############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf netresponse.buildbin-libdir && mkdir netresponse.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netresponse_1.65.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R netresponse.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=netresponse.buildbin-libdir netresponse_1.65.0.tar.gz' >>>>>>> * installing *source* package ‘netresponse’ ... ** 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 netresponse.c -o netresponse.o netresponse.c:264:15: warning: unused variable 'prior_fields' [-Wunused-variable] const char *prior_fields[]={"Mumu","S2mu", ^ netresponse.c:686:6: warning: variable 'Mumu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim1) { ^~~~ netresponse.c:713:21: note: uninitialized use occurs here vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde, ^~~~ netresponse.c:686:3: note: remove the 'if' if its condition is always true if(dim1) { ^~~~~~~~~ netresponse.c:655:15: note: initialize the variable 'Mumu' to silence this warning double *Mumu, *S2mu, *Mubar, *Mutilde, ^ = NULL netresponse.c:686:6: warning: variable 'S2mu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim1) { ^~~~ netresponse.c:713:27: note: uninitialized use occurs here vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde, ^~~~ netresponse.c:686:3: note: remove the 'if' if its condition is always true if(dim1) { ^~~~~~~~~ netresponse.c:655:22: note: initialize the variable 'S2mu' to silence this warning double *Mumu, *S2mu, *Mubar, *Mutilde, ^ = NULL netresponse.c:686:6: warning: variable 'Mubar' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim1) { ^~~~ netresponse.c:713:33: note: uninitialized use occurs here vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde, ^~~~~ netresponse.c:686:3: note: remove the 'if' if its condition is always true if(dim1) { ^~~~~~~~~ netresponse.c:655:30: note: initialize the variable 'Mubar' to silence this warning double *Mumu, *S2mu, *Mubar, *Mutilde, ^ = NULL netresponse.c:686:6: warning: variable 'Mutilde' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim1) { ^~~~ netresponse.c:713:40: note: uninitialized use occurs here vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde, ^~~~~~~ netresponse.c:686:3: note: remove the 'if' if its condition is always true if(dim1) { ^~~~~~~~~ netresponse.c:655:40: note: initialize the variable 'Mutilde' to silence this warning double *Mumu, *S2mu, *Mubar, *Mutilde, ^ = NULL netresponse.c:686:6: warning: variable 'AlphaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim1) { ^~~~ netresponse.c:714:7: note: uninitialized use occurs here AlphaKsi, BetaKsi, KsiAlpha, KsiBeta, ^~~~~~~~ netresponse.c:686:3: note: remove the 'if' if its condition is always true if(dim1) { ^~~~~~~~~ netresponse.c:656:14: note: initialize the variable 'AlphaKsi' to silence this warning *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha, ^ = NULL netresponse.c:686:6: warning: variable 'BetaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim1) { ^~~~ netresponse.c:714:17: note: uninitialized use occurs here AlphaKsi, BetaKsi, KsiAlpha, KsiBeta, ^~~~~~~ netresponse.c:686:3: note: remove the 'if' if its condition is always true if(dim1) { ^~~~~~~~~ netresponse.c:656:24: note: initialize the variable 'BetaKsi' to silence this warning *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha, ^ = NULL netresponse.c:686:6: warning: variable 'KsiAlpha' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim1) { ^~~~ netresponse.c:714:26: note: uninitialized use occurs here AlphaKsi, BetaKsi, KsiAlpha, KsiBeta, ^~~~~~~~ netresponse.c:686:3: note: remove the 'if' if its condition is always true if(dim1) { ^~~~~~~~~ netresponse.c:656:35: note: initialize the variable 'KsiAlpha' to silence this warning *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha, ^ = NULL netresponse.c:686:6: warning: variable 'KsiBeta' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim1) { ^~~~ netresponse.c:714:36: note: uninitialized use occurs here AlphaKsi, BetaKsi, KsiAlpha, KsiBeta, ^~~~~~~ netresponse.c:686:3: note: remove the 'if' if its condition is always true if(dim1) { ^~~~~~~~~ netresponse.c:656:45: note: initialize the variable 'KsiBeta' to silence this warning *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha, ^ = NULL netresponse.c:696:6: warning: variable 'U_p' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim2) { ^~~~ netresponse.c:716:7: note: uninitialized use occurs here U_p, U_hat, ^~~ netresponse.c:696:3: note: remove the 'if' if its condition is always true if(dim2) { ^~~~~~~~~ netresponse.c:656:51: note: initialize the variable 'U_p' to silence this warning *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha, ^ = NULL netresponse.c:696:6: warning: variable 'U_hat' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(dim2) { ^~~~ netresponse.c:716:12: note: uninitialized use occurs here U_p, U_hat, ^~~~~ netresponse.c:696:3: note: remove the 'if' if its condition is always true if(dim2) { ^~~~~~~~~ netresponse.c:661:14: note: initialize the variable 'U_hat' to silence this warning SEXP* U_hat; ^ = NULL 11 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 netresponse.so netresponse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/netresponse.buildbin-libdir/00LOCK-netresponse/00new/netresponse/libs ** R ** data ** 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 (netresponse) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR netresponse.buildbin-libdir/netresponse/libs/netresponse.so >>>>>>> >>>>>>> Paths before fix: netresponse.buildbin-libdir/netresponse/libs/netresponse.so: netresponse.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" "netresponse.buildbin-libdir/netresponse/libs/netresponse.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "netresponse.buildbin-libdir/netresponse/libs/netresponse.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "netresponse.buildbin-libdir/netresponse/libs/netresponse.so" >>>>>>> Paths after fix: netresponse.buildbin-libdir/netresponse/libs/netresponse.so: netresponse.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)