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BioC 3.4: INSTALL report for xcms on malbec1

This page was generated on 2017-04-15 16:09:00 -0400 (Sat, 15 Apr 2017).

Package 1287/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 1.50.1
Steffen Neumann
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/xcms
Last Changed Rev: 125337 / Revision: 128728
Last Changed Date: 2016-12-20 09:03:43 -0500 (Tue, 20 Dec 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: xcms
Version: 1.50.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL xcms
StartedAt: 2017-04-14 18:11:17 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 18:11:40 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 23.7 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL xcms
###
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* installing to library ‘/home/biocbuild/bbs-3.4-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 binners.o
g++ -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fastMatch.c -o fastMatch.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I/home/biocbuild/bbs-3.4-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 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c xcms.c -o xcms.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c binners.c -o binners.o
binners.c: In function ‘_impute_linearly_interpolate_base_x’:
binners.c:707:12: warning: unused variable ‘next_bin_value’ [-Wunused-variable]
     double next_bin_value = base_value;
            ^
binners.c:642:10: warning: unused variable ‘new_value’ [-Wunused-variable]
   double new_value;
          ^
binners.c:641:10: warning: unused variable ‘incrementer’ [-Wunused-variable]
   double incrementer = 0;
          ^
binners.c: In function ‘binYonX’:
binners.c:174:5: warning: ‘index’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(ans_list, 2, index);
     ^
g++ -shared -L/home/biocbuild/bbs-3.4-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 binners.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)