21.3  h659f571_0           conda-forge/linux-64     Cached
  + ld_impl_linux-64                       2.43  h712a8e2_2           conda-forge/linux-64     Cached
  + lerc                                  4.0.0  h27087fc_0           conda-forge/linux-64     Cached
  + libblas                               3.9.0  26_linux64_openblas  conda-forge/linux-64     Cached
  + libcblas                              3.9.0  26_linux64_openblas  conda-forge/linux-64     Cached
  + libcurl                              8.11.1  h332b0f4_0           conda-forge/linux-64     Cached
  + libdeflate                             1.23  h4ddbbb0_0           conda-forge/linux-64     Cached
  + libedit                        3.1.20240808  pl5321h7949ede_0     conda-forge/linux-64     Cached
  + libev                                  4.33  hd590300_2           conda-forge/linux-64     Cached
  + libexpat                              2.6.4  h5888daf_0           conda-forge/linux-64     Cached
  + libffi                                3.4.2  h7f98852_5           conda-forge/linux-64     Cached
  + libgcc                               14.2.0  h77fa898_1           conda-forge/linux-64     Cached
  + libgcc-devel_linux-64                14.2.0  h41c2201_101         conda-forge/noarch       Cached
  + libgcc-ng                            14.2.0  h69a702a_1           conda-forge/linux-64     Cached
  + libgfortran                          14.2.0  h69a702a_1           conda-forge/linux-64     Cached
  + libgfortran-ng                       14.2.0  h69a702a_1           conda-forge/linux-64     Cached
  + libgfortran5                         14.2.0  hd5240d6_1           conda-forge/linux-64     Cached
  + libglib                              2.82.2  h2ff4ddf_0           conda-forge/linux-64     Cached
  + libgomp                              14.2.0  h77fa898_1           conda-forge/linux-64     Cached
  + libiconv                               1.17  hd590300_2           conda-forge/linux-64     Cached
  + libjpeg-turbo                         3.0.0  hd590300_1           conda-forge/linux-64     Cached
  + liblapack                             3.9.0  26_linux64_openblas  conda-forge/linux-64     Cached
  + liblzma                               5.6.3  hb9d3cd8_1           conda-forge/linux-64     Cached
  + libmpdec                              4.0.0  h4bc722e_0           conda-forge/linux-64     Cached
  + libnghttp2                           1.64.0  h161d5f1_0           conda-forge/linux-64     Cached
  + libopenblas                          0.3.28  pthreads_h94d23a6_1  conda-forge/linux-64     Cached
  + libpng                               1.6.44  hadc24fc_0           conda-forge/linux-64     Cached
  + libsanitizer                         14.2.0  h2a3dede_1           conda-forge/linux-64     Cached
  + libsqlite                            3.47.2  hee588c1_0           conda-forge/linux-64     Cached
  + libssh2                              1.11.1  hf672d98_0           conda-forge/linux-64     Cached
  + libstdcxx                            14.2.0  hc0a3c3a_1           conda-forge/linux-64     Cached
  + libstdcxx-devel_linux-64             14.2.0  h41c2201_101         conda-forge/noarch       Cached
  + libstdcxx-ng                         14.2.0  h4852527_1           conda-forge/linux-64     Cached
  + libtiff                               4.7.0  hd9ff511_3           conda-forge/linux-64     Cached
  + libuuid                              2.38.1  h0b41bf4_0           conda-forge/linux-64     Cached
  + libwebp-base                          1.5.0  h851e524_0           conda-forge/linux-64     Cached
  + libxcb                               1.17.0  h8a09558_0           conda-forge/linux-64     Cached
  + libzlib                               1.3.1  hb9d3cd8_2           conda-forge/linux-64     Cached
  + make                                  4.4.1  hb9d3cd8_2           conda-forge/linux-64     Cached
  + ncurses                                 6.5  he02047a_1           conda-forge/linux-64     Cached
  + oniguruma                            6.9.10  hb9d3cd8_0           conda-forge/linux-64     Cached
  + openssl                               3.4.0  h7b32b05_1           conda-forge/linux-64     Cached
  + pango                                1.54.0  h861ebed_4           conda-forge/linux-64     Cached
  + pcre2                                 10.44  hba22ea6_2           conda-forge/linux-64     Cached
  + pip                                  24.3.1  pyh145f28c_2         conda-forge/noarch       Cached
  + pixman                               0.44.2  h29eaf8c_0           conda-forge/linux-64     Cached
  + pthread-stubs                           0.4  hb9d3cd8_1002        conda-forge/linux-64     Cached
  + python                               3.13.1  ha99a958_103_cp313   conda-forge/linux-64     Cached
  + python_abi                             3.13  5_cp313              conda-forge/linux-64     Cached
  + pyyaml                                6.0.2  py313h536fd9c_1      conda-forge/linux-64     Cached
  + r-askpass                             1.2.1  r44h2b5f3a1_0        conda-forge/linux-64     Cached
  + r-base                                4.4.2  hc737e89_2           conda-forge/linux-64     Cached
  + r-bit                               4.5.0.1  r44h2b5f3a1_0        conda-forge/linux-64     Cached
  + r-bit64                               4.5.2  r44h2b5f3a1_0        conda-forge/linux-64     Cached
  + r-blob                                1.2.4  r44hc72bb7e_2        conda-forge/noarch       Cached
  + r-cachem                              1.1.0  r44hb1dbf0f_1        conda-forge/linux-64     Cached
  + r-cli                                 3.6.3  r44h0d4f4ea_1        conda-forge/linux-64     Cached
  + r-cpp11                               0.5.1  r44hc72bb7e_0        conda-forge/noarch       Cached
  + r-crayon                              1.5.3  r44hc72bb7e_1        conda-forge/noarch       Cached
  + r-curl                                6.0.1  r44h2700575_0        conda-forge/linux-64     Cached
  + r-dbi                                 1.2.3  r44hc72bb7e_1        conda-forge/noarch       Cached
  + r-fastmap                             1.2.0  r44ha18555a_1        conda-forge/linux-64     Cached
  + r-glue                                1.8.0  r44h2b5f3a1_0        conda-forge/linux-64     Cached
  + r-httr                                1.4.7  r44hc72bb7e_1        conda-forge/noarch       Cached
  + r-jsonlite                            1.8.9  r44h2b5f3a1_0        conda-forge/linux-64     Cached
  + r-lifecycle                           1.0.4  r44hc72bb7e_1        conda-forge/noarch       Cached
  + r-memoise                             2.0.1  r44hc72bb7e_3        conda-forge/noarch       Cached
  + r-mime                                 0.12  r44hb1dbf0f_3        conda-forge/linux-64     Cached
  + r-openssl                             2.2.2  r44he8289e2_0        conda-forge/linux-64     Cached
  + r-pkgconfig                           2.0.3  r44hc72bb7e_4        conda-forge/noarch       Cached
  + r-plogr                               0.2.0  r44hc72bb7e_1006     conda-forge/noarch       Cached
  + r-png                                 0.1_8  r44h21f035c_2        conda-forge/linux-64     Cached
  + r-r6                                  2.5.1  r44hc72bb7e_3        conda-forge/noarch       Cached
  + r-rlang                               1.1.4  r44ha18555a_1        conda-forge/linux-64     Cached
  + r-rsqlite                             2.3.9  r44h93ab643_0        conda-forge/linux-64     Cached
  + r-sys                                 3.4.3  r44h2b5f3a1_0        conda-forge/linux-64     Cached
  + r-vctrs                               0.6.5  r44h0d4f4ea_1        conda-forge/linux-64     Cached
  + readline                                8.2  h8228510_1           conda-forge/linux-64     Cached
  + sed                                     4.8  he412f7d_0           conda-forge/linux-64     Cached
  + setuptools                           75.6.0  pyhff2d567_1         conda-forge/noarch       Cached
  + sysroot_linux-64                       2.17  h0157908_18          conda-forge/noarch       Cached
  + tk                                   8.6.13  noxft_h4845f30_101   conda-forge/linux-64     Cached
  + tktable                                2.10  h8bc8fbc_6           conda-forge/linux-64     Cached
  + toml                                 0.10.2  pyhd8ed1ab_1         conda-forge/noarch       Cached
  + tomlkit                              0.13.2  pyha770c72_1         conda-forge/noarch       Cached
  + tzdata                                2024b  hc8b5060_0           conda-forge/noarch       Cached
  + xmltodict                            0.14.2  pyhd8ed1ab_1         conda-forge/noarch       Cached
  + xorg-libice                           1.1.2  hb9d3cd8_0           conda-forge/linux-64     Cached
  + xorg-libsm                            1.2.5  he73a12e_0           conda-forge/linux-64     Cached
  + xorg-libx11                          1.8.10  h4f16b4b_1           conda-forge/linux-64     Cached
  + xorg-libxau                          1.0.12  hb9d3cd8_0           conda-forge/linux-64     Cached
  + xorg-libxdmcp                         1.1.5  hb9d3cd8_0           conda-forge/linux-64     Cached
  + xorg-libxext                          1.3.6  hb9d3cd8_0           conda-forge/linux-64     Cached
  + xorg-libxrender                      0.9.12  hb9d3cd8_0           conda-forge/linux-64     Cached
  + xorg-libxt                            1.3.1  hb9d3cd8_0           conda-forge/linux-64     Cached
  + yaml                                  0.2.5  h7f98852_2           conda-forge/linux-64     Cached
  + yq                                    3.4.3  pyhd8ed1ab_1         conda-forge/noarch       Cached
  + zstd                                  1.5.6  ha6fb4c9_0           conda-forge/linux-64     Cached

  Summary:

  Install: 142 packages

  Total download: 0 B

───────────────────────────────────────────────────────────────────────────────────────────────────────


Confirm changes: [Y/n] 
Looking for: ['bioconda::bioconductor-go.db']


Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
ERROR conda.core.link:_execute(745): An error occurred while installing package 'bioconda::bioconductor-go.db-3.20.0-r44hdfd78af_0'.
Rolling back transaction: ...working... done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-go.db-3.20.0-r44hdfd78af_0
location of failed script: /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/.bioconductor-go.db-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0/"GO.db_3.20.0.tar.gz": OK
Error: package ‘AnnotationDbi’ 1.58.0 was found, but >= 1.67.0 is required by ‘GO.db’
In addition: Warning message:
version 1.68.0 of ‘AnnotationDbi’ masked by 1.58.0 in /net/beegfs/scratch/aliyim/R/4.2 
Execution halted

stderr: ++ dirname -- /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/../share/bioconductor-data-packages
+ json=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."go.db-3.20.0".fn' /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GO.db_3.20.0.tar.gz"'
+ IFS=
+ read -r value
++ yq '."go.db-3.20.0".urls[]' /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/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 '."go.db-3.20.0".md5' /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"a41513069bb1ff4a2ecfa1a538110699"'
+ STAGING=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0
+ mkdir -p /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0
+ TARBALL='/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0/"GO.db_3.20.0.tar.gz"'
+ SUCCESS=0
+ for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GO.db_3.20.0.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GO.db_3.20.0.tar.gz
++ echo '"a41513069bb1ff4a2ecfa1a538110699"'
++ tr -d '"'
+ MD5=a41513069bb1ff4a2ecfa1a538110699
+ curl -L https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GO.db_3.20.0.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 25.1M  100 25.1M    0     0  78.3M      0 --:--:-- --:--:-- --:--:-- 78.5M
+ [[ 0 == 0 ]]
++ uname -s
+ [[ Linux == \L\i\n\u\x ]]
+ md5sum -c
+ SUCCESS=1
+ break
+ [[ 1 != 1 ]]
+ R CMD INSTALL --library=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/lib/R/library '/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0/"GO.db_3.20.0.tar.gz"'
* installing *source* package ‘GO.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
ERROR: lazy loading failed for package ‘GO.db’
* removing ‘/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/lib/R/library/GO.db’

return code: 1

kwargs:
{}

class: LinkError
message:
post-link script failed for package bioconda::bioconductor-go.db-3.20.0-r44hdfd78af_0
location of failed script: /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/.bioconductor-go.db-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0/"GO.db_3.20.0.tar.gz": OK
Error: package ‘AnnotationDbi’ 1.58.0 was found, but >= 1.67.0 is required by ‘GO.db’
In addition: Warning message:
version 1.68.0 of ‘AnnotationDbi’ masked by 1.58.0 in /net/beegfs/scratch/aliyim/R/4.2 
Execution halted

stderr: ++ dirname -- /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/../share/bioconductor-data-packages
+ json=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."go.db-3.20.0".fn' /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GO.db_3.20.0.tar.gz"'
+ IFS=
+ read -r value
++ yq '."go.db-3.20.0".urls[]' /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/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 '."go.db-3.20.0".md5' /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"a41513069bb1ff4a2ecfa1a538110699"'
+ STAGING=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0
+ mkdir -p /net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0
+ TARBALL='/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0/"GO.db_3.20.0.tar.gz"'
+ SUCCESS=0
+ for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GO.db_3.20.0.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GO.db_3.20.0.tar.gz
++ echo '"a41513069bb1ff4a2ecfa1a538110699"'
++ tr -d '"'
+ MD5=a41513069bb1ff4a2ecfa1a538110699
+ curl -L https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GO.db_3.20.0.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 25.1M  100 25.1M    0     0  78.3M      0 --:--:-- --:--:-- --:--:-- 78.5M
+ [[ 0 == 0 ]]
++ uname -s
+ [[ Linux == \L\i\n\u\x ]]
+ md5sum -c
+ SUCCESS=1
+ break
+ [[ 1 != 1 ]]
+ R CMD INSTALL --library=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/lib/R/library '/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/share/go.db-3.20.0/"GO.db_3.20.0.tar.gz"'
* installing *source* package ‘GO.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
ERROR: lazy loading failed for package ‘GO.db’
* removing ‘/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/lib/R/library/GO.db’

return code: 1

kwargs:
{}


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

    Traceback (most recent call last):
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 934, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 892, in _wrapped_main
        result = do_call(parsed_args, p)
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 754, in do_call
        exit_code = install(args, parser, "install")
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 599, in install
        handle_txn(conda_transaction, prefix, args, newenv)
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/mamba/linking.py", line 44, in handle_txn
        unlink_link_transaction.execute()
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/conda/core/link.py", line 286, in execute
        self._execute(
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/conda/core/link.py", line 761, in _execute
        raise CondaMultiError(
    conda.CondaMultiError: <unprintable CondaMultiError object>
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/conda/exceptions.py", line 1124, in __call__
        return func(*args, **kwargs)
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line 940, in exception_converter
        print(e, file=sys.stderr)
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/conda/__init__.py", line 112, in __str__
        return "\n".join(str(e) for e in self.errors) + "\n"
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/conda/__init__.py", line 112, in <genexpr>
        return "\n".join(str(e) for e in self.errors) + "\n"
      File "/net/beegfs/scratch/aliyim/local/mambaforge/lib/python3.10/site-packages/conda/__init__.py", line 66, in __str__
        return str(self.message % self._kwargs)
    ValueError: unsupported format character 'T' (0x54) at index 2252

`$ /net/beegfs/scratch/aliyim/local/mambaforge/bin/mamba install bioconda::bioconductor-go.db`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=test
                CONDA_EXE=/net/beegfs/scratch/aliyim/local/mambaforge/bin/conda
             CONDA_PREFIX=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test
           CONDA_PREFIX_1=/net/beegfs/scratch/aliyim/local/mambaforge
    CONDA_PROMPT_MODIFIER=(test)
         CONDA_PYTHON_EXE=/net/beegfs/scratch/aliyim/local/mambaforge/bin/python
               CONDA_ROOT=/net/beegfs/scratch/aliyim/local/mambaforge
              CONDA_SHLVL=2
           CURL_CA_BUNDLE=<not set>
               LD_PRELOAD=<not set>
               MODULEPATH=/etc/scl/modulefiles:/opt/ohpc/pub/modulefiles:/trinity/shared/modulef
                          iles:/trinity/shared/apps/easybuild/modules/all
                     PATH=/net/beegfs/scratch/aliyim/local/mambaforge/envs/test/bin:/net/beegfs/
                          scratch/aliyim/local/mambaforge/condabin:/usr/local/bin:/usr/bin:/usr/
                          local/sbin:/usr/sbin:/trinity/home/aliyim/.local/bin:/trinity/home/ali
                          yim/bin:/trinity/home/aliyim/.local/bin:/trinity/home/aliyim/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
__LMOD_REF_COUNT_MODULEPATH=/opt/ohpc/pub/modulefiles:1

     active environment : test
    active env location : /net/beegfs/scratch/aliyim/local/mambaforge/envs/test
            shell level : 2
       user config file : /trinity/home/aliyim/.condarc
 populated config files : /net/beegfs/scratch/aliyim/local/mambaforge/.condarc
          conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.28=0
                          __linux=4.18.0=0
                          __unix=0=0
       base environment : /net/beegfs/scratch/aliyim/local/mambaforge  (writable)
      conda av data dir : /net/beegfs/scratch/aliyim/local/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
          package cache : /net/beegfs/scratch/aliyim/local/mambaforge/pkgs
                          /trinity/home/aliyim/.conda/pkgs
       envs directories : /net/beegfs/scratch/aliyim/local/mambaforge/envs
                          /trinity/home/aliyim/.conda/envs
               platform : linux-64
             user-agent : conda/23.1.0 requests/2.28.2 CPython/3.10.10 Linux/4.18.0-425.19.2.el8_7.x86_64 rhel/8.7 glibc/2.28
                UID:GID : 1067:1067
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.
@vsuppiyar
Copy link

vsuppiyar commented Jan 13, 2025 •
edited
Loading

@ND91 It seems like version 1.68.0 of ‘AnnotationDbi’ is masked by 1.58.0 in /net/beegfs/scratch/aliyim/R/4.2.

Error: package ‘AnnotationDbi’ 1.58.0 was found, but >= 1.67.0 is required by ‘GO.db’
In addition: Warning message:
version 1.68.0 of ‘AnnotationDbi’ masked by 1.58.0 in /net/beegfs/scratch/aliyim/R/4.2

Could you try unmasking it and retry the installation?

The reason why mamba install bioconda::bioconductor-go.db=3.20.0=r44hdfd78af_1 might fail is that there is no such a build number, see here https://anaconda.org/bioconda/bioconductor-go.db/files.

For me the installation of the package with mamba create -n test bioconda::bioconductor-go.db works fine on Linux x86_64. You might either try one of the other existing build versions from the link above, or look into #53045 where a similar issue was reported for another bioconductor package.

@ND91
Copy link
Author

ND91 commented Jan 14, 2025

@ND91 It seems like version 1.68.0 of ‘AnnotationDbi’ is masked by 1.58.0 in /net/beegfs/scratch/aliyim/R/4.2.

Error: package ‘AnnotationDbi’ 1.58.0 was found, but >= 1.67.0 is required by ‘GO.db’
In addition: Warning message:
version 1.68.0 of ‘AnnotationDbi’ masked by 1.58.0 in /net/beegfs/scratch/aliyim/R/4.2

Could you try unmasking it and retry the installation?

The reason why mamba install bioconda::bioconductor-go.db=3.20.0=r44hdfd78af_1 might fail is that there is no such a build number, see here https://anaconda.org/bioconda/bioconductor-go.db/files.

For me the installation of the package with mamba create -n test bioconda::bioconductor-go.db works fine on Linux x86_64. You might either try one of the other existing build versions from the link above, or look into #53045 where a similar issue was reported for another bioconductor package.

Thank you for your response, it seems indeed that this was an issue specific to my own setup. I'm not entirely sure how to unmask the package, but removing it did solve the issue.

@ND91 ND91 closed this as completed Jan 14, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@ND91 @vsuppiyar