############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh snapCGH_1.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R snapCGH.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=snapCGH.buildbin-libdir snapCGH_1.70.0.tar.gz' >>>>>>> * installing *source* package ‘snapCGH’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optimizer.c -o optimizer.o optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1]; ^ optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1]; ^ optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^ optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1]; ^ optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^ 15 warnings generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/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 (snapCGH) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so >>>>>>> >>>>>>> Paths before fix: snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so: snapCGH.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/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) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so" >>>>>>> Paths after fix: snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so: snapCGH.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/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) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)