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###
### Running command:
###
###   rm -rf MSA2dist.buildbin-libdir && mkdir MSA2dist.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MSA2dist_1.1.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R MSA2dist.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=MSA2dist.buildbin-libdir MSA2dist_1.1.2.tar.gz'
>>>>>>> 

* installing *source* package ‘MSA2dist’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c GY94.cpp -o GY94.o
GY94.cpp:337:27: warning: variable 'status' set but not used [-Wunused-but-set-variable]
   int ii=0, maxround=10, status;
                          ^
GY94.cpp:480:39: warning: variable 'fail' set but not used [-Wunused-but-set-variable]
        int i, j, i1, i2, it, maxround=2000, fail=0, *xmark, *ix, nfree;
                                             ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c KaKs.cpp -o KaKs.o
KaKs.cpp:328:17: warning: variable 'fka' set but not used [-Wunused-but-set-variable]
                float fka,fks,fkaks;
                      ^
KaKs.cpp:328:21: warning: variable 'fks' set but not used [-Wunused-but-set-variable]
                float fka,fks,fkaks;
                          ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LPB93.cpp -o LPB93.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LWL85.cpp -o LWL85.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c MSMA.cpp -o MSMA.o
MSMA.cpp:61:24: warning: variable 'sum' set but not used [-Wunused-but-set-variable]
        double w[MODELCOUNT], sum;
                              ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c MYN.cpp -o MYN.o
MYN.cpp:189:40: warning: variable 'A' set but not used [-Wunused-but-set-variable]
        double tc, ag, Y, R, a1=0, a2=0, b=0, A, B, C;
                                              ^
MYN.cpp:189:43: warning: variable 'B' set but not used [-Wunused-but-set-variable]
        double tc, ag, Y, R, a1=0, a2=0, b=0, A, B, C;
                                                 ^
MYN.cpp:244:37: warning: variable 'B' set but not used [-Wunused-but-set-variable]
        double tc, ag, Y, R, a1, a2, b, A, B, C;
                                           ^
MYN.cpp:244:34: warning: variable 'A' set but not used [-Wunused-but-set-variable]
        double tc, ag, Y, R, a1, a2, b, A, B, C;
                                        ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c NG86.cpp -o NG86.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c YN00.cpp -o YN00.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c base.cpp -o base.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_KaKs.cpp -o rcpp_KaKs.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_distSTRING.cpp -o rcpp_distSTRING.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_pairwiseDeletionAA.cpp -o rcpp_pairwiseDeletionAA.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_pairwiseDeletionDNA.cpp -o rcpp_pairwiseDeletionDNA.o
clang++ -arch arm64 -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/opt/R/arm64/lib -o MSA2dist.so GY94.o KaKs.o LPB93.o LWL85.o MSMA.o MYN.o NG86.o RcppExports.o YN00.o base.o rcpp_KaKs.o rcpp_distSTRING.o rcpp_pairwiseDeletionAA.o rcpp_pairwiseDeletionDNA.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-bioc/meat/MSA2dist.buildbin-libdir/00LOCK-MSA2dist/00new/MSA2dist/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 (MSA2dist)


>>>>>>> 
>>>>>>> FIXING LINKS FOR MSA2dist.buildbin-libdir/MSA2dist/libs/MSA2dist.so
>>>>>>> 

ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib not found!