Steffen Neumann
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/xcms |
| Branch: RELEASE_3_7 |
| Last Commit: 34fb290 |
| Last Changed Date: 2018-04-30 10:35:01 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:32:26 -0400 (Wed, 17 Oct 2018).
| Package 1550/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| xcms 3.2.0 Steffen Neumann
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: xcms |
| Version: 3.2.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:xcms.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings xcms_3.2.0.tar.gz |
| StartedAt: 2018-10-17 05:26:23 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:55:39 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 1755.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: xcms.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:xcms.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings xcms_3.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/xcms.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '3.2.0'
* 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 whether package 'xcms' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
R 2.6Mb
html 1.1Mb
libs 1.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 object imported by a ':::' call: '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:
'XProcessHistory' 'descendMin' '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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/xcms/libs/i386/xcms.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
findPeaks.massifquant-methods 7.36 0.25 7.61
plotChromPeakDensity 6.71 0.05 6.75
fillChromPeaks 4.30 0.09 38.13
adjustRtime-obiwarp 4.12 0.14 35.97
adjustRtime-peakGroups 1.95 0.11 14.09
XCMSnExp-filter-methods 2.04 0.01 11.80
extractMsData-method 1.74 0.28 12.39
chromatogram-method 1.95 0.06 32.31
XCMSnExp-class 1.86 0.13 20.06
applyAdjustedRtime 1.77 0.08 18.30
findChromPeaks-centWave 1.06 0.02 10.64
findChromPeaks-massifquant 0.98 0.00 13.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotChromPeakDensity 6.20 0.08 6.29
findPeaks.massifquant-methods 6.02 0.08 6.09
fillChromPeaks 5.02 0.05 40.02
adjustRtime-obiwarp 4.54 0.13 14.27
XCMSnExp-filter-methods 2.21 0.01 12.55
adjustRtime-peakGroups 2.10 0.01 11.51
chromatogram-method 2.00 0.04 34.04
extractMsData-method 1.75 0.26 9.86
applyAdjustedRtime 1.84 0.10 17.05
XCMSnExp-class 1.72 0.03 18.95
findChromPeaks-centWave 1.09 0.02 10.63
findChromPeaks-massifquant 1.06 0.03 12.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/xcms.Rcheck/00check.log'
for details.
xcms.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/xcms_3.2.0.tar.gz && rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=xcms.buildbin-libdir xcms_3.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL xcms_3.2.0.zip && rm xcms_3.2.0.tar.gz xcms_3.2.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 560k 100 560k 0 0 9652k 0 --:--:-- --:--:-- --:--:-- 10.7M
install for i386
* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/SegProc.cpp -o massifquant/SegProc.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)':
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
float bestscore;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -fno-inline -c mzROI.c -o mzROI.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -fno-inline -c util.c -o util.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
int idx = 0;
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o xcms.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/xcms.buildbin-libdir/xcms/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'sigma' in package 'xcms'
** help
*** installing help indices
converting help for package 'xcms'
finding HTML links ... done
AutoLockMass-methods html
GenericParam html
ProcessHistory-class html
SSgauss html
XCMSnExp-class html
finding level-2 HTML links ... done
XCMSnExp-filter-methods html
XCMSnExp-inherited-methods html
XCMSnExp-peak-grouping-results html
absent-methods html
adjustRtime-obiwarp html
adjustRtime-peakGroups html
adjustRtime html
applyAdjustedRtime html
binYonX html
breaks_on_binSize html
breaks_on_nBins html
c.xcmsSet html
calibrate-calibrant-mass html
calibrate html
chromatogram-method html
chromatographic-peak-detection html
colMax html
collect-methods html
descendZero html
diffreport-methods html
do_adjustRtime_peakGroups html
do_findChromPeaks_centWave html
do_findChromPeaks_centWaveWithPredIsoROIs
html
do_findChromPeaks_massifquant html
do_findChromPeaks_matchedFilter html
do_findPeaks_MSW html
do_groupChromPeaks_density html
do_groupChromPeaks_nearest html
do_groupPeaks_mzClust html
doubleMatrix html
etg html
extractMsData-method html
fillChromPeaks html
fillPeaks-methods html
fillPeaks.MSW-methods html
fillPeaks.chrom-methods html
filtfft html
findChromPeaks-centWave html
findChromPeaks-centWaveWithPredIsoROIs
html
findChromPeaks-massifquant html
findChromPeaks-matchedFilter html
findEqualGreater html
findMZ html
findPeaks-MSW html
findPeaks-methods html
findPeaks.MS1-methods html
findPeaks.MSW-xcmsRaw-method html
findPeaks.addPredictedIsotopeFeatures-methods
html
findPeaks.centWave-methods html
findPeaks.centWaveWithPredictedIsotopeROIs-methods
html
findPeaks.massifquant-methods html
findPeaks.matchedFilter-xcmsRaw-method
html
findneutral html
getEIC-methods html
getPeaks-methods html
getScan-methods html
getSpec-methods html
getXcmsRaw-methods html
group-methods html
group.density html
group.mzClust html
group.nearest html
groupChromPeaks-density html
groupChromPeaks-mzClust html
groupChromPeaks-nearest html
groupChromPeaks html
groupnames-XCMSnExp html
groupnames-methods html
groupval-methods html
highlightChromPeaks html
image.xcmsRaw html
imputeLinInterpol html
levelplot.xcmsRaw html
loadRaw-methods html
medianFilter html
msn2xcmsRaw html
na.flatfill html
panel.cor html
peakPlots-methods html
peakTable-methods html
phenoDataFromPaths html
plot.xcmsEIC html
plotAdjustedRtime html
plotChrom-methods html
plotChromPeakDensity html
plotChromPeaks html
plotEIC-methods html
plotMsData html
plotPeaks-methods html
plotQC html
plotRaw-methods html
plotScan-methods html
plotSpec-methods html
plotSurf-methods html
plotTIC-methods html
plotrt-methods html
profGenerate html
profMat-xcmsSet html
profMedFilt-methods html
profMethod-methods html
profRange-methods html
profStep-methods html
pval html
rawEIC-methods html
rawMat-methods html
rectUnique html
retcor-methods html
retcor.obiwarp-methods html
retcor.peakgroups-methods html
retexp html
sampnames-methods html
showError-xcmsSet-method html
specDist-methods html
specDist.cosine-methods html
specDist.meanMZmatch-methods html
specDist.peakCount-methods html
specNoise html
specPeaks html
split.xcmsRaw html
split.xcmsSet html
stitch-methods html
sub-xcmsRaw-logicalOrNumeric-missing-missing-method
html
updateObject-xcmsSet-method html
useOriginalCode html
verify.mzQuantML html
write.cdf-methods html
write.mzQuantML html
write.mzdata-methods html
writeMzTab html
xcms-deprecated html
xcmsEIC-class html
xcmsFileSource-class html
xcmsFragments-class html
xcmsFragments html
xcmsPapply html
xcmsPeaks-class html
xcmsRaw-class html
xcmsRaw html
xcmsSet-class html
xcmsSet html
xcmsSource-class html
xcmsSource-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/SegProc.cpp -o massifquant/SegProc.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)':
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
float bestscore;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -fno-inline -c mzROI.c -o mzROI.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -fno-inline -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
int idx = 0;
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o xcms.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'xcms' as xcms_3.2.0.zip
* DONE (xcms)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'xcms' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
xcms.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: ProtGenerics
This is MSnbase version 2.6.4
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 3.2.0
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()
+ } else {
+ prm <- SnowParam()
+ }
> 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)
> 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)
Loading required package: xcms
This is xcms version 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
Loading required package: xcms
This is xcms version 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Loading required package: xcms
This is xcms version 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 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
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
Loading required package: 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: ProtGenerics
This is MSnbase version 2.6.4
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 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt22.CDF
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
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt18.CDF
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)
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 41 found.
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: ko15 ko18
center sample: ko18
Processing: ko15 ko16
center sample: ko18
Processing: ko15 ko16
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
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
center sample: ko15
Processing: ko16
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
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
== testthat results ===========================================================
OK: 2287 SKIPPED: 4 FAILED: 0
>
> proc.time()
user system elapsed
383.01 7.70 473.29
There were 50 or more warnings (use warnings() to see the first 50)
Warning messages:
There were 50 or more warnings (use warnings() to see the first 50)
1: There were 50 or more warnings (use warnings() to see the first 50)
In .getPeaks_new(object, peakrange, step = step) :
getPeaks: Peak m/z:246.05-246.1, RT:2502.79243216103-2532.91912290636is out of retention time range for this sample (C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt19.CDF), using zero intensity value.
2: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
3: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
4: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
5: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
6: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
|
xcms.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: ProtGenerics
This is MSnbase version 2.6.4
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 3.2.0
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()
+ } else {
+ prm <- SnowParam()
+ }
> 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)
> 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 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.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
> faahko_xs <- xcmsSet(faahko_3_files, profparam = list(step = 0),
+ method = "centWave", noise = 10000, snthresh = 40)
Loading required package: xcms
This is xcms version 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
Loading required package: xcms
This is xcms version 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Loading required package: xcms
This is xcms version 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 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
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
Loading required package: 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: ProtGenerics
This is MSnbase version 2.6.4
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 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt22.CDF
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
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/KO/ko18.CDF
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)
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 79 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 41 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 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: ko15 ko18
center sample: ko18
Processing: ko15 ko16
center sample: ko18
Processing: ko15 ko16
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
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
center sample: ko15
Processing: ko16
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
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
== testthat results ===========================================================
OK: 2287 SKIPPED: 4 FAILED: 0
>
> proc.time()
user system elapsed
407.82 5.96 503.20
There were 50 or more warnings (use warnings() to see the first 50)
There were 50 or more warnings (use warnings() to see the first 50)
There were 50 or more warnings (use warnings() to see the first 50)
Warning messages:
1: In .getPeaks_new(object, peakrange, step = step) :
getPeaks: Peak m/z:246.05-246.1, RT:2502.79243216103-2532.91912290636is out of retention time range for this sample (C:/Users/biocbuild/bbs-3.7-bioc/R/library/faahKO/cdf/WT/wt19.CDF), using zero intensity value.
2: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
3: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
4: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
5: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
6: In lmrob.S(x, y, control = control) :
S-estimated scale == 0: Probably exact fit; check your data
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xcms.Rcheck/examples_i386/xcms-Ex.timings
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xcms.Rcheck/examples_x64/xcms-Ex.timings
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