findChromPeaks issue (bug?)

[BaylorSci]

I recently updated to R version 4.1.1 and updated XCMS and associated packages to 3.14.1. Using Waters MSe data, I have previously successfully using findChromPeaks for both MS1 and MS2 using the add=TRUE. (script outlined below).

table(msLevel(raw_data1a))
1 2
125773 104078

exp_data=findChromPeaks(raw_data1a,
param=cwp,
msLevel=1)

exp_data=findChromPeaks(raw_data1a,
param=cwp,
add=TRUE,
msLevel=2)

However, when running the msLevel=2, the following error message is being returned:
Error in .local(object, param, ...) : unused argument (add = TRUE)

I have also looked at just starting with msLevel=2L, which returns the following error:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'X' in selecting a method for function 'bplapply': No MS level 2 spectra present

Which makes me suspect that if there is a bug, it is potentially not with XCMS ?

I really should know better then to give in to updates!

[sneumann]

Hi, could you provide your SessionInfo() ? If you upgraded R, how did you upgrade the installed R packages, or did you install everything from fresh ? An inkling says there might be a package version mismatch in one of the dependencies. Yours, Steffen

[sneumann]

Oh, and one more thing would help: after the error occurs please use traceback() for some idea where exactly the error occurs. Yours, Steffen

[BaylorSci]

I installed everything fresh when I updated. SessionInfo outputs the following:
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats4 stats graphics grDevices utils datasets
[7] methods base

other attached packages:
[1] xcms_3.16.0 MSnbase_2.20.0
[3] ProtGenerics_1.26.0 mzR_2.28.0
[5] Rcpp_1.0.7 BiocParallel_1.28.0
[7] SummarizedExperiment_1.24.0 Biobase_2.54.0
[9] GenomicRanges_1.46.0 GenomeInfoDb_1.30.0
[11] IRanges_2.28.0 S4Vectors_0.32.0
[13] BiocGenerics_0.40.0 MatrixGenerics_1.6.0
[15] matrixStats_0.61.0 dplyr_1.0.7

loaded via a namespace (and not attached):
[1] vsn_3.62.0 foreach_1.5.1
[3] BiocManager_1.30.16 affy_1.72.0
[5] GenomeInfoDbData_1.2.7 robustbase_0.93-9
[7] impute_1.68.0 pillar_1.6.4
[9] lattice_0.20-45 glue_1.4.2
[11] limma_3.50.0 digest_0.6.28
[13] RColorBrewer_1.1-2 XVector_0.34.0
[15] colorspace_2.0-2 preprocessCore_1.56.0
[17] Matrix_1.3-4 plyr_1.8.6
[19] MALDIquant_1.20 XML_3.99-0.8
[21] pkgconfig_2.0.3 zlibbioc_1.40.0
[23] purrr_0.3.4 scales_1.1.1
[25] snow_0.4-4 RANN_2.6.1
[27] affyio_1.64.0 tibble_3.1.5
[29] generics_0.1.1 ggplot2_3.3.5
[31] ellipsis_0.3.2 MassSpecWavelet_1.60.0
[33] magrittr_2.0.1 crayon_1.4.1
[35] ncdf4_1.17 fansi_0.5.0
[37] doParallel_1.0.16 MASS_7.3-54
[39] MsFeatures_1.2.0 tools_4.1.1
[41] lifecycle_1.0.1 munsell_0.5.0
[43] cluster_2.1.2 DelayedArray_0.20.0
[45] pcaMethods_1.86.0 compiler_4.1.1
[47] mzID_1.32.0 rlang_0.4.11
[49] grid_4.1.1 RCurl_1.98-1.5
[51] iterators_1.0.13 MsCoreUtils_1.6.0
[53] bitops_1.0-7 gtable_0.3.0
[55] codetools_0.2-18 DBI_1.1.1
[57] R6_2.5.1 utf8_1.2.2
[59] clue_0.3-60 parallel_4.1.1
[61] vctrs_0.3.8 DEoptimR_1.0-9
[63] tidyselect_1.1.1

When I run the following script:
exp_data=findChromPeaks(raw_data1a,
param=cwp,
msLevel=2,
add=TRUE)
It returns:
Error in .local(object, param, ...) : unused argument (add = TRUE)

and then run traceback(), it returns the following :
No traceback available

I'm a bit stumped.

[sneumann]

Hm, can't confirm yet here. We have an add = TRUE in the tests
https://github.com/sneumann/xcms/blob/RELEASE_3_14/tests/testthat/test_methods-XCMSnExp.R#L1272
and that happily works here with 3.16.0: http://bioconductor.org/checkResults/release/bioc-LATEST/xcms/

Could you run R CMD check on the package http://bioconductor.org/packages/release/bioc/html/xcms.html ?
Yours, Steffen

[BaylorSci]

Hi Steffen
So i ran R CMD check on the xcms package; and it returned the following:

Warning: S3 methods ‘plot.xcmsEIC’, ‘split.xcmsSet’, ‘c.xcmsSet’, ‘c.XCMSnExp’, ‘split.xcmsRaw’ were declared in NAMESPACE but not found
Warning in setup_ns_exports(path, export_all, export_imports) :
Objects listed as exports, but not present in namespace: etg, medianFilter, plotQC, retexp, specNoise, specPeaks, SSgauss, msn2xcmsRaw, verify.mzQuantML, xcmsRaw, xcmsSet, xcmsFragments, phenoDataFromPaths, binYonX, breaks_on_binSize, breaks_on_nBins, do_findChromPeaks_centWave, do_findChromPeaks_massifquant, do_findChromPeaks_matchedFilter, do_findPeaks_MSW, do_findChromPeaks_centWaveWithPredIsoROIs, do_findChromPeaks_addPredIsoROIs, imputeLinInterpol, useOriginalCode, do_groupChromPeaks_density, do_groupPeaks_mzClust, do_groupChromPeaks_nearest, do_adjustRtime_peakGroups, processHistoryTypes, adjustRtimePeakGroups, plotAdjustedRtime, highlightChromPeaks, plotChromPeaks, plotChromPeakImage, isCalibrated, plotMsData, applyAdjustedRtime, filterFeatureDefinitions, peaksWithMatchedFilter, peaksWithCentWave, rla, rowRla, featureSummary, overlappingFeatures, fixedMz, fixedRt, exportMetaboAnalyst, imputeRowMin, imputeRowMinRand, chromPeakSpectra, featureSpectra, featureChromatograms, hasFill [... truncated]
Warning in normalizePath(path.expand(path), winslash, mustWork) :

I downloaded the package via Bioconductor using the typical biocmanager::install("xcms), and this has always worked previously.

[BaylorSci]

More verbose output:
-- R CMD build ----------------------------------------------------------------------------
√ checking for file '...\R\win-library\4.1\xcms/DESCRIPTION' ...

• preparing 'xcms': (873ms)
  √ checking DESCRIPTION meta-information ...
• checking whether 'INDEX' is up-to-date ... NO
• use '--force' to remove the existing 'INDEX'
• excluding invalid files
  Subdirectory 'R' contains invalid file names:
  'xcms' 'xcms.rdb' 'xcms.rdx'
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
  Removed empty directory 'xcms/R'
  Removed empty directory 'xcms/man'
  WARNING: Removing directory 'xcms/Meta' which should only occur in an
  installed package
  WARNING: Removing directory 'xcms/help' which should only occur in an
  installed package
  WARNING: Removing directory 'xcms/html' which should only occur in an
  installed package
• looking to see if a 'data/datalist' file should be added
• building 'xcms_3.16.0.tar.gz'

[sneumann]

Can you do an R CMD check xcms_3.16.0.tar.gz ? The above output did not run yet the tests covering the add = TRUE thing we need. The warnings are not dramatic, that is unfortunately a bit noisy.
Yours, Steffen

[BaylorSci]

-- R CMD check ----------------------------------------------------------------------------

• using log directory '..../AppData/Local/Temp/Rtmps3Seps/fileae45c5c1843/xcms.Rcheck' (444ms)

• using R version 4.1.1 (2021-08-10)

• using platform: x86_64-w64-mingw32 (64-bit)

• using session charset: ISO8859-1
  √ checking for file 'xcms/DESCRIPTION' (884ms)

• this is package 'xcms' version '3.16.0'
  √ checking package namespace information ...
  √ checking package dependencies (861ms)
  √ checking if this is a source package ...
  √ checking if there is a namespace
  √ checking for executable files (3.5s)
  N checking for hidden files and directories ...
  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 ...
  √ checking whether package 'xcms' can be installed (54.2s)
  N checking installed package size ...
  installed size is 15.0Mb
  sub-directories of 1Mb or more:
  R 3.1Mb
  doc 9.5Mb
  libs 1.0Mb
  √ checking package directory
  √ checking 'build' directory
  N checking DESCRIPTION meta-information (430ms)
  License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
  √ checking top-level files
  √ checking for left-over files ...
  √ checking index information ...
  √ checking package subdirectories (347ms)
  √ checking R files for non-ASCII characters ...
  √ checking R files for syntax errors ...
  √ checking whether the package can be loaded (5.1s)
  √ checking whether the package can be loaded with stated dependencies (5s)
  √ checking whether the package can be unloaded cleanly (5.1s)
  √ checking whether the namespace can be loaded with stated dependencies (4.9s)
  √ checking whether the namespace can be unloaded cleanly (5.1s)
  √ checking loading without being on the library search path (5.1s)
  N checking dependencies in R code (5.9s)
  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 (5.7s)
  √ checking replacement functions (4.9s)
  √ checking foreign function calls (5.9s)
  N checking R code for possible problems (28.7s)
  .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<- 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 (2.2s)
  √ checking Rd metadata ...
  √ checking Rd cross-references (547ms)
  √ checking for missing documentation entries (5.1s)
  √ checking for code/documentation mismatches (15.4s)
  √ checking Rd \usage sections (6.7s)
  √ checking Rd contents (774ms)
  √ checking for unstated dependencies in examples (774ms)
  √ checking contents of 'data' directory (10s)
  √ checking data for non-ASCII characters (5s)
  √ checking data for ASCII and uncompressed saves ...
  √ checking line endings in C/C++/Fortran sources/headers ...
  √ checking line endings in Makefiles
  √ checking compilation flags in Makevars (889ms)
  √ checking for GNU extensions in Makefiles
  √ checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ...
  √ checking use of PKG_*FLAGS in Makefiles ...
  N checking compiled code (1.6s)
  Note: information on .o files for x64 is not available
  Warning in read_symbols_from_dll(so, rarch) :
  this requires 'objdump.exe' to be on the PATH
  Warning in read_symbols_from_dll(so, rarch) :
  this requires 'objdump.exe' to be on the PATH

  See 'Writing portable packages' in the 'Writing R Extensions' manual.
  √ checking installed files from 'inst/doc' ...
  √ checking files in 'vignettes' ...
  √ checking examples (46.1s)
  √ checking for unstated dependencies in 'tests' ...

• checking tests ...
  √ Running 'testthat.R' (4m 23.4s)
  √ checking for unstated dependencies in vignettes ...
  √ checking package vignettes in 'inst/doc' ...

• checking running R code from vignettes
  'LC-MS-feature-grouping.Rmd' using 'UTF-8'... OK
  'xcms-direct-injection.Rmd' using 'UTF-8'... OK
  'xcms-lcms-ms.Rmd' using 'UTF-8'... OK
  'xcms.Rmd' using 'UTF-8'... OK
  NONE
  √ checking re-building of vignette outputs (2m 15.9s)
  √ checking PDF version of manual (1m 56.1s)

  See
  '..../AppData/Local/Temp/Rtmps3Seps/fileae45c5c1843/xcms.Rcheck/00check.log'
  for details.

-- R CMD check results --------------------------------------------------- xcms 3.16.0 ----
Duration: 12m 37s

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 installed package size ... NOTE
installed size is 15.0Mb
sub-directories of 1Mb or more:
R 3.1Mb
doc 9.5Mb
libs 1.0Mb

checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
GPL (>= 2) + file LICENSE

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 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'
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<- 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
Warning in read_symbols_from_dll(so, rarch) :
this requires 'objdump.exe' to be on the PATH
Warning in read_symbols_from_dll(so, rarch) :
this requires 'objdump.exe' to be on the PATH

See 'Writing portable packages' in the 'Writing R Extensions' manual.

0 errors √ | 0 warnings √ | 6 notes x

[sneumann]

Great, exactly what we needed. So in general everything works because √ Running 'testthat.R' (4m 23.4s).
Next your script needs debugging, can you post a reproducible example that triggers the error, using available data from e.g. the faahKO or mtbls2 packages ?

[BaylorSci]

Just triple checking, but aren't both of the suggested data packages consisting of only msLevel 1, when the error I am reporting is for the addition of msLevel 2 with add=TRUE?

[sneumann]

You're correct. Can you reproduce with this one:
msnfile <- system.file("microtofq/MSMSpos20_6.mzML", package = "msdata")
or any other file of your choice we can download somewhere.
Yours, Steffen

[BaylorSci]

Certainly. Using the file you suggested, I choose the default parameters, with the following scripts:

cwp=CentWaveParam()

files= system.file("microtofq/MSMSpos20_6.mzML", package = "msdata")

pd1=data.frame(sample_name=sub(basename(files), pattern=".mzML",
replacement = "", fixed=TRUE),
sample_group=c(rep("Check", 1)),
stringAsFactors=FALSE)

raw_data1a=readMSData(files=files,
pdata=new("NAnnotatedDataFrame", pd1),
mode="onDisk")

exp_data=findChromPeaks(raw_data1a,
param=cwp,
msLevel=1)

exp_data=findChromPeaks(raw_data1a,
param=cwp,
add=TRUE,
msLevel=2)

returns: Error in .local(object, param, ...) : unused argument (add = TRUE)
traceback: > traceback()
2: findChromPeaks(raw_data1a, param = cwp, add = TRUE, msLevel = 2)
1: findChromPeaks(raw_data1a, param = cwp, add = TRUE, msLevel = 2)

Switching this around, I can pick peaks for msLevel=2 first, and the when I try to add ms 1 data to the onDiskMSnExp, the add=TRUE error comes up.

Outlined below is the session info:
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] beepr_1.3 xcms_3.16.0
[3] MSnbase_2.20.0 ProtGenerics_1.26.0
[5] mzR_2.28.0 Rcpp_1.0.7
[7] BiocParallel_1.28.0 SummarizedExperiment_1.24.0
[9] Biobase_2.54.0 GenomicRanges_1.46.0
[11] GenomeInfoDb_1.30.0 IRanges_2.28.0
[13] S4Vectors_0.32.0 BiocGenerics_0.40.0
[15] MatrixGenerics_1.6.0 matrixStats_0.61.0
[17] dplyr_1.0.7

loaded via a namespace (and not attached):
[1] vsn_3.62.0 foreach_1.5.1 BiocManager_1.30.16
[4] affy_1.72.0 GenomeInfoDbData_1.2.7 robustbase_0.93-9
[7] impute_1.68.0 pillar_1.6.4 lattice_0.20-45
[10] glue_1.4.2 limma_3.50.0 digest_0.6.28
[13] RColorBrewer_1.1-2 XVector_0.34.0 colorspace_2.0-2
[16] preprocessCore_1.56.0 Matrix_1.3-4 plyr_1.8.6
[19] MALDIquant_1.20 XML_3.99-0.8 pkgconfig_2.0.3
[22] zlibbioc_1.40.0 purrr_0.3.4 scales_1.1.1
[25] snow_0.4-4 RANN_2.6.1 affyio_1.64.0
[28] tibble_3.1.5 generics_0.1.1 ggplot2_3.3.5
[31] ellipsis_0.3.2 MassSpecWavelet_1.60.0 magrittr_2.0.1
[34] crayon_1.4.2 ncdf4_1.17 fansi_0.5.0
[37] doParallel_1.0.16 MASS_7.3-54 MsFeatures_1.2.0
[40] tools_4.1.1 lifecycle_1.0.1 stringr_1.4.0
[43] munsell_0.5.0 cluster_2.1.2 DelayedArray_0.20.0
[46] pcaMethods_1.86.0 compiler_4.1.1 mzID_1.32.0
[49] rlang_0.4.12 grid_4.1.1 RCurl_1.98-1.5
[52] iterators_1.0.13 MsCoreUtils_1.6.0 bitops_1.0-7
[55] gtable_0.3.0 codetools_0.2-18 DBI_1.1.1
[58] R6_2.5.1 utf8_1.2.2 clue_0.3-60
[61] stringi_1.7.5 parallel_4.1.1 vctrs_0.3.8
[64] audio_0.1-8 DEoptimR_1.0-9 tidyselect_1.1.1

[jorainer]

OK, I'll have a look into that.

[jorainer]

Note that you are calling findChromPeaks twice on the same object, i.e. the OnDiskMSnExp object with the raw data. The error you are getting (which is indeed very cryptic) comes from the findChromPeaks,OnDiskMSnExp method that does not have a parameter add, while the findChromPeaks,XCMSnExp actually has.

To fix your problem I would suggest to change your workflow to call findChromPeaks with the parameter add = TRUE on the result object you got from the first findChromPeaks call. Something along:

data <- readMSData(fls)

xdata <- findChromPeaks(data, param = cwp)
xdata <- findChromPeaks(xdata, param = cwp, msLevel = 2L, add = TRUE)

Note that in the second findChromPeaks call was done on xdata (an XCMSnExp object with results from the first chromatographic peak detection run), not data (an OnDiskMSnExp object that just represents the raw MS data, without chrom peak results).

[BaylorSci]

ok, that makes sense. I ran this successfully with the suggested "mzml" file, and then when I turned to run this with my own files,
exp_data=findChromPeaks(raw_data1a,
param=cwp,
msLevel=1)
followed by:
exp_data=findChromPeaks(exp_data,
param=cwp,
msLevel=2L,
add=TRUE)
and it returns a new error message:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'X' in selecting a method for function 'bplapply': No MS level 2 spectra present.

This is odd, since the initially imported onDiskMsnExp has both 1 and 2 levels.

The traceback is as follows:
13: h(simpleError(msg, call))
12: .handleSimpleError(function (cond)
.Internal(C_tryCatchHelper(addr, 1L, cond)), "No MS level 2 spectra present.",
base::quote(NULL))
11: stop("No MS level ", msLevel., " spectra present.", call. = FALSE)
10: (function (i, fd, x, to_class)
{
a <- new(to_class)
slot(procd, "files", check = FALSE) <- x@processingData@files[i]
slot(a, "processingData", check = FALSE) <- procd
slot(a, "featureData", check = FALSE) <- extractROWS(fd,
which(fd$msLevel %in% msLevel.))
if (!nrow(a@featureData))
stop("No MS level ", msLevel., " spectra present.", call. = FALSE)
a@featureData$fileIdx <- 1L
slot(a, "experimentData", check = FALSE) <- expd
slot(a, "spectraProcessingQueue", check = FALSE) <- x@spectraProcessingQueue
slot(a, "phenoData", check = FALSE) <- x@phenoData[i, , drop = FALSE]
a
})(dots[[1L]][[6L]], dots[[2L]][[6L]], x = new("XCMSnExp", .processHistory = list(
new("XProcessHistory", param = new("CentWaveParam", ppm = 25,
peakwidth = c(20, 50), snthresh = 10, prefilter = c(3,
100), mzCenterFun = "wMean", integrate = 1L, mzdiff = -0.001,
fitgauss = FALSE, noise = 0, verboseColumns = FALSE,
roiList = list(), firstBaselineCheck = TRUE, roiScales = numeric(0),
...
9: mapply(seq_along(fileNames(x)), fdl, FUN = create_object, MoreArgs = list(x = x,
to_class = to_class))
8: .split_by_file2(object, msLevel. = msLevel)
7: bplapply(.split_by_file2(object, msLevel. = msLevel), FUN = findChromPeaks_OnDiskMSnExp,
method = "centWave", param = param, BPPARAM = BPPARAM)
6: .local(object, param, ...)
5: (new("MethodDefinition", .Data = function (object, param, ...)
{
.local <- function (object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L)
{
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported", call. = FALSE)
centroided <- all(centroided(object)[msLevel(object) %in%
msLevel])
if (is.na(centroided)) {
idx <- which(msLevel(object) %in% msLevel)
idx <- idx[ceiling(length(idx)/3)]
suppressWarnings(centroided <- isCentroided(object[[idx]]))
}
if (is.na(centroided) || !centroided)
warning("Your data appears to be not centroided! CentWave",
...
4: do.call(meth, args = list(object = object, param = param, BPPARAM = BPPARAM,
return.type = return.type, msLevel = msLevel))
3: .local(object, param, ...)
2: findChromPeaks(exp_data, param = cwp, msLevel = 2L, add = TRUE)
1: findChromPeaks(exp_data, param = cwp, msLevel = 2L, add = TRUE)

I know the cwp parameters are not optimized, but the error message is throwing me a bit by saying no MS level 2 spectra present.

[jorainer]

This is indeed strange. What is the output of

table(msLevel(raw_data1a))

on your data? Could it be that you have some files in your data set with only MS1 data?