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### Running command:
###
### rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PICS_2.44.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PICS.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PICS.buildbin-libdir PICS_2.44.0.tar.gz'
>>>>>>>
* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /opt/homebrew/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... no
checking for gcc... clang -arch arm64
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking for gsl-config... /opt/R/arm64/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pics.c -o pics.o
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
double chiSum, etaF, etaR, dd, cc;
^
pics.c:1301:3: warning: variable 'penalty' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
pics.c:1307:97: note: uninitialized use occurs here
bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
^~~~~~~
pics.c:1275:42: note: initialize the variable 'penalty' to silence this warning
double bic, tmp, muF[K], muR[K], penalty, distance;
^
= 0.0
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
6 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c segment.c -o segment.o
segment.c:406:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
pp++;
^
segment.c:395:27: note: incremented here
for (pp=start; pp<=p; pp++) {
^
segment.c:536:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
pp++;
^
segment.c:525:27: note: incremented here
for (pp=start; pp<=p; pp++) {
^
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
SEXP ans, x, y, chr, names;
^
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
SEXP filter1;
^
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
^
5 warnings generated.
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 PICS.so pics.o segment.o -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/PICS.buildbin-libdir/00LOCK-PICS/00new/PICS/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 (PICS)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR PICS.buildbin-libdir/PICS/libs/PICS.so
>>>>>>>
>>>>>>> Paths before fix:
PICS.buildbin-libdir/PICS/libs/PICS.so:
PICS.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "PICS.buildbin-libdir/PICS/libs/PICS.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "PICS.buildbin-libdir/PICS/libs/PICS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "PICS.buildbin-libdir/PICS/libs/PICS.so"
>>>>>>> Paths after fix:
PICS.buildbin-libdir/PICS/libs/PICS.so:
PICS.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
