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CHECK report for xcms on merida1

This page was generated on 2019-04-16 11:54:16 -0400 (Tue, 16 Apr 2019).

Package 1637/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 3.4.4
Steffen Neumann
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/xcms
Branch: RELEASE_3_8
Last Commit: 6a9e67f
Last Changed Date: 2019-02-20 07:54:58 -0400 (Wed, 20 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: xcms
Version: 3.4.4
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_3.4.4.tar.gz
StartedAt: 2019-04-16 03:23:40 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:38:33 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 893.3 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_3.4.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/xcms.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘3.4.4’
* 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          33.253  7.245  17.798
fillChromPeaks                10.972  3.991   9.951
findChromPeaks-massifquant    11.770  2.428   7.805
XCMSnExp-filter-methods        7.703  3.005   5.454
adjustRtime-obiwarp            8.275  2.142   7.805
XCMSnExp-class                 6.219  2.592   5.480
findPeaks.massifquant-methods  8.298  0.286   8.584
plotChromPeakDensity           6.913  0.265   7.178
findChromPeaks-centWave        5.137  1.882   4.179
extractMsData-method           5.264  1.656   4.666
adjustRtime-peakGroups         4.562  1.855   4.239
do_findChromPeaks_massifquant  4.920  0.340   5.274
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘xcms’ ...
** 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++  -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++  -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++  -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++  -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++  -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++  -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++  -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++  -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++  -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++  -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++  -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++ -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/3.5/Resources/library/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
* DONE (xcms)

Tests output

xcms.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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, lengths, 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 2.8.3 
  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 3.4.4 


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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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: 2615 SKIPPED: 4 FAILED: 0
> 
> proc.time()
   user  system elapsed 
408.594  15.784 526.072 

Example timings

xcms.Rcheck/xcms-Ex.timings

nameusersystemelapsed
AutoLockMass-methods000
GenericParam0.0250.0000.026
XCMSnExp-class6.2192.5925.480
XCMSnExp-filter-methods7.7033.0055.454
adjustRtime-obiwarp8.2752.1427.805
adjustRtime-peakGroups4.5621.8554.239
applyAdjustedRtime3.9261.0673.674
binYonX0.0020.0010.003
breaks_on_binSize0.0010.0010.002
breaks_on_nBins0.0000.0000.001
chromatogram-method3.6111.1723.181
descendZero0.0010.0000.001
do_findChromPeaks_centWave2.3190.2292.548
do_findChromPeaks_massifquant4.9200.3405.274
do_findChromPeaks_matchedFilter3.6000.3073.907
do_groupChromPeaks_density1.5610.0641.629
extractMsData-method5.2641.6564.666
featureChromatograms33.253 7.24517.798
fillChromPeaks10.972 3.991 9.951
findChromPeaks-Chromatogram-CentWaveParam1.6770.1691.847
findChromPeaks-Chromatogram-MatchedFilter1.3990.0121.412
findChromPeaks-centWave5.1371.8824.179
findChromPeaks-centWaveWithPredIsoROIs0.0430.0110.056
findChromPeaks-massifquant11.770 2.428 7.805
findChromPeaks-matchedFilter2.9680.2663.235
findMZ0.0010.0000.000
findPeaks-MSW1.8690.1171.989
findPeaks.massifquant-methods8.2980.2868.584
findneutral000
group.mzClust000
group.nearest0.0000.0010.001
groupChromPeaks-density3.3190.1563.475
groupChromPeaks-mzClust1.9140.1202.034
groupChromPeaks-nearest3.4040.1693.573
highlightChromPeaks3.9890.3134.303
imputeLinInterpol0.0050.0020.008
imputeRowMin1.3980.0621.459
imputeRowMinRand1.4520.0831.535
medianFilter0.0000.0000.001
msn2xcmsRaw1.3010.0731.375
overlappingFeatures3.8260.1073.932
peakTable-methods000
peaksWithCentWave1.4420.0261.468
peaksWithMatchedFilter1.2870.0531.341
phenoDataFromPaths0.0010.0000.001
plotAdjustedRtime3.3020.1393.441
plotChromPeakDensity6.9130.2657.178
plotChromPeaks3.9140.2464.162
plotMsData1.3660.0601.426
plotQC1.6700.0531.725
profGenerate000
profMat-xcmsSet1.1840.1171.302
profStep-methods0.0000.0000.001
rectUnique0.0020.0000.003
rla0.0020.0000.002
stitch-methods0.0010.0000.001
sub-xcmsRaw-logicalOrNumeric-missing-missing-method0.9900.0311.022
writeMzTab1.4010.0581.460
xcmsPapply000
xcmsRaw0.0010.0000.000