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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:xcms.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings xcms_4.3.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/xcms.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '4.3.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'xcms' can be installed ... WARNING
Found the following significant warnings:
  fastMatch.c:32:69: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:79:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:102:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:331:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:629:74: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:633:74: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
See 'F:/biocbuild/bbs-3.20-bioc/meat/xcms.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    help   1.0Mb
    libs   1.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'MALDIquant:::.localMaxima' 'MSnbase:::.MSnExpReqFvarLabels'
  'MSnbase:::.plotXIC' 'MSnbase:::.vertical_sub_layout'
  'MSnbase:::formatFileSpectrumNames' 'Spectra:::.concatenate_spectra'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.copy_env' 'MSW.cwt' 'MSW.getLocalMaximumCWT' 'MSW.getRidge'
  'descendMin' 'descendMinTol' 'estimateChromNoise'
  'getLocalNoiseEstimate' 'na.flatfill' 'patternVsRowScore'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.xcmsFragments.plotTree: no visible global function definition for
  'edgemode<-'
.xcmsFragments.plotTree: no visible global function definition for
  'addEdge'
buildAnalysisSummary: no visible global function definition for
  'newXMLNode'
buildAssayList : <anonymous>: no visible global function definition for
  'newXMLNode'
buildAssayList: no visible global function definition for 'newXMLNode'
buildAuditCollection: no visible global function definition for
  'newXMLNode'
buildCVlist: no visible global function definition for 'newXMLNode'
buildCVlist: no visible global function definition for 'addChildren'
buildCvParams : <anonymous>: no visible global function definition for
  'newXMLNode'
buildDataProcessingList: no visible global function definition for
  'newXMLNode'
buildFeatureList : <anonymous>: no visible global function definition
  for 'newXMLNode'
buildInputFiles : <anonymous>: no visible global function definition
  for 'newXMLNode'
buildInputFiles: no visible global function definition for 'newXMLNode'
buildMzq: no visible global function definition for 'xmlTree'
buildSmallMoleculeList : <anonymous>: no visible global function
  definition for 'newXMLNode'
buildSmallMoleculeList: no visible global function definition for
  'newXMLNode'
buildSoftwareList: no visible global function definition for
  'newXMLNode'
buildStudyVariableList : <anonymous>: no visible global function
  definition for 'newXMLNode'
buildStudyVariableList : <anonymous> : <anonymous>: no visible global
  function definition for 'newXMLNode'
buildStudyVariableList: no visible global function definition for
  'newXMLNode'
plotPrecursorIons: no visible global function definition for
  'filterEmptySpectra'
plotQC: no visible global function definition for 'sampleNames'
running: multiple local function definitions for 'funct' with different
  formal arguments
verify.mzQuantML: no visible global function definition for
  'xmlTreeParse'
verify.mzQuantML: no visible global function definition for
  'xmlInternalTreeParse'
verify.mzQuantML: no visible global function definition for
  'xmlSchemaValidate'
xcmsClusterApply: no visible global function definition for
  'checkCluster'
xcmsClusterApply : submit: no visible global function definition for
  'sendCall'
xcmsClusterApply: no visible global function definition for
  'recvOneResult'
xcmsClusterApply: no visible global function definition for
  'checkForRemoteErrors'
xcmsPapply: no visible global function definition for 'mpi.comm.size'
xcmsPapply: no visible global function definition for
  'mpi.spawn.Rslaves'
xcmsPapply: no visible global function definition for 'mpi.comm.rank'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.send.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.recv.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.any.source'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.any.tag'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for
  'mpi.bcast.Robj2slave'
xcmsPapply: no visible global function definition for 'mpi.bcast.cmd'
xcmsPapply: no visible global function definition for 'mpi.recv.Robj'
xcmsPapply: no visible global function definition for 'mpi.any.source'
xcmsPapply: no visible global function definition for 'mpi.any.tag'
xcmsPapply: no visible global function definition for
  'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for 'mpi.send.Robj'
xcmsParallelSetup: no visible global function definition for
  'mpi.spawn.Rslaves'
xcmsParallelSetup: no visible global function definition for
  'mpi.comm.size'
xcmsParallelSetup: no visible global function definition for
  'mpi.comm.rank'
xcmsParallelSetup: no visible global function definition for
  'makeCluster'
xcmsSet: no visible global function definition for 'bpstopOnError'
xcmsSet: no visible global function definition for 'bptry'
xcmsSet: no visible global function definition for 'bpok'
plotSurf,xcmsRaw: no visible global function definition for 'clear3d'
plotSurf,xcmsRaw: no visible global function definition for 'surface3d'
plotSurf,xcmsRaw: no visible global function definition for 'points3d'
plotSurf,xcmsRaw: no visible global function definition for 'bbox3d'
plotTree,xcmsFragments: no visible global function definition for
  'edgemode<-'
plotTree,xcmsFragments: no visible global function definition for
  'addEdge'
write.cdf,xcmsRaw: no visible global function definition for
  'ncdim_def'
write.cdf,xcmsRaw: no visible global function definition for
  'ncvar_def'
write.cdf,xcmsRaw: no visible global function definition for
  'nc_create'
write.cdf,xcmsRaw: no visible global function definition for
  'ncvar_put'
write.cdf,xcmsRaw: no visible global function definition for
  'ncatt_put'
write.cdf,xcmsRaw: no visible global function definition for 'nc_close'
write.mzQuantML,xcmsSet: no visible global function definition for
  'saveXML'
write.mzdata,xcmsRaw: no visible global function definition for
  'base64encode'
Undefined global functions or variables:
  addChildren addEdge base64encode bbox3d bpok bpstopOnError bptry
  checkCluster checkForRemoteErrors clear3d edgemode<-
  filterEmptySpectra makeCluster mpi.any.source mpi.any.tag
  mpi.bcast.Robj2slave mpi.bcast.cmd mpi.comm.rank mpi.comm.size
  mpi.get.sourcetag mpi.recv.Robj mpi.send.Robj mpi.spawn.Rslaves
  nc_close nc_create ncatt_put ncdim_def ncvar_def ncvar_put newXMLNode
  points3d recvOneResult sampleNames saveXML sendCall surface3d
  xmlInternalTreeParse xmlSchemaValidate xmlTree xmlTreeParse
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/xcms/libs/x64/xcms.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
XcmsExperiment                11.25   0.90   13.00
findPeaks.massifquant-methods  7.48   0.22    7.70
findChromPeaks-massifquant     4.38   1.86    6.29
LamaParama                     4.78   0.48  180.72
chromPeakChromatograms         3.12   1.80    5.01
PlainTextParam                 1.17   0.25   28.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/xcms.Rcheck/00check.log'
for details.