############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:xcms.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings xcms_3.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/xcms.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'xcms/DESCRIPTION' ... OK * this is package 'xcms' version '3.14.1' * 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 ... OK * checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: R 3.0Mb help 2.3Mb html 1.4Mb libs 2.2Mb * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'MALDIquant:::.localMaxima' 'MSnbase:::.MSnExpReqFvarLabels' 'MSnbase:::.plotXIC' 'MSnbase:::.vertical_sub_layout' 'MSnbase:::formatFileSpectrumNames' 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' '.getChromPeakData' '.get_closest_index' '.spectra_for_peaks' '.split_by_file2' '.validChromPeaksMatrix' '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 .spectra_for_peaks: no visible global function definition for 'featureData' .spectra_for_peaks: no visible global function definition for 'featureData<-' .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 : : 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 : : no visible global function definition for 'newXMLNode' buildDataProcessingList: no visible global function definition for 'newXMLNode' buildFeatureList : : no visible global function definition for 'newXMLNode' buildInputFiles : : no visible global function definition for 'newXMLNode' buildInputFiles: no visible global function definition for 'newXMLNode' buildMzq: no visible global function definition for 'xmlTree' buildSmallMoleculeList : : no visible global function definition for 'newXMLNode' buildSmallMoleculeList: no visible global function definition for 'newXMLNode' buildSoftwareList: no visible global function definition for 'newXMLNode' buildStudyVariableList : : no visible global function definition for 'newXMLNode' buildStudyVariableList : : : no visible global function definition for 'newXMLNode' buildStudyVariableList: no visible global function definition for 'newXMLNode' chromPeakSpectra: no visible global function definition for 'List' featureSpectra: no visible global function definition for 'List' 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' [,XChromatograms-ANY-ANY-ANY: no visible global function definition for 'pData<-' plotSurf,xcmsRaw: no visible global function definition for 'rgl.clear' plotSurf,xcmsRaw: no visible global function definition for 'rgl.surface' plotSurf,xcmsRaw: no visible global function definition for 'rgl.points' plotSurf,xcmsRaw: no visible global function definition for 'rgl.bbox' plotTree,xcmsFragments: no visible global function definition for 'edgemode<-' plotTree,xcmsFragments: no visible global function definition for 'addEdge' refineChromPeaks,XCMSnExp-FilterIntensityParam: no visible binding for global variable 'value' 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: List addChildren addEdge base64encode checkCluster checkForRemoteErrors edgemode<- featureData featureData<- 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 pData<- recvOneResult rgl.bbox rgl.clear rgl.points rgl.surface sampleNames saveXML sendCall value 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 i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/xcms/libs/i386/xcms.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/xcms/libs/x64/xcms.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) 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. 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findPeaks.massifquant-methods 7.67 0.15 7.82 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findPeaks.massifquant-methods 6.50 0.06 6.56 findChromPeaks-Chromatogram-CentWaveParam 5.05 0.11 5.15 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/xcms.Rcheck/00check.log' for details.