############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf geneXtendeR.buildbin-libdir && mkdir geneXtendeR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh geneXtendeR_1.33.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R geneXtendeR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=geneXtendeR.buildbin-libdir geneXtendeR_1.33.0.tar.gz' >>>>>>> * installing *source* package ‘geneXtendeR’ ... ** 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 annotate.c -o annotate.o annotate.c:159:94: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer)); ~~ ^~~~~~~~~~~~~~ %lu annotate.c:191:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); ~~ ^~~~~~~~~~~~~~ %lu annotate.c:199:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); ~~ ^~~~~~~~~~~~~~ %lu annotate.c:208:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); ~~ ^~~~~~~~~~~~~~ %lu annotate.c:228:97: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer)); ~~ ^~~~~~~~~~~~~~ %lu 5 warnings generated. 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 extract_number.c -o extract_number.o extract_number.c:50:12: warning: variable 'pvcfcol1_1' set but not used [-Wunused-but-set-variable] char * pvcfcol1_1; ^ extract_number.c:51:12: warning: variable 'pvcfcol2_2' set but not used [-Wunused-but-set-variable] char * pvcfcol2_2; ^ extract_number.c:52:12: warning: variable 'pvcfcol3_3' set but not used [-Wunused-but-set-variable] char * pvcfcol3_3; ^ extract_number.c:66:10: warning: variable 'j_1' set but not used [-Wunused-but-set-variable] long j_1; ^ extract_number.c:53:12: warning: variable 'pvcfcol4_4' set but not used [-Wunused-but-set-variable] char * pvcfcol4_4; ^ extract_number.c:54:12: warning: variable 'pvcfcol5_5' set but not used [-Wunused-but-set-variable] char * pvcfcol5_5; ^ extract_number.c:72:10: warning: variable 'n_1' set but not used [-Wunused-but-set-variable] long n_1; ^ 7 warnings generated. 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 extract_peaks.c -o extract_peaks.o extract_peaks.c:202:94: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer)); ~~ ^~~~~~~~~~~~~~ %lu 1 warning generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/geneXtendeR.buildbin-libdir/00LOCK-geneXtendeR/00new/geneXtendeR/libs ** R ** data *** moving datasets to lazyload DB ** 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 (geneXtendeR) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR geneXtendeR.buildbin-libdir/geneXtendeR/libs/geneXtendeR.so >>>>>>> >>>>>>> Paths before fix: geneXtendeR.buildbin-libdir/geneXtendeR/libs/geneXtendeR.so: geneXtendeR.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "geneXtendeR.buildbin-libdir/geneXtendeR/libs/geneXtendeR.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "geneXtendeR.buildbin-libdir/geneXtendeR/libs/geneXtendeR.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "geneXtendeR.buildbin-libdir/geneXtendeR/libs/geneXtendeR.so" >>>>>>> Paths after fix: geneXtendeR.buildbin-libdir/geneXtendeR/libs/geneXtendeR.so: geneXtendeR.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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)