############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:xcms.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings xcms_4.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/xcms.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘xcms/DESCRIPTION’ ... OK * this is package ‘xcms’ version ‘4.4.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘xcms’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: R 3.5Mb help 1.0Mb libs 2.4Mb * 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 loading without being on the library search path ... 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 : : 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’ 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’ estimatePrecursorIntensity,MsExperiment: no visible global function definition for ‘spectraSampleIndex’ 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<- 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 spectraSampleIndex 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed XcmsExperiment 9.238 0.510 10.411 findPeaks.massifquant-methods 6.526 0.010 6.542 LamaParama 4.523 0.888 5.574 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/xcms.Rcheck/00check.log’ for details.