############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf puma.buildbin-libdir && mkdir puma.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh puma_3.47.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R puma.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=puma.buildbin-libdir puma_3.47.0.tar.gz' >>>>>>> * installing *source* package ‘puma’ ... ** 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 PMmultimgmos.c -o PMmultimgmos.o 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 cregistration.c -o cregistration.o 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 donlp2.c -o donlp2.o donlp2.c:471:33: warning: variable 'infiny' set but not used [-Wunused-but-set-variable] static DDOUBLE tol1,term, infiny; ^ donlp2.c:2034:1: warning: '/*' within block comment [-Wcomment] /* **************************************************************************** */ ^ donlp2.c:2707:1: warning: '/*' within block comment [-Wcomment] /* inactive ^ donlp2.c:2079:44: warning: variable 'iumin' set but not used [-Wunused-but-set-variable] static DDOUBLE delsig,delx,sum,term, iumin; ^ 4 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 gme.c -o gme.o gme.c:266:9: warning: variable 'fstart' set but not used [-Wunused-but-set-variable] double fstart; ^ 1 warning 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 ipplr_c.c -o ipplr_c.o ipplr_c.c:255:118: warning: '&&' within '||' [-Wlogical-op-parentheses] while((fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps)||(fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps)&& (n<2000)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ ipplr_c.c:255:118: note: place parentheses around the '&&' expression to silence this warning while((fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps)||(fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps)&& (n<2000)) ^ ( ) 1 warning 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 multimgmos.c -o multimgmos.o multimgmos.c:893:95: warning: suggest braces around initialization of subobject [-Wmissing-braces] double alphaii[MAX_NUM_COND]={0.0}, s1[MAX_NUM_COND]={0.0}, s2[MAX_NUM_PROBE][MAX_NUM_COND]={0.0}, c, d_mmgmos, t1, s3, s4; ^~~ { } 1 warning 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 newx.c -o newx.o 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 pplr_c.c -o pplr_c.o pplr_c.c:185:65: warning: unused variable 'x_temp' [-Wunused-variable] double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND]; ^ 1 warning 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 pumaclust_c.c -o pumaclust_c.o pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] while (foptold-fopt > abs(in_param.eps*fopt)) ^ pumaclust_c.c:181:24: note: use function 'fabs' instead while (foptold-fopt > abs(in_param.eps*fopt)) ^~~ fabs 1 warning 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 pumaclustii_c.c -o pumaclustii_c.o pumaclustii_c.c:255:42: warning: variable 'temp2' set but not used [-Wunused-but-set-variable] double *exprs=NULL, *vars=NULL, temp, *temp2, temp3, **t3=NULL, *t4=NULL; ^ 1 warning 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 user_eval.c -o user_eval.o 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 puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/puma.buildbin-libdir/00LOCK-puma/00new/puma/libs ** R ** data ** demo ** 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 (puma) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR puma.buildbin-libdir/puma/libs/puma.so >>>>>>> >>>>>>> Paths before fix: puma.buildbin-libdir/puma/libs/puma.so: puma.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "puma.buildbin-libdir/puma/libs/puma.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "puma.buildbin-libdir/puma/libs/puma.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "puma.buildbin-libdir/puma/libs/puma.so" >>>>>>> Paths after fix: puma.buildbin-libdir/puma/libs/puma.so: puma.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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)