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mamba install freezes #38

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arisp99 opened this issue Apr 29, 2022 · 1 comment
Closed

mamba install freezes #38

arisp99 opened this issue Apr 29, 2022 · 1 comment
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bug unexpected problem or unintended behavior
Milestone
1.0.0

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@arisp99
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arisp99 commented Apr 29, 2022

Bug Description

When trying to build the container, mamba freezes when trying to install packages.

Reprex

gh repo clone bailey-lab/miptools
sudo singularity build --force miptools_dev.sif MIPTools.def

Additional Information

  • Printing the info during mamba installation, mamba seems to fail when installing openssl. It prints the following info message: info libmamba Parsing MatchSpec openssl and never moves on from this.
  • I have attempted to build the development version and the latest stable release (v0.4.0) and both never move past this line.
  • I have also attempted to change mamba versions to no avail.

cc @aydemiro. Do you have any experience with this problem?
@arisp99 arisp99 added the bug unexpected problem or unintended behavior label Apr 29, 2022
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arisp99 commented Apr 30, 2022

After more investigation, this issue appears to be caused by the installation of libgfortran. We currently try to manually install libgfortran4 but one of the other packages we install requires libgfortran5. mamba is unable to resolve these conflicts and gets stuck at the installation stage. To solve this, we can remove the manual installation of libgfortran4.

@arisp99 arisp99 added this to the 1.0.0 milestone Apr 30, 2022
arisp99 added a commit that referenced this issue Apr 30, 2022
@arisp99
Don't install libgfortran4
dd7b60c 
This was causing building errors (#38)
arisp99 added a commit that referenced this issue May 2, 2022
@arisp99
Specify version number for installed software (#32)
c4001d2 
* Specify version number for R packages, git software, and the basespace CLI

* Install mamba packages using an environment file

After installation, we save an `environment_versioned.yml` file that contains all the installed versions of our software

* Don't install `libgfortran4`

This was causing building errors (#38)

* Clean installation docs, adding instructions on reproducible builds, and update changelog
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