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###
### Running command:
###
###   rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifcounter_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R motifcounter.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=motifcounter.buildbin-libdir motifcounter_1.22.0.tar.gz'
>>>>>>> 

* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rbackground.c -o Rbackground.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rcombinatorial.c -o Rcombinatorial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rminmaxscore.c -o Rminmaxscore.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Roption.c -o Roption.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Roverlap.c -o Roverlap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rscore1d.c -o Rscore1d.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rsequence.c -o Rsequence.o
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
    int mins, maxs, noscores;
                    ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rsimulate.c -o Rsimulate.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c background.c -o background.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c combinatorial.c -o combinatorial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c compoundpoisson.c -o compoundpoisson.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c markovchain.c -o markovchain.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c markovchain_single.c -o markovchain_single.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c matrix.c -o matrix.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c mdist_register.c -o mdist_register.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c minmaxscore.c -o minmaxscore.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c overlap.c -o overlap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c score1d.c -o score1d.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c score2d.c -o score2d.o
score2d.c:597:25: warning: variable 'p1' set but not used [-Wunused-but-set-variable]
    double p, p0 = 0.0, p1 = 0.0, ptmp;
                        ^
score2d.c:597:15: warning: variable 'p0' set but not used [-Wunused-but-set-variable]
    double p, p0 = 0.0, p1 = 0.0, ptmp;
              ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
    int j, i, index, cindex, ds;
                     ^
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
  int s, index, cindex;
                ^
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
    int s, index, cindex;
                  ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c sequence.c -o sequence.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c simulate.c -o simulate.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/motifcounter.buildbin-libdir/00LOCK-motifcounter/00new/motifcounter/libs
** R
** 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 (motifcounter)


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

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so"