[Bioc-devel] msPurity check failure on Windows

[Thomas Lawson]

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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>>
>>
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