DROP installation issue on linux cluster

[gianfilippo]

Hi,

in trying to reinstall DROP, I foud it to 'interact' with the local R packages.
This resulted in an error at line 35 in installRPackages.R at (dry-)run time. Here the compareVersion function expects two strings to compare, while
installed[Package == pckg_name, Version]
can result in 2 (or more?) strings, crashing the compareVersion function.
I solved this by replacing the original line 35
if (!pckg_name %in% installed$Package || (!is.na(version) && compareVersion(installed[Package == pckg_name, Version]), version) < 0) {

with the one below

if (!pckg_name %in% installed$Package || (!is.na(version) && max(sapply(installed[Package == pckg_name, Version],compareVersion,version)) < 0)) {

I believe this error could be probably resolved by unsetting the R_LIBS_USER var. A better way could be probably to add
conda-ecosystem-user-package-isolation
to the installation.

Best

[gaynora7]

Hi everyone,
I was having the same initial issue as @gianfilippo with the original language in installRpackages.R.
I then tried replacing line 35 of installRPackages.R with the proposed code:
if (!pckg_name %in% installed$Package || (!is.na(version) && max(sapply(installed[Package == pckg_name, Version],compareVersion,version)) < 0)){

Now I am getting the error:

**WARNING: 7 files missing in samples annotation. Ignoring...
/vcu_gpfs2/home/gaynora/DROP/udx_1015/Output/processed_data/aberrant_expression/params/config/AberrantExpression_config.tsv Param Files do not match. Updating to current Sample Annotation

/vcu_gpfs2/home/gaynora/DROP/udx_1015/Output/processed_data/aberrant_splicing/params/config/AberrantSplicing_config.tsv Param Files do not match. Updating to current Sample Annotation

check for missing R packages
OSError in file /vcu_gpfs2/home/gaynora/DROP/udx_1015/Snakefile, line 13:
[Errno 8] Exec format error: PosixPath('/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/site-packages/drop/installRPackages.R')
File "/vcu_gpfs2/home/gaynora/DROP/udx_1015/Snakefile", line 13, in
File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/site-packages/drop/setupDrop.py", line 40, in installRPackages
File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/subprocess.py", line 493, in run
File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/subprocess.py", line 858, in init
File "/vcu_gpfs2/home/gaynora/mambaforge/envs/drop_env_133/lib/python3.8/subprocess.py", line 1720, in _execute_child**

Not quite sure where to go to from here. Any ideas?

Thanks!