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BioC 3.5: INSTALL report for xcms on tokay2

This page was generated on 2017-08-16 13:18:56 -0400 (Wed, 16 Aug 2017).

Package 1373/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 1.52.0
Steffen Neumann
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/xcms
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: xcms
Version: 1.52.0
Command: rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/xcms_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=xcms.buildbin-libdir --merge-multiarch xcms_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL xcms_1.52.0.zip && rm xcms_1.52.0.tar.gz xcms_1.52.0.zip
StartedAt: 2017-08-15 18:48:12 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:49:24 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 71.8 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/xcms_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=xcms.buildbin-libdir --merge-multiarch xcms_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL xcms_1.52.0.zip  && rm xcms_1.52.0.tar.gz xcms_1.52.0.zip
###
##############################################################################
##############################################################################


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100  590k  100  590k    0     0  1448k      0 --:--:-- --:--:-- --:--:-- 1455k

install for i386

* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzROI.c -o mzROI.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c util.c -o util.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:334:7: 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˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzROI.c -o mzROI.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:334:7: 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˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'xcms' as xcms_1.52.0.zip
* DONE (xcms)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'xcms' successfully unpacked and MD5 sums checked