Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

BUILD BIN report for nem on celaya2

This page was generated on 2019-10-16 12:46:11 -0400 (Wed, 16 Oct 2019).

Package 1092/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nem 2.58.0
Holger Froehlich
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/nem
Branch: RELEASE_3_9
Last Commit: 3ab2aad
Last Changed Date: 2019-05-02 11:53:06 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: nem
Version: 2.58.0
Command: rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh nem_2.58.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R nem.buildbin-libdir
StartedAt: 2019-10-16 09:02:10 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 09:02:30 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 20.2 seconds
RetCode: 0
Status:  OK 
PackageFile: nem_2.58.0.tgz
PackageFileSize: 3.923 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh nem_2.58.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R nem.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=nem.buildbin-libdir nem_2.58.0.tar.gz'
>>>>>>> 

* installing *source* package ‘nem’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c MCMC.c -o MCMC.o
MCMC.c:44:45: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
                                p -= inv_nu*abs(net[s][k]-prior[s][k]);
                                            ^
MCMC.c:44:45: note: use function 'fabs' instead
                                p -= inv_nu*abs(net[s][k]-prior[s][k]);
                                            ^~~
                                            fabs
MCMC.c:72:62: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
                                        if(Psi[p][s] != 0 && abs(Psi[p][s]) <= t){ // p is a parent
                                                             ^
MCMC.c:72:62: note: use function 'fabs' instead
                                        if(Psi[p][s] != 0 && abs(Psi[p][s]) <= t){ // p is a parent
                                                             ^~~
                                                             fabs
MCMC.c:359:35: warning: unused variable 'mutinf' [-Wunused-variable]
    double loglikMean, loglikSum, mutinf, delta, logPrior_cur_scale;  
                                  ^
MCMC.c:403:10: warning: unused variable 'stored2' [-Wunused-variable]
    long stored2 = 0;
         ^
MCMC.c:402:10: warning: unused variable 'stored' [-Wunused-variable]
    long stored = 0;
         ^
5 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c netlearn.c -o netlearn.o
netlearn.c:171:13: warning: variable 'negenes' used in loop condition not modified in loop body [-Wfor-loop-analysis]
                for (i=0; negenes; i++) {
                          ^~~~~~~
netlearn.c:168:9: warning: unused variable 'lik_switch' [-Wunused-variable]
        double lik_switch;
               ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c wrapper.c -o wrapper.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 nem.so MCMC.o netlearn.o wrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/nem.buildbin-libdir/00LOCK-nem/00new/nem/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nem)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "nem.buildbin-libdir/nem/libs//nem.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "nem.buildbin-libdir/nem/libs//nem.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "nem.buildbin-libdir/nem/libs//nem.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "nem.buildbin-libdir/nem/libs//nem.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "nem.buildbin-libdir/nem/libs//nem.so"