############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ClassifyR_3.7.4.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ClassifyR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ClassifyR.buildbin-libdir ClassifyR_3.7.4.tar.gz' >>>>>>> * installing *source* package ‘ClassifyR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coxformatrices.cpp -o coxformatrices.o coxformatrices.cpp:23:16: warning: unused variable 'sclback2' [-Wunused-variable] double sclback2=*sctest2; ^ coxformatrices.cpp:24:16: warning: unused variable 'sclback3' [-Wunused-variable] double sclback3=*sctest3; ^ coxformatrices.cpp:81:9: warning: suggest braces around initialization of subobject [-Wmissing-braces] NULL ^~~~ { } /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/stddef.h:84:18: note: expanded from macro 'NULL' # define NULL __null ^~~~~~ coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j; ^~~~~~~~~ coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j; ^~~~~~~~~ coxformatrices.cpp:529:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register double temp; ^~~~~~~~~ coxformatrices.cpp:569:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register double temp; ^~~~~~~~~ coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j,k; ^~~~~~~~~ coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j,k; ^~~~~~~~~ coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j,k; ^~~~~~~~~ coxformatrices.cpp:656:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register double **pointer; ^~~~~~~~~ 12 warnings generated. clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ClassifyR.so coxformatrices.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/ClassifyR.buildbin-libdir/00LOCK-ClassifyR/00new/ClassifyR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘ROCplot’ with signature ‘"ClassifyResult"’: no definition for class “ClassifyResult” ** help *** installing help indices *** copying figures ** 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 (ClassifyR) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so >>>>>>> >>>>>>> Paths before fix: ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so: ClassifyR.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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /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" "ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.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" "ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.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" "ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so" >>>>>>> Paths after fix: ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so: ClassifyR.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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)