############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PICS_2.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PICS.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PICS.buildbin-libdir PICS_2.50.0.tar.gz' >>>>>>> * installing *source* package ‘PICS’ ... ** using staged installation checking for pkg-config... /opt/R/arm64/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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:1963:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] if((gsl_matrix_get(Index,kMerge,k)==1) | (gsl_matrix_get(Index,kMerge+1,k)==1)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || pics.c:1963:10: note: cast one or both operands to int to silence this warning pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable] int i=0,j=0,k=0,l=0,kMerge=0,flag=0; ^ pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable] int i=0,j=0,k=0,l=0,kMerge=0,flag=0; ^ 7 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:123:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((length(contF)>0) & (length(contR)>0)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && segment.c:123:6: note: cast one or both operands to int to silence this warning 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:1489:11: warning: unused variable 'muFilter' [-Wunused-variable] double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score; ^ segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable] SEXP filter1; ^ segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable] SEXP ans, x, y, chr, names; ^ 6 warnings generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o PICS.so pics.o segment.o -L/opt/R/arm64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/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/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /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/4.4-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/4.4-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/4.4-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/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)