Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:47 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2322/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
xcms 4.6.3 (landing page) Steffen Neumann
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
To the developers/maintainers of the xcms package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/xcms.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: xcms |
Version: 4.6.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:xcms.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings xcms_4.6.3.tar.gz |
StartedAt: 2025-08-02 14:58:57 -0400 (Sat, 02 Aug 2025) |
EndedAt: 2025-08-02 15:23:57 -0400 (Sat, 02 Aug 2025) |
EllapsedTime: 1499.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: xcms.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:xcms.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings xcms_4.6.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/xcms.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘xcms/DESCRIPTION’ ... OK * this is package ‘xcms’ version ‘4.6.3’ * 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... INFO installed size is 5.8Mb sub-directories of 1Mb or more: R 3.6Mb help 1.0Mb * 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’ 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'xcmsRaw-class.Rd': ‘[xcms:image.xcmsRaw]{image}’ ‘[xcms:levelplot.xcmsRaw]{levelplot}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: XCMSnExp-class.Rd: OnDiskMSnExp, Spectrum, MSnExp, bpparam, Chromatogram, quantify, SummarizedExperiment, pSet XCMSnExp-filter-methods.Rd: OnDiskMSnExp XCMSnExp-inherited-methods.Rd: OnDiskMSnExp, bin, clean, filterAcquisitionNum, normalize, pickPeaks, removePeaks XCMSnExp-peak-grouping-results.Rd: SummarizedExperiment XChromatogram.Rd: Chromatogram, transformIntensity chromPeakSpectra.Rd: Spectra, MSpectra, Spectrum-class, Spectrum2-class chromatogram-method.Rd: OnDiskMSnExp, MChromatograms, Chromatogram correlate-Chromatogram.Rd: compareChromatograms dirname.Rd: OnDiskMSnExp-class do_findPeaks_MSW.Rd: peakDetectionCWT, tuneInPeakInfo estimatePrecursorIntensity.Rd: bpparam feature-grouping.Rd: AbundanceSimilarityParam fillPeaks.chrom-methods.Rd: bpparam findChromPeaks-Chromatogram-CentWaveParam.Rd: Chromatogram, MChromatograms findChromPeaks-Chromatogram-MatchedFilter.Rd: Chromatogram, MChromatograms findChromPeaks-centWave.Rd: OnDiskMSnExp, bpparam, register findChromPeaks-centWaveWithPredIsoROIs.Rd: OnDiskMSnExp, bpparam, register findChromPeaks-massifquant.Rd: OnDiskMSnExp, bpparam, register findChromPeaks-matchedFilter.Rd: OnDiskMSnExp, bpparam, register findPeaks-MSW.Rd: OnDiskMSnExp, identifyMajorPeaks, peakDetectionCWT, bpparam, tuneInPeakInfo, register findPeaks.MSW-xcmsRaw-method.Rd: peakDetectionCWT, identifyMajorPeaks, tuneInPeakInfo groupFeatures-abundance-correlation.Rd: AbundanceSimilarityParam groupFeatures-eic-similarity.Rd: compareChromatograms, alignRt, groupSimilarityMatrix, SimilarRtimeParam highlightChromPeaks.Rd: Chromatogram, MChromatograms isolationWindowTargetMz-OnDiskMSnExp-method.Rd: OnDiskMSnExp-class manualChromPeaks.Rd: OnDiskMSnExp plotFeatureGroups.Rd: featureGroups, groupFeatures profMat-xcmsSet.Rd: bpparam removeIntensity-Chromatogram.Rd: filterIntensity useOriginalCode.Rd: SnowParam xcmsSet.Rd: SerialParam, MulticoreParam, SnowParam Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed XcmsExperiment 15.752 0.983 16.759 findPeaks.massifquant-methods 8.353 0.299 8.693 LamaParama 5.567 0.959 5.665 plotPrecursorIons 5.633 0.250 5.848 findChromPeaks-massifquant 5.432 0.190 5.640 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Error in object@backend$getPeakList(scans): dims [product 4504] do not match the length of object [2252] Backtrace: ▆ 1. ├─xcms::reconstructChromPeakSpectra(pest_swth) at test_XcmsExperiment.R:1421:5 2. └─xcms::reconstructChromPeakSpectra(pest_swth) 3. └─xcms (local) .local(object, ...) 4. ├─BiocParallel::bplapply(...) 5. └─BiocParallel::bplapply(...) 6. └─BiocParallel:::.bpinit(...) [ FAIL 1 | WARN 984 | SKIP 14 | PASS 4255 ] Error: Test failures Execution halted * 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 ERROR, 6 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/xcms.Rcheck/00check.log’ for details.
xcms.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL xcms ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘xcms’ ... ** this is package ‘xcms’ version ‘4.6.3’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o In file included from massifquant/Tracker.cpp:8: massifquant/Tracker.h:49:16: warning: private field 'r_val_i' is not used [-Wunused-private-field] double r_val_i; ^ massifquant/Tracker.h:50:16: warning: private field 'p_val_i' is not used [-Wunused-private-field] double p_val_i; ^ massifquant/Tracker.h:53:16: warning: private field 'r_val_m' is not used [-Wunused-private-field] double r_val_m; ^ massifquant/Tracker.h:54:16: warning: private field 'p_val_m' is not used [-Wunused-private-field] double p_val_m; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o In file included from massifquant/DataKeeper.cpp:4: massifquant/DataKeeper.h:36:26: warning: private field 'scbuf' is not used [-Wunused-private-field] struct scanBuf * scbuf; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o obiwarp/mat.cpp:137:9: warning: variable 'linelength' set but not used [-Wunused-but-set-variable] int linelength = 0; ^ obiwarp/mat.cpp:545:9: warning: variable 'linelength' set but not used [-Wunused-but-set-variable] int linelength = 0; ^ obiwarp/mat.cpp:953:9: warning: variable 'linelength' set but not used [-Wunused-but-set-variable] int linelength = 0; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable] float bestscore; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastMatch.c -o fastMatch.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mzROI.c -o mzROI.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.c -o util.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c xcms.c -o xcms.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c binners.c -o binners.o binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable] int idx = 0; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-xcms/00new/xcms/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘group’ in package ‘xcms’ Creating a new generic function for ‘sigma’ in package ‘xcms’ ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (xcms)
xcms.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(xcms) Loading required package: BiocParallel This is xcms version 4.6.3 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma > library(faahKO) > library(MSnbase) Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.34.1 Visit https://lgatto.github.io/MSnbase/ to get started. Consider switching to the 'R for Mass Spectrometry' packages - see https://RforMassSpectrometry.org for details. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws > library(msdata) > library(BiocParallel) > prm <- SerialParam() > > register(SerialParam()) > > ## Create some objects we can re-use in different tests: > faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"), + system.file('cdf/KO/ko16.CDF', package = "faahKO"), + system.file('cdf/KO/ko18.CDF', package = "faahKO")) > > cwp <- CentWaveParam(noise = 10000, snthresh = 40, prefilter = c(3, 10000)) > faahko_od <- readMSData(faahko_3_files, mode = "onDisk") Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method. > faahko_xod <- findChromPeaks(faahko_od, param = cwp, BPPARAM = SerialParam()) Detecting mass traces at 25 ppm ... OK Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found. Detecting mass traces at 25 ppm ... OK Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found. Detecting mass traces at 25 ppm ... OK Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found. > od_x <- faahko_od > mzr <- matrix(c(335, 335, 344, 344), ncol = 2, byrow = TRUE) > od_chrs <- chromatogram(od_x, mz = mzr) > xod_x <- faahko_xod > pdp <- PeakDensityParam(sampleGroups = rep(1, 3)) > xod_xg <- groupChromPeaks(xod_x, param = pdp) > xod_xgr <- adjustRtime(xod_xg, param = PeakGroupsParam(span = 0.4)) Performing retention time correction using 19 peak groups. Applying retention time adjustment to the identified chromatographic peaks ... OK > xod_xgrg <- groupChromPeaks(xod_xgr, param = pdp) > xod_r <- adjustRtime(as(od_x, "XCMSnExp"), param = ObiwarpParam()) Sample number 2 used as center sample. Aligning ko15.CDF against ko16.CDF ... OK Aligning ko18.CDF against ko16.CDF ... OK > > xod_chr <- findChromPeaks(filterMz(filterRt(od_x, rt = c(2500, 3500)), + mz = c(334.9, 344.1)), + param = CentWaveParam()) Detecting mass traces at 25 ppm ... OK Detecting chromatographic peaks in 514 regions of interest ... OK: 23 found. Detecting mass traces at 25 ppm ... OK Detecting chromatographic peaks in 551 regions of interest ... OK: 29 found. Detecting mass traces at 25 ppm ... OK Detecting chromatographic peaks in 515 regions of interest ... OK: 20 found. Warning message: In .local(object, param, ...) : Your data appears to be not centroided! CentWave works best on data in centroid mode. > > microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"), + system.file("microtofq/MM8.mzML", package = "msdata")) > microtofq_od <- readMSData(microtofq_fs, mode = "onDisk") > > ## Direct injection data: > fticrf <- list.files(system.file("fticr-mzML", package = "msdata"), + recursive = TRUE, full.names = TRUE) > fticr <- readMSData(fticrf[1:2], msLevel. = 1, mode = "onDisk") > fticr_xod <- findChromPeaks(fticr, MSWParam(scales = c(1, 7), + peakThr = 80000, ampTh = 0.005, + SNR.method = "data.mean", + winSize.noise = 500)) > > ## Pesticide data > fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML", package = "msdata") > pest_swth <- readMSData(fl, mode = "onDisk") > cwp2 <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10, + peakwidth = c(3, 20), prefilter = c(3, 1000)) > pest_swth <- findChromPeaks(pest_swth, param = cwp2) Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 11 regions of interest ... OK: 11 found. > pest_swth <- findChromPeaksIsolationWindow(pest_swth, param = cwp2) Detecting mass traces at 10 ppm ... OK Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 2 regions of interest ... OK: 2 found. Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 7 regions of interest ... OK: 7 found. Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 3 regions of interest ... OK: 3 found. Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 17 regions of interest ... OK: 17 found. Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 3 regions of interest ... OK: 2 found. Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 10 regions of interest ... OK: 10 found. Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 3 regions of interest ... OK: 3 found. Warning messages: 1: In .centWave_orig(mz = mz, int = int, scantime = scantime, valsPerSpect = valsPerSpect, : No ROIs found! 2: In .processResultList(resList, getProcHist = return.type == "xcmsSet", : No peaks found in sample number 1. > > fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata") > pest_dda <- readMSData(fl, mode = "onDisk") > pest_dda <- findChromPeaks(pest_dda, param = cwp2) Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 29 regions of interest ... OK: 27 found. > > ## Sciex test data. > ## fl <- dir(system.file("sciex", package = "msdata"), full.names = TRUE) > ## sciex_data <- readMSData(fl, mode = "onDisk") > ## sciex_data <- pickPeaks(sciex_data) > > library(MsExperiment) > fls <- normalizePath(faahko_3_files) > df <- data.frame(mzML_file = basename(fls), + dataOrigin = fls, + sample = c("ko15", "ko16", "ko18")) > mse <- readMsExperiment(spectraFiles = fls, sampleData = df) > xmse <- findChromPeaks(mse, param = cwp) > expect_true(length(processHistory(xmse)) == 1L) > pdp <- PeakDensityParam(sampleGroups = rep(1, 3)) > xmseg <- groupChromPeaks(xmse, param = pdp, add = FALSE) > expect_true(length(processHistory(xmseg)) == 2L) > > ## Data for LamaParama checks > ref <- loadXcmsData("xmse") > f <- sampleData(ref)$sample_type > f[f == "QC"] <- NA > ref <- filterFeatures(ref, PercentMissingFilter(threshold = 0, f = f)) 5 features were removed > ref_mz_rt <- featureDefinitions(ref)[, c("mzmed","rtmed")] > tst <- loadXcmsData("faahko_sub2") > > test_check("xcms") Object of class: CleanPeaksParam Parameters: - maxPeakwidth: [1] 13.2 Object of class: MergeNeighboringPeaksParam Parameters: - expandRt: [1] 5 - expandMz: [1] 0.1 - ppm: [1] 20 - minProp: [1] 0.9 8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00 8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00 Sizes of mz and intensity arrays don't match. 8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00 8.00 16.00 28.00 32.00 40.00 64.00 80.00 96.00 100.00 8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00 8.00 16.00 28.00 32.00 40.00 56.00 64.00 80.00 88.00 96.00 100.00 8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00 Object of class: XChromatogram length of object: 0 from file: mz range: [NA, NA] MS level: 1 Identified chromatographic peaks (0): rt rtmin rtmax into maxo sn [ FAIL 1 | WARN 984 | SKIP 14 | PASS 4255 ] ══ Skipped tests (14) ══════════════════════════════════════════════════════════ • empty test (14): 'test_XcmsExperiment-plotting.R:14:1', 'test_XcmsExperiment-plotting.R:45:1', 'test_XcmsExperiment-plotting.R:69:1', 'test_functions-XCMSnExp.R:80:1', 'test_functions-XCMSnExp.R:91:1', 'test_functions-XCMSnExp.R:466:1', 'test_functions-XChromatogram.R:60:1', 'test_functions-utils.R:49:1', 'test_matchpeaks.R:1:1', 'test_methods-MChromatograms.R:181:1', 'test_methods-XCMSnExp.R:2278:1', 'test_methods-XChromatogram.R:1:1', 'test_methods-XChromatogram.R:60:1', 'test_methods-XChromatograms.R:140:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_XcmsExperiment.R:1421:5'): findChromPeaksIsolationWindow, etc, MsExperiment works ── <bplist_error/bperror/error/condition> Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error in object@backend$getPeakList(scans): dims [product 4504] do not match the length of object [2252] Backtrace: ▆ 1. ├─xcms::reconstructChromPeakSpectra(pest_swth) at test_XcmsExperiment.R:1421:5 2. └─xcms::reconstructChromPeakSpectra(pest_swth) 3. └─xcms (local) .local(object, ...) 4. ├─BiocParallel::bplapply(...) 5. └─BiocParallel::bplapply(...) 6. └─BiocParallel:::.bpinit(...) [ FAIL 1 | WARN 984 | SKIP 14 | PASS 4255 ] Error: Test failures Execution halted
xcms.Rcheck/xcms-Ex.timings
name | user | system | elapsed | |
AutoLockMass-methods | 0.000 | 0.001 | 0.000 | |
GenericParam | 0.001 | 0.000 | 0.002 | |
LamaParama | 5.567 | 0.959 | 5.665 | |
XCMSnExp-class | 1.412 | 0.319 | 1.818 | |
XCMSnExp-filter-methods | 0.610 | 0.041 | 0.654 | |
XChromatogram | 1.844 | 0.108 | 1.956 | |
XcmsExperiment | 15.752 | 0.983 | 16.759 | |
applyAdjustedRtime | 2.352 | 0.174 | 2.535 | |
binYonX | 0.001 | 0.002 | 0.004 | |
breaks_on_binSize | 0.001 | 0.002 | 0.003 | |
breaks_on_nBins | 0.000 | 0.000 | 0.001 | |
chromPeakChromatograms | 2.750 | 0.161 | 2.927 | |
chromPeakSpectra | 2.796 | 0.120 | 2.907 | |
chromatogram-method | 1.850 | 0.087 | 1.941 | |
correlate-Chromatogram | 0.198 | 0.013 | 0.212 | |
descendZero | 0.001 | 0.000 | 0.001 | |
do_findChromPeaks_centWave | 0.964 | 0.040 | 1.014 | |
do_findChromPeaks_massifquant | 1.476 | 0.120 | 1.600 | |
do_findChromPeaks_matchedFilter | 2.388 | 0.083 | 2.477 | |
do_groupChromPeaks_density | 0.278 | 0.015 | 0.293 | |
extractMsData-method | 0.590 | 0.062 | 0.653 | |
featureChromatograms | 1.917 | 0.093 | 2.012 | |
fillChromPeaks | 1.153 | 0.049 | 1.205 | |
filter-MChromatograms | 0.383 | 0.011 | 0.393 | |
filterFeatures | 0.265 | 0.011 | 0.276 | |
findChromPeaks-Chromatogram-CentWaveParam | 1.670 | 0.082 | 1.754 | |
findChromPeaks-Chromatogram-MatchedFilter | 0.436 | 0.020 | 0.457 | |
findChromPeaks-centWave | 1.044 | 0.038 | 1.085 | |
findChromPeaks-centWaveWithPredIsoROIs | 0.011 | 0.001 | 0.012 | |
findChromPeaks-massifquant | 5.432 | 0.190 | 5.640 | |
findChromPeaks-matchedFilter | 3.153 | 0.036 | 3.192 | |
findMZ | 0.000 | 0.001 | 0.000 | |
findPeaks-MSW | 2.129 | 0.080 | 2.230 | |
findPeaks.massifquant-methods | 8.353 | 0.299 | 8.693 | |
findneutral | 0.000 | 0.000 | 0.001 | |
group.mzClust | 0.000 | 0.000 | 0.001 | |
group.nearest | 0.000 | 0.000 | 0.001 | |
groupFeatures-abundance-correlation | 0.380 | 0.014 | 0.394 | |
groupFeatures-eic-similarity | 2.793 | 0.178 | 2.977 | |
groupFeatures-similar-rtime | 0.329 | 0.011 | 0.340 | |
groupOverlaps | 0.001 | 0.001 | 0.001 | |
highlightChromPeaks | 1.354 | 0.091 | 1.454 | |
imputeLinInterpol | 0.006 | 0.003 | 0.012 | |
imputeRowMin | 1.435 | 0.115 | 1.554 | |
imputeRowMinRand | 1.357 | 0.053 | 1.411 | |
loadXcmsData | 0.083 | 0.005 | 0.089 | |
manualChromPeaks | 0.446 | 0.033 | 0.485 | |
medianFilter | 0.000 | 0.000 | 0.001 | |
msn2xcmsRaw | 1.684 | 0.057 | 1.742 | |
overlappingFeatures | 0.467 | 0.024 | 0.490 | |
peakTable-methods | 0 | 0 | 0 | |
peaksWithCentWave | 0.331 | 0.028 | 0.360 | |
peaksWithMatchedFilter | 0.500 | 0.035 | 0.535 | |
phenoDataFromPaths | 0.001 | 0.001 | 0.003 | |
plotAdjustedRtime | 0.342 | 0.008 | 0.356 | |
plotChromPeakDensity | 0.197 | 0.013 | 0.212 | |
plotChromPeaks | 0.354 | 0.015 | 0.371 | |
plotChromatogramsOverlay | 3.184 | 0.110 | 3.326 | |
plotPrecursorIons | 5.633 | 0.250 | 5.848 | |
plotQC | 1.752 | 0.047 | 1.804 | |
profGenerate | 0.000 | 0.001 | 0.001 | |
profMat-xcmsSet | 1.728 | 0.145 | 1.875 | |
profStep-methods | 0.000 | 0.000 | 0.001 | |
rectUnique | 0.002 | 0.002 | 0.003 | |
refineChromPeaks | 1.455 | 0.076 | 1.538 | |
removeIntensity-Chromatogram | 0.184 | 0.013 | 0.198 | |
rla | 0.000 | 0.000 | 0.001 | |
stitch-methods | 0.000 | 0.000 | 0.001 | |
sub-xcmsRaw-logicalOrNumeric-missing-missing-method | 1.380 | 0.056 | 1.437 | |
writeMzTab | 1.184 | 0.024 | 1.215 | |
xcmsRaw | 0.001 | 0.001 | 0.001 | |