Package: CellNOptR

Version: 1.29.0

Command: rm -rf CellNOptR.buildbin-libdir && mkdir CellNOptR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CellNOptR_1.29.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CellNOptR.buildbin-libdir

StartedAt: 2019-04-09 06:46:53 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 06:47:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 22.3 seconds

RetCode: 0

Status:  OK

PackageFile: CellNOptR_1.29.0.tgz

PackageFileSize: 1.91 MiB

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### Running command:
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###   rm -rf CellNOptR.buildbin-libdir && mkdir CellNOptR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CellNOptR_1.29.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CellNOptR.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CellNOptR.buildbin-libdir CellNOptR_1.29.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CellNOptR’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -I./include  -fPIC  -Wall -g -O2  -c getFit.c -o getFit.o
getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable]
        int nReacs = INTEGER(nReacs_in)[0];
            ^
getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable]
        int selection[40];
            ^
getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable]
        int selCounter = 0;
            ^
getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable]
        int or_max = 0;
            ^
getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable]
        int curr_max = 0;
            ^
5 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -I./include  -fPIC  -Wall -g -O2  -c simulatorT1.c -o simulatorT1.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -I./include  -fPIC  -Wall -g -O2  -c simulatorTN.c -o simulatorTN.o
simulatorTN.c:303:24: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if((track_cond == nCond)) {
            ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorTN.c:303:24: note: remove extraneous parentheses around the comparison to silence this warning
        if((track_cond == nCond)) {
           ˜           ^       ˜
simulatorTN.c:303:24: note: use '=' to turn this equality comparison into an assignment
        if((track_cond == nCond)) {
                       ^˜
                       =
simulatorTN.c:501:28: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
            if((track_cond == nCond)) {
                ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorTN.c:501:28: note: remove extraneous parentheses around the comparison to silence this warning
            if((track_cond == nCond)) {
               ˜           ^       ˜
simulatorTN.c:501:28: note: use '=' to turn this equality comparison into an assignment
            if((track_cond == nCond)) {
                           ^˜
                           =
2 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 CellNOptR.so getFit.o simulatorT1.o simulatorTN.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/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 (CellNOptR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR CellNOptR.buildbin-libdir/CellNOptR/libs//CellNOptR.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" "CellNOptR.buildbin-libdir/CellNOptR/libs//CellNOptR.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "CellNOptR.buildbin-libdir/CellNOptR/libs//CellNOptR.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" "CellNOptR.buildbin-libdir/CellNOptR/libs//CellNOptR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "CellNOptR.buildbin-libdir/CellNOptR/libs//CellNOptR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "CellNOptR.buildbin-libdir/CellNOptR/libs//CellNOptR.so"