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).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 2322/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 4.6.3  (landing page)
Steffen Neumann
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/xcms
git_branch: RELEASE_3_21
git_last_commit: 4b1f7c6
git_last_commit_date: 2025-06-20 09:07:15 -0400 (Fri, 20 Jun 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for xcms on kjohnson1

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

xcms.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
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Platform: aarch64-apple-darwin20

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'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

Example timings

xcms.Rcheck/xcms-Ex.timings

nameusersystemelapsed
AutoLockMass-methods0.0000.0010.000
GenericParam0.0010.0000.002
LamaParama5.5670.9595.665
XCMSnExp-class1.4120.3191.818
XCMSnExp-filter-methods0.6100.0410.654
XChromatogram1.8440.1081.956
XcmsExperiment15.752 0.98316.759
applyAdjustedRtime2.3520.1742.535
binYonX0.0010.0020.004
breaks_on_binSize0.0010.0020.003
breaks_on_nBins0.0000.0000.001
chromPeakChromatograms2.7500.1612.927
chromPeakSpectra2.7960.1202.907
chromatogram-method1.8500.0871.941
correlate-Chromatogram0.1980.0130.212
descendZero0.0010.0000.001
do_findChromPeaks_centWave0.9640.0401.014
do_findChromPeaks_massifquant1.4760.1201.600
do_findChromPeaks_matchedFilter2.3880.0832.477
do_groupChromPeaks_density0.2780.0150.293
extractMsData-method0.5900.0620.653
featureChromatograms1.9170.0932.012
fillChromPeaks1.1530.0491.205
filter-MChromatograms0.3830.0110.393
filterFeatures0.2650.0110.276
findChromPeaks-Chromatogram-CentWaveParam1.6700.0821.754
findChromPeaks-Chromatogram-MatchedFilter0.4360.0200.457
findChromPeaks-centWave1.0440.0381.085
findChromPeaks-centWaveWithPredIsoROIs0.0110.0010.012
findChromPeaks-massifquant5.4320.1905.640
findChromPeaks-matchedFilter3.1530.0363.192
findMZ0.0000.0010.000
findPeaks-MSW2.1290.0802.230
findPeaks.massifquant-methods8.3530.2998.693
findneutral0.0000.0000.001
group.mzClust0.0000.0000.001
group.nearest0.0000.0000.001
groupFeatures-abundance-correlation0.3800.0140.394
groupFeatures-eic-similarity2.7930.1782.977
groupFeatures-similar-rtime0.3290.0110.340
groupOverlaps0.0010.0010.001
highlightChromPeaks1.3540.0911.454
imputeLinInterpol0.0060.0030.012
imputeRowMin1.4350.1151.554
imputeRowMinRand1.3570.0531.411
loadXcmsData0.0830.0050.089
manualChromPeaks0.4460.0330.485
medianFilter0.0000.0000.001
msn2xcmsRaw1.6840.0571.742
overlappingFeatures0.4670.0240.490
peakTable-methods000
peaksWithCentWave0.3310.0280.360
peaksWithMatchedFilter0.5000.0350.535
phenoDataFromPaths0.0010.0010.003
plotAdjustedRtime0.3420.0080.356
plotChromPeakDensity0.1970.0130.212
plotChromPeaks0.3540.0150.371
plotChromatogramsOverlay3.1840.1103.326
plotPrecursorIons5.6330.2505.848
plotQC1.7520.0471.804
profGenerate0.0000.0010.001
profMat-xcmsSet1.7280.1451.875
profStep-methods0.0000.0000.001
rectUnique0.0020.0020.003
refineChromPeaks1.4550.0761.538
removeIntensity-Chromatogram0.1840.0130.198
rla0.0000.0000.001
stitch-methods0.0000.0000.001
sub-xcmsRaw-logicalOrNumeric-missing-missing-method1.3800.0561.437
writeMzTab1.1840.0241.215
xcmsRaw0.0010.0010.001