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.
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.