Version on Bioc has bug, fixed on github

[lgatto]

The version on Bioconductor uses dQuote the create the java path, which wrap the path in uni-code inverted quotes and fails in R. This has been confirmed on Linux and Windows.

The version on github works as expected (confirmed on linux). Could you commit the fix to Bioc, please.

[lgatto]

In msgfPar.R on hedgehog:

if(async) {
            if(length(rawfiles) > 1) warning('Multiple rawfiles. Only the first will be used when running with "async=TRUE"')

            if(basename(savenames[1]) == savenames[1]){
                savenames[1] <- file.path(getwd(), savenames[1])
            }
            fileCall <- createFileCall(rawfiles[1], savenames[1])
            systemCall <- paste0(dQuote(.javaExecutable()), ' -Xmx', memory, 'M -jar ', msgfPath, ' ', fileCall, ' ', parameterCall)
            checkfile <- tempfile('checkfile', fileext='.txt')
            if(Sys.info()["sysname"] == 'Windows') {
                shell(paste0(systemCall, ' && echo "">', checkfile), wait=FALSE, ignore.stdout=TRUE, ignore.stderr=TRUE)
            } else {
                system(paste0(systemCall, ' && echo "">', checkfile), wait=FALSE, ignore.stdout=TRUE, ignore.stderr=TRUE)
            }
            return(new('msgfAsync', checkfile, savenames[1]))
        }

        for(i in 1:length(rawfiles)){
            if(basename(savenames[i]) == savenames[i]){
                savenames[i] <- file.path(getwd(), savenames[i])
            }
            fileCall <- createFileCall(rawfiles[i], savenames[i])
            systemCall <- paste0(dQuote(.javaExecutable()), ' -Xmx', memory, 'M -jar ', msgfPath, ' ', fileCall, ' ', parameterCall)
            cat(systemCall, '\n\n')
            system(systemCall)
        }

but on github, no sight of dQuote.

[lgatto]

And, no sign of any dQuote in all commits. Quote (positive control) works

$ git grep Quote $(git rev-list --all)
776b70ca1d3c5cac859dae27e0c81a64a09f5ed8:aaa.R:    paste0('-s ', shQuote(rawfile), ' -o ', shQuote(savename))
776b70ca1d3c5cac859dae27e0c81a64a09f5ed8:msgfPar.R:        db <- shQuote(object@database)
776b70ca1d3c5cac859dae27e0c81a64a09f5ed8:msgfPar.R:        msgfPath <- shQuote(msgfPath)
776b70ca1d3c5cac859dae27e0c81a64a09f5ed8:msgfParIsotopeError.R:                    range <- shQuote(range)
776b70ca1d3c5cac859dae27e0c81a64a09f5ed8:msgfParModificationList.R:                modFile <- shQuote(modFile)
a8fef82c311e266c1cf6d353b2737e16b53a44ce:aaa.R:    paste0('-s ', shQuote(rawfile), ' -o ', shQuote(savename))
a8fef82c311e266c1cf6d353b2737e16b53a44ce:msgfPar.R:        db <- shQuote(object@database)
a8fef82c311e266c1cf6d353b2737e16b53a44ce:msgfPar.R:        msgfPath <- shQuote(msgfPath)
a8fef82c311e266c1cf6d353b2737e16b53a44ce:msgfParIsotopeError.R:                    range <- shQuote(range)
a8fef82c311e266c1cf6d353b2737e16b53a44ce:msgfParModificationList.R:                modFile <- shQuote(modFile)
afc10624521c8688504eb725a1ae2b271153df28:aaa.R:    paste0('-s ', shQuote(rawfile), ' -o ', shQuote(savename))
afc10624521c8688504eb725a1ae2b271153df28:msgfPar.R:        db <- shQuote(object@database)
afc10624521c8688504eb725a1ae2b271153df28:msgfPar.R:        msgfPath <- shQuote(msgfPath)
afc10624521c8688504eb725a1ae2b271153df28:msgfParIsotopeError.R:                    range <- shQuote(range)
afc10624521c8688504eb725a1ae2b271153df28:msgfParModificationList.R:                modFile <- shQuote(modFile)
9e44a2efd8d8c43b9a097bed552b9ed7501d51ff:aaa.R:    paste0('-s ', shQuote(rawfile), ' -o ', shQuote(savename))
9e44a2efd8d8c43b9a097bed552b9ed7501d51ff:msgfPar.R:        db <- shQuote(object@database)
9e44a2efd8d8c43b9a097bed552b9ed7501d51ff:msgfPar.R:        msgfPath <- shQuote(msgfPath)
9e44a2efd8d8c43b9a097bed552b9ed7501d51ff:msgfParIsotopeError.R:                    range <- shQuote(range)
9e44a2efd8d8c43b9a097bed552b9ed7501d51ff:msgfParModificationList.R:                modFile <- shQuote(modFile)
f33e7ca0090bd793c35ff052cf4b64e53f475b0c:aaa.R:    paste0('-s ', shQuote(rawfile), ' -o ', shQuote(savename))
f33e7ca0090bd793c35ff052cf4b64e53f475b0c:msgfPar.R:        db <- shQuote(object@database)
f33e7ca0090bd793c35ff052cf4b64e53f475b0c:msgfPar.R:        msgfPath <- shQuote(msgfPath)
f33e7ca0090bd793c35ff052cf4b64e53f475b0c:msgfParIsotopeError.R:                    range <- shQuote(range)
f33e7ca0090bd793c35ff052cf4b64e53f475b0c:msgfParModificationList.R:                modFile <- shQuote(modFile)
967381dcbd3e8989bfec4709c7b2ccf82844571e:aaa.R:    paste0('-s ', shQuote(rawfile), ' -o ', shQuote(savename))
967381dcbd3e8989bfec4709c7b2ccf82844571e:msgfPar.R:        db <- shQuote(object@database)
967381dcbd3e8989bfec4709c7b2ccf82844571e:msgfPar.R:        msgfPath <- shQuote(msgfPath)
967381dcbd3e8989bfec4709c7b2ccf82844571e:msgfParIsotopeError.R:                    range <- shQuote(range)
967381dcbd3e8989bfec4709c7b2ccf82844571e:msgfParModificationList.R:                modFile <- shQuote(modFile)
ba2e1ae83d045d91dd21f3e6e506a0ba6713a7a2:aaa.R:    paste0('-s ', shQuote(rawfile), ' -o ', shQuote(savename))
ba2e1ae83d045d91dd21f3e6e506a0ba6713a7a2:msgfPar.R:        db <- shQuote(object@database)
ba2e1ae83d045d91dd21f3e6e506a0ba6713a7a2:msgfPar.R:        msgfPath <- shQuote(msgfPath)
ba2e1ae83d045d91dd21f3e6e506a0ba6713a7a2:msgfParIsotopeError.R:                    range <- shQuote(range)
ba2e1ae83d045d91dd21f3e6e506a0ba6713a7a2:msgfParModificationList.R:                modFile <- shQuote(modFile)
3320a08126194816da6a7a2a7c8efe6fe8602de0:aaa.R:    paste0('-s ', shQuote(rawfile), ' -o ', shQuote(savename))
3320a08126194816da6a7a2a7c8efe6fe8602de0:msgfPar.R:        db <- shQuote(object@database)
3320a08126194816da6a7a2a7c8efe6fe8602de0:msgfPar.R:        msgfPath <- shQuote(msgfPath)
3320a08126194816da6a7a2a7c8efe6fe8602de0:msgfParIsotopeError.R:                    range <- shQuote(range)
3320a08126194816da6a7a2a7c8efe6fe8602de0:msgfParModificationList.R: 

[thomasp85]

Can you confirm the GitHub version works on windows as well? My faint memory of this was that it was used to avoid failing on directories with space...

[lgatto]

Unfortunately, I can't test on windows. The windows tests I referred to above were done with a students computer, but the workshop is over now. But the symptoms and tests on linux and windows were the same.

• running runMSGF in R failed on linux with sh: 1: “/usr/bin/java”: not found and on windows with error 127, and in both cases the system calls included unicodes produced by dQuote.
• Copy/pasting the command printed in the R terminal in the window terminal worked, and, on linux, not calling dQuote produced a valid system call.

[lgatto]

@thomasp85 any news on this?

[thomasp85]

I need to set up a windows test somehow. Don't feel good about just removing dQuote in blindness. Also perplexed why this suddenly is a problem. It has worked fine before...

[thomasp85]

Will try to find room for it tonight

[lgatto]

Thanks. Have you considered a unit test running MSGFplus on a small raw file that (1) checks that a mzid is created and (2) it is equivalent to a pre-existing one? This error would have been caught.