[Bioc-devel] msPurity check failure on Windows

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

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