Hi Martin, That's great thanks!
After running the following code in my unit test: ------------------------------------------------------------------------------------------------------------- msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS") xset <- xcms::xcmsSet(msmsPths, nSlaves = 1) xset <- xcms::group(xset) xset <- xcms::retcor(xset) xset <- xcms::group(xset) ------------------------------------------------------------------------------------------------------------- I get an error that is coming from either xcms::xcmsSet or xcms::group, see the bottom of the message for full error. ------------------------------------------------------------------------------------------------------------- Error in signalCondition(e) : no function to return from, jumping to top level Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition ------------------------------------------------------------------------------------------------------------- I was thinking it was do with how I was calling the XCMS functions but perhaps it is more likely to do with the "nSlaves" parameter for xcmsSet that is now deprecated. Either way I am now finding it difficult to repeat the error on my local windows machine. I think the following updated code should now pass (I have also removed the additional retcor and group function calls as they were not required for the testing). ------------------------------------------------------------------------------------------------------------- library(xcms) msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS") xset <- xcmsSet(msmsPths) xset <- group(xset) ------------------------------------------------------------------------------------------------------------- My most recent code should is now on the git mirror [1] and the test script in question is called test.lcms.R [2] Kind regards, Tom [1] https://github.com/Bioconductor-mirror/msPurity/ [2] https://github.com/Bioconductor-mirror/msPurity/blob/master/tests/testthat/test.lcms.R Error message 1: xcms::xcmsSet at testthat/test.lcms.R:7 2: getExportedValue(pkg, name) 3: asNamespace(ns) 4: getNamespace(ns) 5: tryCatch(loadNamespace(name), error = function(e) stop(e)) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: doTryCatch(return(expr), name, parentenv, handler) 9: loadNamespace(name) 10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 11: asNamespace(ns) 12: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 13: methods::cacheMetaData(ns, TRUE, ns) 14: .updateMethodsInTable(fdef, where, attach) 15: .mergeMethodsTable(generic, mtable, tt, attach) 16: .resetTable(table, ns, signames) 17: as(ifelse(seqN > length(newSig), anyLabel, newSig), "signature") 18: asMethod(object) 19: `as<-`(`*tmp*`, "character", value = c("ANY", "ANY")) 20: asMethod(object, Class, value) 21: setDataPart(structure(character(0), .Names = character(0), package = character(0), class = structure("signature", package = "methods")), c("ANY", "ANY")) 22: .dataSlot(names(slots)) 23: match(dataSlot, slotNames, 0) 24: (function (x) x$.self$finalize())(<environment>) Error in signalCondition(e) : no function to return from, jumping to top level Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition 166 229 291 354 416 479 Retention Time Correction Groups: 351 166 229 291 354 416 479 164 227 289 352 414 477 Retention Time Correction Groups: 762 164 227 289 352 414 477 testthat results ================================================================ OK: 63 SKIPPED: 0 FAILED: 1 1. Error: checking lcms based functions (@test.lcms.R#7) Error: testthat unit tests failed Execution halted On Thu, Oct 13, 2016 at 1:57 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 10/13/2016 08:17 AM, Thomas Lawson wrote: > >> Hi all, >> >> Thanks for everybody who worked to get mzR to build and pass on Windows. >> >> The package msPurity, which relies on mzR, was building and passing all >> checks after the mzR updates but then unfortunately started failing on a >> unit test on the Windows server. >> >> The problem seems to be from when I call xcms::group in a unit test. The >> error message goes away on my local Windows machine when I load in the >> XCMS >> library as 'library(xcms)' rather than calling directly 'xcms::group' in >> the test script. >> >> I know we are well past the package deadline for this release, but I was >> just checking if there is perhaps a small chance of getting my package >> into >> the stable release (if it passes the CMD check on Windows by tomorrow)? >> > > yes, your package will be included in the release. > > But your approach sounds like a workaround rather than the right solution > to the problem. What specifically was the error on Windows? > > Martin > > >> Kind regards, >> Tom >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > This email message may contain legally privileged and/or confidential > information. 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