############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gaga_2.52.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gaga.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gaga.buildbin-libdir gaga_2.52.0.tar.gz' >>>>>>> * installing *source* package ‘gaga’ ... ** using staged installation ** 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 cseqdesma.c -o cseqdesma.o cseqdesma.c:4524:14: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ((*usesumx==0)) { //if suff stat not pre-computed ~~~~~~~~^~~ cseqdesma.c:4524:14: note: remove extraneous parentheses around the comparison to silence this warning if ((*usesumx==0)) { //if suff stat not pre-computed ~ ^ ~ cseqdesma.c:4524:14: note: use '=' to turn this equality comparison into an assignment if ((*usesumx==0)) { //if suff stat not pre-computed ^~ = cseqdesma.c:5836:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ((*usel==0)) { ~~~~~^~~ cseqdesma.c:5836:13: note: remove extraneous parentheses around the comparison to silence this warning if ((*usel==0)) { ~ ^ ~ cseqdesma.c:5836:13: note: use '=' to turn this equality comparison into an assignment if ((*usel==0)) { ^~ = cseqdesma.c:6070:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ((*usel==0)) { ~~~~~^~~ cseqdesma.c:6070:13: note: remove extraneous parentheses around the comparison to silence this warning if ((*usel==0)) { ~ ^ ~ cseqdesma.c:6070:13: note: use '=' to turn this equality comparison into an assignment if ((*usel==0)) { ^~ = cseqdesma.c:6340:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ((*usel==0)) { //If l values have to be generated ~~~~~^~~ cseqdesma.c:6340:13: note: remove extraneous parentheses around the comparison to silence this warning if ((*usel==0)) { //If l values have to be generated ~ ^ ~ cseqdesma.c:6340:13: note: use '=' to turn this equality comparison into an assignment if ((*usel==0)) { //If l values have to be generated ^~ = 4 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 cstat.c -o cstat.o cstat.c:26:15: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] FILE *ifile, *fopen(), *ofile; ^ cstat.c:1477:14: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype] double gamdev(); ^ ./cstat.h:172:8: note: conflicting prototype is here double gamdev(double ); ^ cstat.c:1838:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] if(abs(ndf - 2.0) < eps) { /* df ~= 2 */ ^ cstat.c:1838:6: note: use function 'fabs' instead if(abs(ndf - 2.0) < eps) { /* df ~= 2 */ ^~~ fabs cstat.c:18:19: warning: unused variable 'interface_c_sccs_id' [-Wunused-const-variable] static const char interface_c_sccs_id[] = "%W%"; ^ cstat.c:19:19: warning: unused variable 'mess_c_sccs_id' [-Wunused-const-variable] static const char mess_c_sccs_id[] = "%W%"; ^ cstat.c:20:19: warning: unused variable 'nrutil_c_sccs_id' [-Wunused-const-variable] static const char nrutil_c_sccs_id[] = "%W%"; ^ cstat.c:21:19: warning: unused variable 'vector_c_sccs_id' [-Wunused-const-variable] static const char vector_c_sccs_id[] = "%W%"; ^ cstat.c:22:19: warning: unused variable 'css_c_sccs_id' [-Wunused-const-variable] static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$"; ^ 8 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 gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/gaga.buildbin-libdir/00LOCK-gaga/00new/gaga/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 (gaga) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR gaga.buildbin-libdir/gaga/libs/gaga.so >>>>>>> >>>>>>> Paths before fix: gaga.buildbin-libdir/gaga/libs/gaga.so: gaga.so (compatibility version 0.0.0, current version 0.0.0) /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) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "gaga.buildbin-libdir/gaga/libs/gaga.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "gaga.buildbin-libdir/gaga/libs/gaga.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "gaga.buildbin-libdir/gaga/libs/gaga.so" >>>>>>> Paths after fix: gaga.buildbin-libdir/gaga/libs/gaga.so: gaga.so (compatibility version 0.0.0, current version 0.0.0) /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) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)