Hi Martin/all It looks like the build/check [1] is still using an older version of the code (v0.99.9) so it is still failing the check in Windows. i.e. it has not updated to version (v0.99.12) [2] of the code.
Is this going to be a problem for the package to be accepted into the next stable release? Please let me know if there is anything I can do. Kind regards, Tom [1] http://bioconductor.org/checkResults/devel/bioc-LATEST/msPurity/ [2] https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msPurity/ On Thu, Oct 13, 2016 at 4:16 PM, Thomas Lawson < thomas.nigel.law...@gmail.com> wrote: > 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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