Package: birta

Version: 1.27.0

Command: rm -rf birta.buildbin-libdir && mkdir birta.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh birta_1.27.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R birta.buildbin-libdir

StartedAt: 2019-04-09 04:50:47 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:52:07 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 80.5 seconds

RetCode: 0

Status:  OK

PackageFile: birta_1.27.0.tgz

PackageFileSize: 718.3 KiB

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### Running command:
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###   rm -rf birta.buildbin-libdir && mkdir birta.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh birta_1.27.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R birta.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=birta.buildbin-libdir birta_1.27.0.tar.gz'
>>>>>>> 

* installing *source* package ‘birta’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BayesNetwork.cpp -o BayesNetwork.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BayesNetworkNC.cpp -o BayesNetworkNC.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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++ -std=gnu++11 -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-3.9-bioc/meat/birta.buildbin-libdir/birta/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
* 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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "birta.buildbin-libdir/birta/libs//birta.so"