[Bioc-devel] msPurity check failure on Windows
Martin Morgan
martin.morgan at roswellpark.org
Fri Oct 14 17:05:29 CEST 2016
On 10/14/2016 09:07 AM, Thomas Lawson wrote:
> 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?
no worries on your end. Note the date at the top of the page, and the
svn 'Snapshot Date' -- for reasons that I do not know, the build report
for Wednesday night's build did not post, and you are looking at
Tuesday's build. Wait until the build report is updated to be after your
commits.
Martin
>
> 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.lawson at gmail.com <mailto:thomas.nigel.lawson at 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/
> <https://github.com/Bioconductor-mirror/msPurity/>
>
> [2]
> https://github.com/Bioconductor-mirror/msPurity/blob/master/tests/testthat/test.lcms.R
> <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.morgan at roswellpark.org
> <mailto:martin.morgan at 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]]
>
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