linuxcondamathjax

Conda environment fails to create due to mathjax package


I'm trying to create a Conda enviroment from this YAML:

channels:
- bioconda
- conda-forge
- defaults
dependencies:
- fastqc=0.12.1
- multiqc=1.21

According to Conda, these packages are going to be installed (I only paste the first lines so you can see mathjax is the only one not cached):

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

  + ld_impl_linux-64                2.38  h1181459_1       pkgs/main       Cached
  + ca-certificates            2024.3.11  h06a4308_0       pkgs/main       Cached
  + libstdcxx-ng                  11.2.0  h1234567_1       pkgs/main       Cached
  + _libgcc_mutex                    0.1  main             pkgs/main       Cached
  + mathjax                        2.7.5  h06a4308_0       pkgs/main         18MB
  + blas                             1.0  openblas         pkgs/main       Cached
  + libgfortran5                  11.2.0  h1234567_1       pkgs/main       Cached

Then, this keeps happening:

mathjax                                             18.0MB @  82.2MB/s  0.2s
[+] 3m:18.9s
Downloading      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━  18.0MB /  18.0MB                               0.2s
Extracting  (13) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━      50 /      63 openjdk                   3m:19.2s
error    libmamba Error when extracting package: Can't create 'lib/python3.11/site-packages/plotly/validators/icicle/legendgrouptitle/__pycache__/
_text.cpython-311.pyc'
error    libmamba Error when extracting package: filesystem error: cannot create directories: Disk quota exceeded [/home/salias/miniconda3/pkgs/co
ntourpy-1.2.0-py311hdb19cb5_0]
error    libmamba Error when extracting package: filesystem error: cannot create directories: Disk quota exceeded [/home/salias/miniconda3/pkgs/ri
ch-13.3.5-py311h06a4308_0]
plotly-5.19.0-py311h92b7b1e_0.conda extraction failed                                                                                             
contourpy-1.2.0-py311hdb19cb5_0.conda extraction failed
rich-13.3.5-py311h06a4308_0.conda extraction failed
openjdk-11.0.13-h87a67e3_0.conda extraction failed
[+] 3m:22.4s
Downloading      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━  18.0MB /  18.0MB                               0.2s
Extracting   (5) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━      58 /      63 mathjax                   3m:22.7s
error    libmamba Error when extracting package: Can't create 'site-packages/fontTools/ttLib/tables/S__i_l_l.py'
error    libmamba Error when extracting package: filesystem error: cannot create directories: Disk quota exceeded [/home/salias/miniconda3/pkgs/py
thon-dateutil-2.8.2-pyhd3eb1b0_0]
error    libmamba Error when extracting package: filesystem error: cannot create directories: Disk quota exceeded [/home/salias/miniconda3/pkgs/re
quests-2.31.0-py311h06a4308_1]
error    libmamba Error when extracting package: filesystem error: cannot create directories: Disk quota exceeded [/home/salias/miniconda3/pkgs/ma
tplotlib-base-3.8.0-py311ha02d727_0]
fonttools-4.25.0-pyhd3eb1b0_0.conda extraction failed                                                                                             python-dateutil-2.8.2-pyhd3eb1b0_0.conda extraction failed
requests-2.31.0-py311h06a4308_1.conda extraction failed
matplotlib-base-3.8.0-py311ha02d727_0.conda extraction failed
mathjax-2.7.5-h06a4308_0.conda extraction failed

Anyone has any clue about what is happening here? I find really strange that the error seems to be something related with disk space (although I only want FastQC and MultiQC) but if I try to create a really big Conda environment (like QIIME2) it works fine. Just in case it is useful, I'm creating the environment in the login machine of a Linux cluster.


Solution

  • The line

    error    libmamba Error when extracting package: filesystem error: cannot create directories: Disk quota exceeded [/home/salias/miniconda3/pkgs/co
    ntourpy-1.2.0-py311hdb19cb5_0]
    

    suggests that your disk quota is exceeded. That is, you have used all the disk space you are allowed, and so can't extract any more of the needed packages. It has nothing to do with MathJax specifically, and while MathJax is the last file listed at the bottom of the text you have supplied, there are three other packages above it that are also have failed to be installed.