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BioC 3.2: INSTALL report for xcms on linux1.bioconductor.org

This page was generated on 2015-10-27 17:23:41 -0400 (Tue, 27 Oct 2015).

Package 1098/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 1.46.0
Steffen Neumann
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/xcms
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: xcms
Version: 1.46.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL xcms
StartedAt: 2015-10-26 20:17:13 -0400 (Mon, 26 Oct 2015)
EndedAt: 2015-10-26 20:17:32 -0400 (Mon, 26 Oct 2015)
EllapsedTime: 19.0 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL xcms
###
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* installing to library ‘/home/biocbuild/bbs-3.2-bioc/R/library’
* installing *source* package ‘xcms’ ...
** libs
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function ‘SEXPREC* massifquant(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
massifquant/xcms_massifquant.cpp:122:6: warning: unused variable ‘scanLength’ [-Wunused-variable]
  int scanLength = int(featInfo.at(5) - featInfo.at(4) + 1);
      ^
massifquant/xcms_massifquant.cpp:33:58: warning: unused variable ‘vstcenter’ [-Wunused-variable]
     SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
                                                          ^
massifquant/xcms_massifquant.cpp:33:93: warning: unused variable ‘vintenmax’ [-Wunused-variable]
     SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
                                                                                             ^
massifquant/xcms_massifquant.cpp:76:12: warning: unused variable ‘maxScanNums’ [-Wunused-variable]
     double maxScanNums = double(scanrangeTo);
            ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp: In member function ‘void SegProc::collapseSubsets()’:
massifquant/SegProc.cpp:119:13: warning: variable ‘combinedUnions’ set but not used [-Wunused-but-set-variable]
         int combinedUnions = 0;
             ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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;
         ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fastMatch.c -o fastMatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mzROI.c -o mzROI.o
mzROI.c: In function ‘getMZ’:
mzROI.c:486:17: warning: variable ‘pintensity’ set but not used [-Wunused-but-set-variable]
   double *pmz, *pintensity,*p_res, mzrangeFrom,mzrangeTo;
                 ^
mzROI.c: In function ‘findmzROI’:
mzROI.c:538:41: warning: variable ‘mzrangeTo’ set but not used [-Wunused-but-set-variable]
   double *pmz, *pintensity, mzrangeFrom,mzrangeTo;
                                         ^
mzROI.c:538:29: warning: variable ‘mzrangeFrom’ set but not used [-Wunused-but-set-variable]
   double *pmz, *pintensity, mzrangeFrom,mzrangeTo;
                             ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c xcms.c -o xcms.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/R/library/xcms/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xcms)