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BioC 3.3: BUILD BIN report for birta on oaxaca

This page was generated on 2016-10-13 12:58:15 -0700 (Thu, 13 Oct 2016).

Package 122/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birta 1.16.0
Benedikt Zacher , Holger Froehlich
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/birta
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: birta
Version: 1.16.0
Command: rm -rf birta.buildbin-libdir && mkdir birta.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh birta_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R birta.buildbin-libdir
StartedAt: 2016-10-13 07:25:32 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 07:25:38 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 5.9 seconds
RetCode: 0
Status:  OK 
PackageFile: birta_1.16.0.tgz
PackageFileSize: 680.2 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf birta.buildbin-libdir && mkdir birta.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh birta_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R birta.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=birta.buildbin-libdir birta_1.16.0.tar.gz'
>>>>>>> 

* installing *source* package ‘birta’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c BayesNetwork.cpp -o BayesNetwork.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c BayesNetworkNC.cpp -o BayesNetworkNC.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c getStates.cpp -o getStates.o
getStates.cpp:259:13: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                                else if(c == 1) {
                                        ^˜˜˜˜˜
getStates.cpp:262:49: note: uninitialized use occurs here
                                Otf[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                            ^˜˜˜˜
getStates.cpp:259:10: note: remove the 'if' if its condition is always true
                                else if(c == 1) {
                                     ^˜˜˜˜˜˜˜˜˜˜
getStates.cpp:255:14: note: initialize the variable 'nreps' to silence this warning
                                int nreps;
                                         ^
                                          = 0
getStates.cpp:228:12: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if(c == 1) {
                                ^˜˜˜˜˜
getStates.cpp:231:46: note: uninitialized use occurs here
                        O[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                  ^˜˜˜˜
getStates.cpp:228:9: note: remove the 'if' if its condition is always true
                        else if(c == 1) {
                             ^˜˜˜˜˜˜˜˜˜˜
getStates.cpp:224:13: note: initialize the variable 'nreps' to silence this warning
                        int nreps;
                                 ^
                                  = 0
getStates.cpp:201:13: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                                else if(c == 1) {
                                        ^˜˜˜˜˜
getStates.cpp:204:47: note: uninitialized use occurs here
                                A[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                          ^˜˜˜˜
getStates.cpp:201:10: note: remove the 'if' if its condition is always true
                                else if(c == 1) {
                                     ^˜˜˜˜˜˜˜˜˜˜
getStates.cpp:197:14: note: initialize the variable 'nreps' to silence this warning
                                int nreps;
                                         ^
                                          = 0
3 warnings 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 birta.so BayesNetwork.o BayesNetworkNC.o getStates.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/birta.buildbin-libdir/birta/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (birta)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "birta.buildbin-libdir/birta/libs//birta.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "birta.buildbin-libdir/birta/libs//birta.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "birta.buildbin-libdir/birta/libs//birta.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "birta.buildbin-libdir/birta/libs//birta.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "birta.buildbin-libdir/birta/libs//birta.so"