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CHECK report for xcms on celaya2

This page was generated on 2019-04-09 12:50:19 -0400 (Tue, 09 Apr 2019).

Package 1690/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 3.5.1
Steffen Neumann
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/xcms
Branch: master
Last Commit: 1bd12fa
Last Changed Date: 2019-01-04 13:12:44 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: xcms
Version: 3.5.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:xcms.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings xcms_3.5.1.tar.gz
StartedAt: 2019-04-09 06:19:01 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:37:35 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 1114.8 seconds
RetCode: 0
Status:  OK 
CheckDir: xcms.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:xcms.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings xcms_3.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/xcms.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘3.5.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xcms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘MALDIquant:::.localMaxima’ ‘MSnbase:::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:
  ‘MSW.cwt’ ‘MSW.getLocalMaximumCWT’ ‘MSW.getRidge’ ‘XProcessHistory’
  ‘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’
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’
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’
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 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
  recvOneResult rgl.bbox rgl.clear rgl.points rgl.surface saveXML
  sendCall xmlInternalTreeParse xmlSchemaValidate xmlTree xmlTreeParse
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
featureChromatograms          41.221 12.779  24.923
fillChromPeaks                18.271  7.279  17.928
findChromPeaks-massifquant    14.075  4.218  10.087
XCMSnExp-filter-methods        8.300  5.068   6.974
adjustRtime-obiwarp            8.660  3.456   8.957
XCMSnExp-class                 7.249  4.098   6.894
findChromPeaks-centWave        7.403  3.606   6.365
extractMsData-method           6.581  2.978   6.407
adjustRtime-peakGroups         6.106  3.353   6.186
findPeaks.massifquant-methods  8.624  0.503   9.127
plotChromPeakDensity           8.005  0.374   8.380
chromatogram-method            4.946  1.986   4.508
applyAdjustedRtime             4.988  1.608   4.862
do_findChromPeaks_massifquant  5.580  0.566   6.150
highlightChromPeaks            4.966  0.431   5.398
plotChromPeaks                 4.757  0.409   5.166
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/xcms.Rcheck/00check.log’
for details.



Installation output

xcms.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL xcms
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘xcms’ ...
** using staged installation
** libs
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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c obiwarp/mat.cpp -o obiwarp/mat.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c obiwarp/vec.cpp -o obiwarp/vec.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastMatch.c -o fastMatch.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c mzClust_hclust.c -o mzClust_hclust.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c mzROI.c -o mzROI.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c util.c -o util.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c xcms.c -o xcms.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -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++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-xcms/00new/xcms/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘sigma’ in package ‘xcms’
** help
*** installing help indices
** 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


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
Loading required package: MSnbase
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:base':

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.9.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws


This is xcms version 3.5.1 


Attaching package: 'xcms'

The following object is masked from 'package:stats':

    sigma

> library(faahKO)
> library(msdata)
> 
> attr(faahko, "filepaths") <- sapply(
+     as.list(basename(attr(faahko, "filepaths"))),
+     function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else "WT",
+                             x, package = "faahKO"))
> if (.Platform$OS.type == "unix") {
+     prm <- MulticoreParam(2)
+ } else {
+     prm <- SnowParam(2)
+ }
> register(bpstart(prm))
> 
> ## 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"))
> 
> ## An xcmsRaw for the first file:
> faahko_xr_1 <- xcmsRaw(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+                        profstep = 0)
Error in R_nc4_close: NetCDF: Not a valid ID
> 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 = CentWaveParam(noise = 10000,
+                                                               snthresh = 40))
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.
> faahko_xs <- xcmsSet(faahko_3_files, profparam = list(step = 0),
+                      method = "centWave", noise = 10000, snthresh = 40)
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
> faahko_xsg <- group(faahko_xs)
Processing 2572 mz slices ... OK
> ## Doing also the retention time correction etc
> od_x <- faahko_od
> xod_x <- faahko_xod
> pdp <- PeakDensityParam(sampleGroups = rep(1, 3))
> xod_xg <- groupChromPeaks(xod_x, param = pdp)
Processing 2572 mz slices ... OK
> 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)
Processing 2572 mz slices ... OK
> 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
> 
> faahko_grouped_filled <- fillPeaks(group(faahko))
Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
> faahko_grouped_retcor_filled <-
+     fillPeaks(group(retcor(group(updateObject(faahko)))))
Processing 3195 mz slices ... OK
Performing retention time correction using 132 peak groups.
Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
>     
> microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+                   system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_xr <- xcmsRaw(microtofq_fs[1], profstep = 0)
> microtofq_od <- readMSData(microtofq_fs, mode = "onDisk")
> 
> ## Direct injection data:
> fticrf <- list.files(system.file("fticr", 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))
> fticr_xs <- xcmsSet(method="MSW", files=fticrf[1:2], scales=c(1,7),
+                     SNR.method='data.mean' , winSize.noise=500,
+                     peakThr=80000,  amp.Th=0.005)
> 
> fs <- 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"),
+         system.file('cdf/KO/ko19.CDF', package = "faahKO"))
> xs_1 <- xcmsSet(fs, profparam = list(step = 0), method = "centWave",
+                 noise = 10000, snthresh = 50)
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 41 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 79 found.
> 
> test_check("xcms")
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  
center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID
ko18  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko18 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID
ko16  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko18 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID
ko16  Error in R_nc4_close: NetCDF: Not a valid ID

Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
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  
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  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  
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  
HAM004_641fE_14-11-07--Exp1.extracted HAM004_641fE_14-11-07--Exp2.extracted 
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
method:  bin 
step:  0.3 
method:  binlin 
step:  0.2 
method:  binlinbase 
step:  0.2 
method:  intlin 
step:  0.2 
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
center sample:  ko15 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko16  Error in R_nc4_close: NetCDF: Not a valid ID

Error in R_nc4_close: NetCDF: Not a valid ID
center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Comparing peaks...OK
Comparing peaks...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Error in R_nc4_close: NetCDF: Not a valid ID
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 2613 SKIPPED: 4 FAILED: 0
> 
> proc.time()
   user  system elapsed 
496.626  28.831 653.433 

Example timings

xcms.Rcheck/xcms-Ex.timings

nameusersystemelapsed
AutoLockMass-methods0.0010.0010.001
GenericParam0.0280.0010.029
XCMSnExp-class7.2494.0986.894
XCMSnExp-filter-methods8.3005.0686.974
adjustRtime-obiwarp8.6603.4568.957
adjustRtime-peakGroups6.1063.3536.186
applyAdjustedRtime4.9881.6084.862
binYonX0.0030.0040.008
breaks_on_binSize0.0030.0030.005
breaks_on_nBins0.0010.0010.001
chromatogram-method4.9461.9864.508
descendZero0.0010.0020.003
do_findChromPeaks_centWave2.8820.4723.354
do_findChromPeaks_massifquant5.5800.5666.150
do_findChromPeaks_matchedFilter4.2850.5174.801
do_groupChromPeaks_density1.5430.1151.658
extractMsData-method6.5812.9786.407
featureChromatograms41.22112.77924.923
fillChromPeaks18.271 7.27917.928
findChromPeaks-Chromatogram-CentWaveParam2.0270.1252.153
findChromPeaks-Chromatogram-MatchedFilter2.0580.1042.162
findChromPeaks-centWave7.4033.6066.365
findChromPeaks-centWaveWithPredIsoROIs0.0810.0270.107
findChromPeaks-massifquant14.075 4.21810.087
findChromPeaks-matchedFilter3.4790.4533.933
findMZ000
findPeaks-MSW2.1770.1652.349
findPeaks.massifquant-methods8.6240.5039.127
findneutral0.0000.0000.001
group.mzClust000
group.nearest0.0010.0000.001
groupChromPeaks-density4.0570.2634.320
groupChromPeaks-mzClust2.2050.1552.358
groupChromPeaks-nearest4.2190.2644.482
highlightChromPeaks4.9660.4315.398
imputeLinInterpol0.0080.0020.011
imputeRowMin1.5780.1301.709
imputeRowMinRand1.5440.0771.621
medianFilter0.0000.0000.001
msn2xcmsRaw1.5630.1471.713
overlappingFeatures4.6430.2514.893
peakTable-methods0.0000.0010.000
peaksWithCentWave1.7710.0471.819
peaksWithMatchedFilter1.5700.0861.655
phenoDataFromPaths0.0010.0010.002
plotAdjustedRtime4.0150.2354.249
plotChromPeakDensity8.0050.3748.380
plotChromPeaks4.7570.4095.166
plotMsData1.6510.0681.719
plotQC1.8120.1151.928
profGenerate0.0010.0000.001
profMat-xcmsSet1.4080.1831.590
profStep-methods0.0000.0000.001
rectUnique0.0020.0010.003
rla0.0010.0000.001
stitch-methods0.0010.0010.000
sub-xcmsRaw-logicalOrNumeric-missing-missing-method1.2040.0551.259
writeMzTab1.4450.0611.505
xcmsPapply000
xcmsRaw0.0000.0010.001