Hi all, I'm trying to upgrade a package that uses R and python together with temp files generated by the system. I encounter an error when building via the command line, but can build the package with no errors using RStudio.
*Do I need to worry about any command line errors if the package can be built correctly using RStudio?* More detail about my error: I'm currently updating the package 'seq2pathway'. Saving the 'seq2pathway' directory as an R package and building it in RStudio gives me a couple warnings but no errors. However, building it in console gives this error: > R CMD build seq2pathway * checking for file ‘seq2pathway/DESCRIPTION’ ... OK * preparing ‘seq2pathway’: * checking DESCRIPTION meta-information ... OK * checking whether ‘INDEX’ is up-to-date ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘seq2pathwaypackage.Rnw’ using Sweave Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’ Warning in system2(mypython, args = script_path, stdout = TRUE, stderr = TRUE) : running command ''/Library/Frameworks/Python.framework/Versions/3.8/bin/python3' /var/folders/9r/bgcsznps6sz6kcn851gqf47m0000gp/T//Rtmp4ADNbj/inputfile_20210323_13_33_30_seq2gene_log.py 2>&1' had status 1 Error: processing vignette 'seq2pathwaypackage.Rnw' failed with diagnostics: chunk 7 (label = runseq2gene) Error in read.table(file = tmpoutfile_UTR3, header = TRUE, sep = "\t") : no lines available in input --- failed re-building ‘seq2pathwaypackage.Rnw’ SUMMARY: processing the following file failed: ‘seq2pathwaypackage.Rnw’ Error: Vignette re-building failed. Execution halted I've encountered and debugged this error before, and it usually means that python encountered an error when trying to read the input file from the temp folder, and exits before writing anything to the output temp file. However, I have tested the same R function with the same command outside of building the package, and am sure that it can be run without error if I directly source the .R file containing the function. Any help on this would be greatly appreciated, but once again I'm not sure it's even necessary if I can just build the package in RStudio and submit it to Bioconductor. Thank you, AJ Kinstlick [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel