Gene Set Enrichment Analysis error with gateway+VIP

[angelasanzo]

Hi there,

so I have started a cellxgene project and as I want to use multiple datasets and also keep the plug in VIP, I have combined both extensions () Jonbioinfo's answer, however, I kept getting errors in regards of the gene set enrichment analysis. I solved those related to ggplot and other libraries, nevertheless, this one keeps going on:

ERROR @server: Traceback (most recent call last):
  File "<string>", line None
SyntaxError: in fgsea.R: Error in gmtPathways(strGMT) : could not find function "gmtPathways"
Execution halted

Thank you so much for your help.

[z5ouyang]

could you make sure you did install "fgsea" package? Since you mentioned that multiple datasets, you might also interested in this: https://pubmed.ncbi.nlm.nih.gov/34971674/ with github: https://github.com/interactivereport/CellDepot

[angelasanzo]

Thank you so much for your reply @z5ouyang ! This is what I do in the command line (in VIP env): conda install -c bioconda bioconductor-fgsea

And this is the outcome I get:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                    

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libstdcxx-ng conflicts for:
bioconductor-fgsea -> libstdcxx-ng[version='>=10.3.0|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9']
bioconductor-fgsea -> r-rcpp -> libstdcxx-ng[version='7.2.0.*|>=7.2.0']

Package ncurses conflicts for:
python=3.8.5 -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='>=6.1,<7.0a0|>=6.3,<7.0a0|>=6.2,<7.0.0a0']
bioconductor-fgsea -> r-base[version='>=3.6,<3.7.0a0'] -> ncurses[version='5.9.*|>=6.1,<7.0a0|>=6.2,<7.0a0|6.0.*|>=6.0,<7.0a0|>=5.9*|>=5.9.*']
python=3.8.5 -> ncurses[version='>=6.2,<7.0a0']

Package libgcc-ng conflicts for:
bioconductor-fgsea -> r-data.table -> libgcc-ng[version='7.2.0.*|>=7.2.0']
bioconductor-fgsea -> libgcc-ng[version='>=10.3.0|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - feature:|@/linux-64::__glibc==2.31=0
  - python=3.8.5 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

However if I do conda list the package is not found.

[interactivereport]

Did you install it under R? Please see step 4 of installation guide,

R -q -e 'if(!require(fgsea)) BiocManager::install("fgsea")'

[angelasanzo]

Yes, I have! all of them

R -q -e 'if(!require(fgsea)) BiocManager::install("fgsea")'
> if(!require(fgsea)) BiocManager::install("fgsea")
Loading required package: fgsea
> 

Still got the outcome at enrichment analysis:

ERROR @server: SyntaxError: in fgsea.R: Error in gmtPathways(strGMT) : could not find function "gmtPathways"
Execution halted

If I check the version of fgsea that I have, I get this outcome:

R -q -e "packageVersion('fgsea')"
> packageVersion('fgsea')
[1] ‘1.20.0’
> 

thanks a lot @interactivereport

[z5ouyang]

@angelasanzo, just want to double check with you, does the fgsea installed in the same conda env as the VIP?

[angelasanzo]

@z5ouyang hi there,

so I have tried several ways to install within the VIP environment (all the comments before), however, if I do "conda list" it does not appear as installed. Although, when i have the conda env activated I can check the version in R:

R -q -e "packageVersion('fgsea')"
> packageVersion('fgsea')
[1] ‘1.20.0’