[Bioc-devel] msPurity check failure on Windows

[Thomas Lawson]

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.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/
>
> [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.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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>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
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