############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gmapR ### ############################################################################## ############################################################################## * checking for file ‘gmapR/DESCRIPTION’ ... OK * preparing ‘gmapR’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘gmapR’ ... ** using staged installation ** libs ** arch - cd gstruct/; \ CFLAGS="-g -O3" \ ./configure --enable-static --disable-shared \ --prefix=/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr --includedir=/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/include/gstruct \ --libdir=/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/lib \ --with-samtools-lib=/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/samtools \ --disable-maintainer-mode \ --disable-binaries checking package version... 2017-01-01 checking whether to enable maintainer-specific portions of Makefiles... no loading default site script ./config.site checking CFLAGS... -g -O3 checking build system type... arm-apple-darwin22.1.0 checking host system type... arm-apple-darwin22.1.0 checking target system type... arm-apple-darwin22.1.0 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... rm: conftest.dSYM: is a directory yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... config/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 for style of include used by make... GNU checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking bindir... /private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/bin checking whether to link statically... not specified so disabled by default checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes 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 arm-apple-darwin22.1.0 file names to arm-apple-darwin22.1.0 format... func_convert_file_noop checking how to convert arm-apple-darwin22.1.0 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... darwin22.1.0 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 for X... libraries /usr/X11/lib, headers checking whether -R must be followed by a space... neither works checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for qsub... no checking gmap program directory... checking for get-genome... false checking for iit_store... false checking for iit_get... false checking for gmap_build... false checking for gmap... false checking for gsnap... false checking for sam_sort... false checking for uniqscan... false checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... -D_THREAD_SAFE checking for cc_r... gcc checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking for working mmap with MAP_FIXED... no checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... yes checking for sigaction... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... yes checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for builtin popcount/clz/ctz features... not specified so enabled by default ./configure: line 16917: ACX_BUILTIN_POPCOUNT: command not found checking for bsr instruction in assembly... no checking whether sse2 is enabled... not specified so enabled by default checking compiler is defective and requires an immediate in sse2 shift commands... yes checking whether ssse3 is enabled... not specified so enabled by default checking whether sse4.1 is enabled... not specified so enabled by default checking whether sse4.2 is enabled... not specified so enabled by default checking whether avx is enabled... not specified so enabled by default checking whether avx2 is enabled... not specified so enabled by default checking whether simd is enabled... not specified so enabled by default checking gmapdb... /private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share checking whether to make binaries... disabled checking for zlib support... enabled checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for samtools program... checking for samtools library... provided by --with-samtools-lib checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating lib/gstruct-1.0.pc config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: WARNING: You don't seem to have gsnap specified. checking Standard compiler and flags to be used... gcc -g -O3 checking Standard linker flags to be used... checking pthread compiler flags to be used... -D_THREAD_SAFE checking popcnt compiler flags to be used... checking SIMD features available on computer... checking SIMD compiler flags to be used... cd gstruct; \ make install Making install in src /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c -o 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-DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c assert.c -o libgstruct_1.0_la-assert.o mv -f .deps/libgstruct_1.0_la-assert.Tpo .deps/libgstruct_1.0_la-assert.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c -o libgstruct_1.0_la-mem.lo `test -f 'mem.c' || echo './'`mem.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c mem.c -o libgstruct_1.0_la-mem.o mv -f .deps/libgstruct_1.0_la-mem.Tpo .deps/libgstruct_1.0_la-mem.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c -o libgstruct_1.0_la-intlist.lo `test -f 'intlist.c' || echo './'`intlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c intlist.c -o libgstruct_1.0_la-intlist.o mv -f .deps/libgstruct_1.0_la-intlist.Tpo .deps/libgstruct_1.0_la-intlist.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c -o libgstruct_1.0_la-list.lo `test -f 'list.c' || echo './'`list.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c list.c -o libgstruct_1.0_la-list.o mv -f .deps/libgstruct_1.0_la-list.Tpo .deps/libgstruct_1.0_la-list.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c -o libgstruct_1.0_la-littleendian.lo `test -f 'littleendian.c' || echo './'`littleendian.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c littleendian.c -o libgstruct_1.0_la-littleendian.o mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c -o libgstruct_1.0_la-bigendian.lo `test -f 'bigendian.c' || echo './'`bigendian.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" 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libgstruct_1.0_la-interval.o mv -f .deps/libgstruct_1.0_la-interval.Tpo .deps/libgstruct_1.0_la-interval.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c -o libgstruct_1.0_la-uintlist.lo `test -f 'uintlist.c' || echo './'`uintlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c uintlist.c -o libgstruct_1.0_la-uintlist.o mv -f .deps/libgstruct_1.0_la-uintlist.Tpo .deps/libgstruct_1.0_la-uintlist.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c -o libgstruct_1.0_la-stopwatch.lo `test -f 'stopwatch.c' || echo './'`stopwatch.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c stopwatch.c -o libgstruct_1.0_la-stopwatch.o mv -f .deps/libgstruct_1.0_la-stopwatch.Tpo .deps/libgstruct_1.0_la-stopwatch.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c -o libgstruct_1.0_la-access.lo `test -f 'access.c' || echo './'`access.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"arm-apple-darwin22.1.0\" -DGMAPDB=\"/private/tmp/RtmpvhZixh/Rbuild6f1a783e2295/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c access.c -o libgstruct_1.0_la-access.o access.c:59:7: error: implicit declaration of function 'stat64' is invalid in C99 [-Werror,-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c:59:7: note: did you mean 'stat'? /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stat.h:386:9: note: 'stat' declared here int stat(const char *, struct stat *) __DARWIN_INODE64(stat); ^ access.c:79:3: error: implicit declaration of function 'stat64' is invalid in C99 [-Werror,-Wimplicit-function-declaration] stat64(filename,&sb); ^ 2 errors generated. make[2]: *** [libgstruct_1.0_la-access.lo] Error 1 make[1]: *** [install-recursive] Error 1 make: *** [gstruct] Error 2 ERROR: compilation failed for package ‘gmapR’ * removing ‘/private/tmp/RtmpvhZixh/Rinst6f1a3750a1df/gmapR’ ----------------------------------- ERROR: package installation failed