Steffen Neumann
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/xcms |
| Branch: RELEASE_3_6 |
| Last Commit: 232eb7f |
| Last Changed Date: 2018-03-03 15:33:06 -0400 (Sat, 03 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:17:49 -0400 (Thu, 12 Apr 2018).
| Package 1461/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| xcms 3.0.2 Steffen Neumann
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: xcms |
| Version: 3.0.2 |
| Command: rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/xcms_3.0.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=xcms.buildbin-libdir --merge-multiarch xcms_3.0.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL xcms_3.0.2.zip && rm xcms_3.0.2.tar.gz xcms_3.0.2.zip |
| StartedAt: 2018-04-11 18:56:53 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:59:44 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 171.1 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/xcms_3.0.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=xcms.buildbin-libdir --merge-multiarch xcms_3.0.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL xcms_3.0.2.zip && rm xcms_3.0.2.tar.gz xcms_3.0.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/xcms.buildbin-libdir/xcms/libs/i386
** R
** inst
** preparing 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
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-class.Rd:311: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-class.Rd:392: missing file link 'Spectrum'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-class.Rd:199: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-class.Rd:287: missing file link 'Spectrum'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-class.Rd:547: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-class.Rd:547: missing file link 'MSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-class.Rd:548: missing file link 'pSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-class.Rd:558: missing file link 'chromatogram'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-class.Rd:559: missing file link 'Chromatogram'
XCMSnExp-filter-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-filter-methods.Rd:86: missing file link 'Spectrum'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-filter-methods.Rd:92: missing file link 'filterMsLevel'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-filter-methods.Rd:100: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-filter-methods.Rd:48: missing file link 'filterMz'
XCMSnExp-inherited-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:87: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:94: missing file link 'bin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:97: missing file link 'clean'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:102: missing file link 'filterAcquisitionNum'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:106: missing file link 'normalize'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:110: missing file link 'pickPeaks'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:116: missing file link 'removePeaks'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:120: missing file link 'smooth'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:32: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:57: missing file link 'normalize'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:59: missing file link 'pickPeaks'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:61: missing file link 'smooth'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:67: missing file link 'pickPeaks'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:67: missing file link 'smooth'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:71: missing file link 'pickPeaks'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:76: missing file link 'removePeaks'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:78: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/XCMSnExp-inherited-methods.Rd:126: missing file link 'OnDiskMSnExp'
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
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:63: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:65: missing file link 'chromatogram'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:66: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:14: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:51: missing file link 'Chromatogram'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:76: missing file link 'Chromatogram'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:85: missing file link 'Chromatogram'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:142: missing file link 'Chromatogram'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:145: missing file link 'Chromatograms'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/chromatogram-method.Rd:148: missing file link 'plot'
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
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/fillPeaks.chrom-methods.Rd:33: missing file link 'bpparam'
filtfft html
findChromPeaks-centWave html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWave.Rd:238: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWave.Rd:239: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWave.Rd:190: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWave.Rd:199: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWave.Rd:312: missing file link 'MSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWave.Rd:312: missing file link 'OnDiskMSnExp'
findChromPeaks-centWaveWithPredIsoROIs
html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.Rd:200: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.Rd:201: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.Rd:146: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.Rd:155: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.Rd:242: missing file link 'MSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.Rd:243: missing file link 'OnDiskMSnExp'
findChromPeaks-massifquant html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-massifquant.Rd:268: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-massifquant.Rd:269: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-massifquant.Rd:215: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-massifquant.Rd:224: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-massifquant.Rd:355: missing file link 'MSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-massifquant.Rd:356: missing file link 'OnDiskMSnExp'
findChromPeaks-matchedFilter html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-matchedFilter.Rd:207: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-matchedFilter.Rd:208: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-matchedFilter.Rd:149: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-matchedFilter.Rd:158: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-matchedFilter.Rd:273: missing file link 'MSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findChromPeaks-matchedFilter.Rd:274: missing file link 'OnDiskMSnExp'
findEqualGreater html
findMZ html
findPeaks-MSW html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findPeaks-MSW.Rd:192: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findPeaks-MSW.Rd:193: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findPeaks-MSW.Rd:146: missing file link 'OnDiskMSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findPeaks-MSW.Rd:155: missing file link 'bpparam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findPeaks-MSW.Rd:260: missing file link 'MSnExp'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/findPeaks-MSW.Rd:260: missing file link 'OnDiskMSnExp'
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-methods html
groupval-methods html
highlightChromPeaks html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/highlightChromPeaks.Rd:43: missing file link 'Chromatogram'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/highlightChromPeaks.Rd:44: missing file link 'Chromatograms'
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
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/xcms-deprecated.Rd:30: missing file link 'Chromatogram'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/xcms-deprecated.Rd:31: missing file link 'Chromatograms'
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
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/xcmsSet.Rd:44: missing file link 'SerialParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/xcmsSet.Rd:45: missing file link 'MulticoreParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi2nvLF/R.INSTALL14d865265ede/xcms/man/xcmsSet.Rd:46: missing file link 'SnowParam'
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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'xcms' as xcms_3.0.2.zip
* DONE (xcms)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'xcms' successfully unpacked and MD5 sums checked
In R CMD INSTALL