############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL msa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘msa’ ... ** this is package ‘msa’ version ‘1.39.1’ ** 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 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c R_init_msa.cpp -o R_init_msa.o In file included from R_init_msa.cpp:3: In file included from ./Muscle/RMuscle.h:4: ./Muscle/muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from R_init_msa.cpp:3: In file included from ./Muscle/RMuscle.h:4: In file included from ./Muscle/muscle.h:38: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c SplitCharVector2List.cpp -o SplitCharVector2List.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o make --file=msaMakefile --directory=gc-8.2.2 ./configure --enable-cplusplus --enable-threads=pthreads --enable-shared=no --with-pic checking build system type... x86_64-apple-darwin21.6.0 checking host system type... x86_64-apple-darwin21.6.0 checking target system type... x86_64-apple-darwin21.6.0 checking GC version numbers... major=8 minor=2 micro=2 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking dependency style of gcc... gcc3 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 786432 checking how to convert x86_64-apple-darwin21.6.0 file names to x86_64-apple-darwin21.6.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin21.6.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin21.6.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin21.6.0 dyld checking how to hardcode library paths into programs... immediate checking for emscripten... no checking for inline... inline configure: WARNING: "Explicit GC_INIT() calls may be required." checking for pthread_self in -lpthread... yes checking for clock_gettime without additional libraries... yes checking whether compiler supports -Wextra... yes checking whether compiler supports -Wpedantic... yes checking for xlc... no checking whether compiler supports -fno-strict-aliasing... yes checking for getcontext... yes checking for dl_iterate_phdr... no checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking whether to build shared libraries... no checking which machine-dependent code should be used... checking whether AIX gcc optimization fix is necessary... no checking whether -Wno-frame-address works... yes checking for dladdr... yes checking for sigsetjmp... yes checking for pthread_setname_np... yes (w/o tid) checking sys/dg_sys_info.h usability... no checking sys/dg_sys_info.h presence... no checking for sys/dg_sys_info.h... no checking for compiler intrinsics support... yes checking which libatomic_ops to use... none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bdw-gc.pc config.status: creating include/config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing default commands make depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile -DHAVE_CONFIG_H -I./include -I./include -fexceptions -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\ mv -f $depbase.Tpo $depbase.Plo Usage: /Users/biocbuild/bbs-3.21-bioc/meat/msa/src/gc-8.2.2/libtool [OPTION]... [MODE-ARG]... Try 'libtool --help' for more information. libtool: error: unrecognised option: '-DHAVE_CONFIG_H' make[3]: *** [allchblk.lo] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [build_gc] Error 2 make: *** [build_gc] Error 2 ERROR: compilation failed for package ‘msa’ * removing ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/msa’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/msa’