demo failig

[gianfilippo]

Hi,

I installed the package as described, without any issue.

I then issue the commands to run the demo
conda activate drop_env
mkdir ~/drop_demo
cd ~/drop_demo
drop demo
snakemake --cores 1 -n

The last command results in the following error
WARNING: Less than 30 IDs in DROP_GROUP outrider
WARNING: Less than 30 IDs in DROP_GROUP outrider_external
WARNING: Less than 30 IDs in DROP_GROUP fraser
WARNING: Less than 30 IDs in DROP_GROUP fraser_external
check for missing R packages
Error in if (is.na(a)) return(-1L) : the condition has length > 1
Calls: compareVersion
Execution halted
CalledProcessError in file /demo_dir/Snakefile, line 13:
Command '['Rscript', PosixPath('$HOME/.conda/envs/drop_env/lib/python3.12/site-packages/drop/installRPackages.R'), PosixPath('$HOME/.conda/envs/drop_env/lib/python3.12/site-packages/drop/requirementsR.txt')]' returned non-zero exit status 1.
File "/demo_dir/Snakefile", line 13, in
File "$HOME/.conda/envs/drop_env/lib/python3.12/site-packages/drop/setupDrop.py", line 35, in installRPackages
File "$HOME/.conda/envs/drop_env/lib/python3.12/subprocess.py", line 502, in check_returncode

Can you please help ?

Thanks

[gianfilippo]

Hi,
I resolved then issue.
In your installRPackages.R, the line
if (!pckg_name %in% installed$Package || (!is.na(version) && compareVersion(installed[Package == pckg_name, Version], version) < 0))

expects to find at most one entry in the "installed" matrix for a specific package.
The "installed.packages" command in the script reports also packages installed outside the conda env, which can result in more than one entry in the "installed" matrix for a specific package.

Best