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BioC 3.6: BUILD BIN report for xcms on veracruz1

This page was generated on 2017-08-16 13:39:01 -0400 (Wed, 16 Aug 2017).

Package 1399/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 2.99.6
Steffen Neumann
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms
Last Changed Rev: 131862 / Revision: 131943
Last Changed Date: 2017-08-09 05:24:08 -0400 (Wed, 09 Aug 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: xcms
Version: 2.99.6
Command: rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh xcms_2.99.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R xcms.buildbin-libdir
StartedAt: 2017-08-16 11:34:27 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 11:35:00 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 33.9 seconds
RetCode: 0
Status:  OK 
PackageFile: xcms_2.99.6.tgz
PackageFileSize: 4.566 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh xcms_2.99.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R xcms.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=xcms.buildbin-libdir xcms_2.99.6.tar.gz'
>>>>>>> 

* 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
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
In file included from massifquant/Tracker.cpp:8:
massifquant/Tracker.h:49:16: warning: private field 'r_val_i' is not used [-Wunused-private-field]
        double r_val_i;
               ^
massifquant/Tracker.h:50:16: warning: private field 'p_val_i' is not used [-Wunused-private-field]
        double p_val_i;
               ^
massifquant/Tracker.h:53:16: warning: private field 'r_val_m' is not used [-Wunused-private-field]
        double r_val_m;
               ^
massifquant/Tracker.h:54:16: warning: private field 'p_val_m' is not used [-Wunused-private-field]
        double p_val_m;
               ^
4 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
In file included from massifquant/DataKeeper.cpp:4:
massifquant/DataKeeper.h:36:26: warning: private field 'scbuf' is not used [-Wunused-private-field]
        struct scanBuf * scbuf;
                         ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c obiwarp/mat.cpp -o obiwarp/mat.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c obiwarp/vec.cpp -o obiwarp/vec.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastMatch.c -o fastMatch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mzClust_hclust.c -o mzClust_hclust.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mzROI.c -o mzROI.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c util.c -o util.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c xcms.c -o xcms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c binners.c -o binners.o
binners.c:334:7: warning: unused variable 'idx' [-Wunused-variable]
  int idx = 0;
      ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/xcms.buildbin-libdir/xcms/libs
** 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
* DONE (xcms)


>>>>>>> 
>>>>>>> FIXING LINKS FOR xcms.buildbin-libdir/xcms/libs//xcms.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "xcms.buildbin-libdir/xcms/libs//xcms.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "xcms.buildbin-libdir/xcms/libs//xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "xcms.buildbin-libdir/xcms/libs//xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "xcms.buildbin-libdir/xcms/libs//xcms.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "xcms.buildbin-libdir/xcms/libs//xcms.so"