bioconda-recipes: bioconductor-genomeinfodbdata postlink failure

It seems like suddenly, the genomeinfodbdata package cannot be installed anymore, because the post-link script fails. The failure reason is not shown by conda, and when I try to run the script manually, it seems to work. Any idea what could be wrong?

conda create -n test-genominfodbdata bioconductor-genomeinfodbdata
Collecting package metadata: done
Solving environment: done

## Package Plan ##

  environment location: /home/johannes/.local/opt/miniconda3/envs/test-genominfodbdata

  added / updated specs:
    - bioconductor-genomeinfodbdata


The following NEW packages will be INSTALLED:

  _r-mutex           pkgs/r/linux-64::_r-mutex-1.0.0-anacondar_1
  binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.28.1-had2808c_3
  binutils_linux-64  pkgs/main/linux-64::binutils_linux-64-7.2.0-had2808c_27
  bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.0-r351_0
  bwidget            pkgs/main/linux-64::bwidget-1.9.11-1
  bzip2              conda-forge/linux-64::bzip2-1.0.6-h14c3975_1002
  ca-certificates    conda-forge/linux-64::ca-certificates-2018.11.29-ha4d7672_0
  cairo              conda-forge/linux-64::cairo-1.14.12-h80bd089_1005
  curl               conda-forge/linux-64::curl-7.64.0-h646f8bb_2
  fontconfig         conda-forge/linux-64::fontconfig-2.13.1-h2176d3f_1000
  freetype           conda-forge/linux-64::freetype-2.9.1-h94bbf69_1005
  gcc_impl_linux-64  pkgs/main/linux-64::gcc_impl_linux-64-7.2.0-habb00fd_3
  gcc_linux-64       pkgs/main/linux-64::gcc_linux-64-7.2.0-h550dcbe_27
  gettext            conda-forge/linux-64::gettext-0.19.8.1-h9745a5d_1001
  gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-7.2.0-hdf63c60_3
  gfortran_linux-64  pkgs/main/linux-64::gfortran_linux-64-7.2.0-h550dcbe_27
  glib               conda-forge/linux-64::glib-2.56.2-had28632_1001
  graphite2          conda-forge/linux-64::graphite2-1.3.13-hf484d3e_1000
  gxx_impl_linux-64  pkgs/main/linux-64::gxx_impl_linux-64-7.2.0-hdf63c60_3
  gxx_linux-64       pkgs/main/linux-64::gxx_linux-64-7.2.0-h550dcbe_27
  harfbuzz           conda-forge/linux-64::harfbuzz-1.9.0-he243708_1001
  icu                conda-forge/linux-64::icu-58.2-hf484d3e_1000
  jpeg               conda-forge/linux-64::jpeg-9c-h14c3975_1001
  krb5               conda-forge/linux-64::krb5-1.16.3-h05b26f9_1001
  libcurl            conda-forge/linux-64::libcurl-7.64.0-h541490c_2
  libedit            conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001
  libffi             conda-forge/linux-64::libffi-3.2.1-hf484d3e_1005
  libgcc-ng          conda-forge/linux-64::libgcc-ng-7.3.0-hdf63c60_0
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.2.0-hdf63c60_3
  libiconv           conda-forge/linux-64::libiconv-1.15-h14c3975_1004
  libpng             conda-forge/linux-64::libpng-1.6.36-h84994c4_1000
  libssh2            conda-forge/linux-64::libssh2-1.8.0-h90d6eec_1004
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-7.3.0-hdf63c60_0
  libtiff            conda-forge/linux-64::libtiff-4.0.10-h648cc4a_1001
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
  libxcb             conda-forge/linux-64::libxcb-1.13-h14c3975_1002
  libxml2            conda-forge/linux-64::libxml2-2.9.8-h143f9aa_1005
  make               conda-forge/linux-64::make-4.2.1-h14c3975_2004
  ncurses            conda-forge/linux-64::ncurses-6.1-hf484d3e_1002
  openssl            conda-forge/linux-64::openssl-1.1.1b-h14c3975_0
  pango              conda-forge/linux-64::pango-1.40.14-hf0c64fd_1003
  pcre               conda-forge/linux-64::pcre-8.41-hf484d3e_1003
  pixman             conda-forge/linux-64::pixman-0.34.0-h14c3975_1003
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
  r-base             conda-forge/linux-64::r-base-3.5.1-he45234b_1005
  readline           conda-forge/linux-64::readline-7.0-hf8c457e_1001
  tk                 conda-forge/linux-64::tk-8.6.9-h84994c4_1000
  tktable            pkgs/main/linux-64::tktable-2.10-h14c3975_0
  wget               pkgs/main/linux-64::wget-1.19.5-h20c2e04_0
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.0.9-h14c3975_1004
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.3-h4937e3b_1000
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.6.7-h14c3975_1000
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.2-h14c3975_1007
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.3-h14c3975_1004
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.10-h14c3975_1002
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002
  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007
  xz                 conda-forge/linux-64::xz-5.2.4-h14c3975_1001
  zlib               conda-forge/linux-64::zlib-1.2.11-h14c3975_1004


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: failed
ERROR conda.core.link:_execute(543): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.0-r351_0'.
LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.0-r351_0
running your command again with `-v` will provide additional information
location of failed script: /home/johannes/.local/opt/miniconda3/envs/test-genominfodbdata/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>

Attempting to roll back.

Rolling back transaction: done

LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.0-r351_0
running your command again with `-v` will provide additional information
location of failed script: /home/johannes/.local/opt/miniconda3/envs/test-genominfodbdata/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>

About this issue

Original URL
State: closed
Created 5 years ago
Comments: 33 (26 by maintainers)

Commits related to this issue

Use curl instead of wget for data packages. This fixes issue bioconda/bioconda-recipes#13846. — committed to bioconda/bioconda-utils by johanneskoester 5 years ago
Use curl instead of wget for data packages. (#430) * Use curl instead of wget for data packages. This fixes issue bioconda/bioconda-recipes#13846. * adapt test cases * omit constraints when ... — committed to bioconda/bioconda-utils by johanneskoester 5 years ago
Increase conda version Xref: https://github.com/bioconda/bioconda-recipes/issues/13846 @bgruening It's not entirely clear to me if this will suffice to fix the PRs broken due to the aforementioned... — committed to bioconda/bioconda-common by dpryan79 5 years ago

Most upvoted comments

I got the post-link error using conda 4.4.10, 4.5.12, and 4.6.7. As a temporary workaround, I was able to install GenomeInfoDbData by pinning wget to its previous version of 1.19.4:

conda --version
## conda 4.6.7
conda create -n test-wget bioconductor-genomeinfodbdata wget=1.19.4

jdblischak on Mar 4, 2019

Actually the wget seems to come from the anaconda channel. We could switch to curl.

johanneskoester on Mar 4, 2019

Hmm, this works for me for some reason. Can those of you still experiencing this please try again after doing the following?

Find and remove all environments with bioconductor-genomeinfodb and bioconductor-genomeinfodbdata
Run conda clean -all
Create a new env with bioconductor-genomeinfodb

dpryan79 on Apr 16, 2019

So the error has nothing to do with a wrong link or something like that, isn’t it?

You are right, this seems to be a conda 4.6 bug.

nsoranzo on Mar 1, 2019