Steffen Neumann
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/xcms |
| Branch: RELEASE_3_11 |
| Last Commit: 4ff8895 |
| Last Changed Date: 2020-09-18 09:32:16 -0400 (Fri, 18 Sep 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:00 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE xcms PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1892/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| xcms 3.10.2 Steffen Neumann
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | TIMEOUT | skipped | skipped |
| Package: xcms |
| Version: 3.10.2 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/xcms_3.10.2.tar.gz && rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=xcms.buildbin-libdir xcms_3.10.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL xcms_3.10.2.zip && rm xcms_3.10.2.tar.gz xcms_3.10.2.zip |
| StartedAt: 2020-10-16 18:51:42 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 18:55:09 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 206.2 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/xcms_3.10.2.tar.gz && rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=xcms.buildbin-libdir xcms_3.10.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL xcms_3.10.2.zip && rm xcms_3.10.2.tar.gz xcms_3.10.2.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 693k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 693k 100 693k 0 0 1416k 0 --:--:-- --:--:-- --:--:-- 1433k
install for i386
* installing *source* package 'xcms' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/Tracker.cpp -o massifquant/Tracker.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/SegProc.cpp -o massifquant/SegProc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/mat.cpp -o obiwarp/mat.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/vec.cpp -o obiwarp/vec.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xcms_obiwarp.cpp -o xcms_obiwarp.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c fastMatch.c -o fastMatch.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzROI.c -o mzROI.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c util.c -o util.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c xcms.c -o xcms.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/g++ -std=gnu++11 -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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/xcms.buildbin-libdir/00LOCK-xcms/00new/xcms/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'sigma' in package 'xcms'
Creating a generic function from function 'hasFilledChromPeaks' 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
XChromatogram html
absent-methods html
adjustRtime-obiwarp html
adjustRtime-peakGroups html
adjustRtime html
align-Chromatogram html
applyAdjustedRtime html
binYonX html
breaks_on_binSize html
breaks_on_nBins html
c.xcmsSet html
calibrate-calibrant-mass html
calibrate html
chromPeakSpectra html
chromatogram-method html
chromatographic-peak-detection html
colMax html
collect-methods html
correlate-Chromatogram html
descendZero html
diffreport-methods html
dirname 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
exportMetaboAnalyst html
extractMsData-method html
featureChromatograms html
featureSpectra html
featureSummary html
fillChromPeaks html
fillPeaks-methods html
fillPeaks.MSW-methods html
fillPeaks.chrom-methods html
filtfft html
findChromPeaks-Chromatogram-CentWaveParam
html
findChromPeaks-Chromatogram-MatchedFilter
html
findChromPeaks-centWave html
findChromPeaks-centWaveWithPredIsoROIs
html
findChromPeaks-massifquant html
findChromPeaks-matchedFilter html
findChromPeaksIsolationWindow 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
groupOverlaps html
groupnames-XCMSnExp html
groupnames-methods html
groupval-methods html
highlightChromPeaks html
image.xcmsRaw html
imputeLinInterpol html
imputeRowMin html
imputeRowMinRand html
isolationWindowTargetMz-OnDiskMSnExp-method
html
levelplot.xcmsRaw html
loadRaw-methods html
medianFilter html
msn2xcmsRaw html
na.flatfill html
overlappingFeatures html
panel.cor html
peakPlots-methods html
peakTable-methods html
peaksWithCentWave html
peaksWithMatchedFilter 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
reconstructChromPeakSpectra html
rectUnique html
refineChromPeaks-clean html
refineChromPeaks-merge html
retcor-methods html
retcor.obiwarp-methods html
retcor.peakgroups-methods html
retexp html
rla 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
writeMSData-XCMSnExp-character-method 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'xcms' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/Tracker.cpp -o massifquant/Tracker.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/SegProc.cpp -o massifquant/SegProc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/mat.cpp -o obiwarp/mat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/vec.cpp -o obiwarp/vec.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xcms_obiwarp.cpp -o xcms_obiwarp.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c fastMatch.c -o fastMatch.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzROI.c -o mzROI.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c util.c -o util.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c xcms.c -o xcms.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/g++ -std=gnu++11 -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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'xcms' as xcms_3.10.2.zip
* DONE (xcms)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'xcms' successfully unpacked and MD5 sums checked