methylation.sif container not working on BU cluster

[Alexandre Pelletier]

Hello,
When I used the methylation_calling sesame pipeline using the methylation.sif container, the run fail, while when I used my own environment, the pipeline run.
Here is the command used:
sos run /projectnb/tcwlab-adsp/member/adpelle1/projects/fungen-xqtl/xqtl-pipeline/pipeline/methylation_calling.ipynb sesame --cwd outputs/01-methylation_preprocessing_sesame_pipeline --sample-sheet /restricted/projectnb/tcwlab-adsp/ROSMAP/methylation/ROSMAP_assay_methylationArray_metadata.csv --idat-folder /restricted/projectnb/tcwlab-adsp/ROSMAP/methylation/IDAT\\ Files/ --sample-sheet-header-rows 0 --mem 64G --numThreads 20 --container xqtl-pipeline/container/singularity//methylation.sif -c csg.yml -q scc -s build
and the error message:

 Error: package or namespace load failed for ‘AnnotationHub’ in dyn.load(file, DLLpath = DLLpath, ...):
  unable to load shared object '/usr2/postdoc/adpelle1/R/x86_64-pc-linux-gnu-library/4.2/png/libs/png.so':
  libpng15.so.15: cannot open shared object file: No such file or directory
Error: package ‘AnnotationHub’ could not be loaded

Based on this, it could be that AnnotationHub seek libpng15.so.15 at a wrong place

[hsun3163]

This is due to a existed .Rprofile file in the home dir overwriting the .libPath() file in our R script. Potentially this can be hacked by creating a temp empty .Rprofile file in the directory sos were run via the new entrypoint feature according to https://community.rstudio.com/t/why-does-r-ignore-rprofile/23897