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BioC 3.5: BUILD BIN report for bgx on toluca2

This page was generated on 2017-04-23 14:34:08 -0400 (Sun, 23 Apr 2017).

Package 103/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bgx 1.41.0
Ernest Turro
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bgx
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: bgx
Version: 1.41.0
Command: rm -rf bgx.buildbin-libdir && mkdir bgx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bgx_1.41.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bgx.buildbin-libdir
StartedAt: 2017-04-23 11:40:50 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 11:41:20 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 29.8 seconds
RetCode: 0
Status:  OK 
PackageFile: bgx_1.41.0.tgz
PackageFileSize: 260 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf bgx.buildbin-libdir && mkdir bgx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bgx_1.41.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bgx.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bgx.buildbin-libdir bgx_1.41.0.tar.gz'
>>>>>>> 

* installing *source* package ‘bgx’ ...
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... i386-apple-darwin13.4.0
checking host system type... i386-apple-darwin13.4.0
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 306e4:5200800:7fbee3ff:bfebfbff
checking whether C compiler accepts -march=pentiumpro... no
checking whether C compiler accepts -mcpu=pentiumpro... yes
checking for gcc architecture flag... -mcpu=pentiumpro
checking for clang option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
In file included from bgx.cc:29:
./bgx_updates.hh:47:8: warning: private field 'categories' is not used [-Wunused-private-field]
  int* categories;
       ^
./bgx_updates.hh:310:8: warning: private field 'categories' is not used [-Wunused-private-field]
  int *categories;
       ^
./bgx_updates.hh:311:7: warning: private field 'numberCategories' is not used [-Wunused-private-field]
  int numberCategories;
      ^
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
bgx_frontend.cc:251:16: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(SampleSets==NULL){
     ˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:261:15: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(ProbeSets==NULL){
     ˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:271:16: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(Categories==NULL){
     ˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:281:22: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(UnknownProbeSeqs==NULL){
     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:291:18: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(GenesToWatch==NULL){
     ˜˜˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:301:33: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(FirstProbeInEachGeneToWatch==NULL){
     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:311:8: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(PM==NULL){
     ˜˜^ ˜˜˜˜
bgx_frontend.cc:316:8: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(MM==NULL){
     ˜˜^ ˜˜˜˜
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -g -O2 -mcpu=pentiumpro  -ffast-math -O3 -c qnorm.c -o qnorm.o
clang: warning: argument unused during compilation: '-mcpu=pentiumpro'
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
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 bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl
installing to /Users/biocbuild/bbs-3.5-bioc/meat/bgx.buildbin-libdir/bgx/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 (bgx)


>>>>>>> 
>>>>>>> FIXING LINKS FOR bgx.buildbin-libdir/bgx/libs//bgx.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" "bgx.buildbin-libdir/bgx/libs//bgx.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.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" "bgx.buildbin-libdir/bgx/libs//bgx.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.so"