############################################################################## ############################################################################## ### ### 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’ ... ** this is package ‘gmapR’ version ‘1.51.0’ ** using staged installation ** libs cd gstruct/; \ ./configure --enable-static --disable-shared \ --prefix=/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr --includedir=/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include/gstruct \ --libdir=/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib \ --with-samtools-lib=/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/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... not set by user so using default -O3 checking build system type... aarch64-apple-darwin22.6.0 checking host system type... aarch64-apple-darwin22.6.0 checking target system type... aarch64-apple-darwin22.6.0 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for gcc option to enable large file support... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 2 checking whether build environment is sane... yes checking for a race-free mkdir -p... mkdir -p 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 the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... gcc3 checking bindir... /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/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 the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (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 aarch64-apple-darwin22.6.0 file names to aarch64-apple-darwin22.6.0 format... func_convert_file_noop checking how to convert aarch64-apple-darwin22.6.0 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 file... file 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 ranlib... ranlib checking for ar... ar checking for archiver @FILE support... no checking for strip... strip 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... ld: warning: -single_module is obsolete no checking for -no_fixup_chains linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.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... darwin22.6.0 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... gcc -E checking for X... libraries /usr/X11/lib, headers /usr/X11/include 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 dirent.h that defines DIR... yes checking for library containing opendir... none required checking for fcntl.h... yes checking for limits.h... 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 declarations of fseeko and ftello... yes checking for working mmap with MAP_FIXED... yes 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 19293: 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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share checking whether to make binaries... disabled checking for zlib support... enabled 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 -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 CC="clang -arch arm64 -std=gnu2x" install Making install in src /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-except.lo -MD 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-DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -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 clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -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: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c bigendian.c -o libgstruct_1.0_la-bigendian.o mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c -o libgstruct_1.0_la-interval.lo `test -f 'interval.c' || echo './'`interval.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c interval.c -o 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 clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -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: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -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 clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -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: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -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 clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -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: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -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 mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c -o libgstruct_1.0_la-iit-read.lo `test -f 'iit-read.c' || echo './'`iit-read.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c iit-read.c -o libgstruct_1.0_la-iit-read.o iit-read.c:1611:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1611:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1638:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1638:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1650:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1650:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1672:21: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,divno,offset,filesize); ^~~~~~ iit-read.c:1672:28: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,divno,offset,filesize); ^~~~~~~~ iit-read.c:1693:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1693:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1742:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1742:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1779:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1779:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:1810:25: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (new->version >= 2 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)+sizeof(int)) { ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1810:25: note: use '&' for a bitwise operation if (new->version >= 2 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)+sizeof(int)) { ^~ & iit-read.c:1810:25: note: remove constant to silence this warning if (new->version >= 2 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)+sizeof(int)) { ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1812:32: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] } else if (new->version <= 1 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)) { ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1812:32: note: use '&' for a bitwise operation } else if (new->version <= 1 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)) { ^~ & iit-read.c:1812:32: note: remove constant to silence this warning } else if (new->version <= 1 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)) { ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1834:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:1834:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2344:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2344:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2360:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2360:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2372:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2372:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2381:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2381:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2408:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2408:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2429:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2429:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2446:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2446:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2466:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2466:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2495:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2495:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2608:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2608:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2626:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2626:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2643:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2643:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2652:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2652:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2681:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2681:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2702:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2702:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2719:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2719:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2744:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2744:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2770:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2770:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:2823:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:2823:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3010:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3010:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3026:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3026:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3043:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3043:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3052:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3052:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3081:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3081:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3107:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3107:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3124:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3124:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3149:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3149:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3175:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3175:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ iit-read.c:3220:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~ iit-read.c:3220:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filename,offset,filesize); ^~~~~~~~ 76 warnings generated. mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c -o libgstruct_1.0_la-chrom.lo `test -f 'chrom.c' || echo './'`chrom.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c chrom.c -o libgstruct_1.0_la-chrom.o chrom.c:108:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/libgstruct_1.0_la-chrom.Tpo .deps/libgstruct_1.0_la-chrom.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c -o libgstruct_1.0_la-genomicpos.lo `test -f 'genomicpos.c' || echo './'`genomicpos.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c genomicpos.c -o libgstruct_1.0_la-genomicpos.o mv -f .deps/libgstruct_1.0_la-genomicpos.Tpo .deps/libgstruct_1.0_la-genomicpos.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c -o libgstruct_1.0_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c md5.c -o libgstruct_1.0_la-md5.o mv -f .deps/libgstruct_1.0_la-md5.Tpo .deps/libgstruct_1.0_la-md5.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c -o libgstruct_1.0_la-sequence.lo `test -f 'sequence.c' || echo './'`sequence.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c sequence.c -o libgstruct_1.0_la-sequence.o mv -f .deps/libgstruct_1.0_la-sequence.Tpo .deps/libgstruct_1.0_la-sequence.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC 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-DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo `test -f 'translation.c' || echo './'`translation.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o mv -f .deps/libgstruct_1.0_la-translation.Tpo .deps/libgstruct_1.0_la-translation.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c -o libgstruct_1.0_la-expr.lo `test -f 'expr.c' || echo './'`expr.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c expr.c -o libgstruct_1.0_la-expr.o mv -f .deps/libgstruct_1.0_la-expr.Tpo .deps/libgstruct_1.0_la-expr.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo `test -f 'bamtally.c' || echo './'`bamtally.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o mv -f .deps/libgstruct_1.0_la-bamtally.Tpo .deps/libgstruct_1.0_la-bamtally.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c -o libgstruct_1.0_la-datadir.lo `test -f 'datadir.c' || echo './'`datadir.c libtool: compile: clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c datadir.c -o libgstruct_1.0_la-datadir.o mv -f .deps/libgstruct_1.0_la-datadir.Tpo .deps/libgstruct_1.0_la-datadir.Plo /bin/sh ../libtool --tag=CC --mode=link clang -arch arm64 -std=gnu2x -D_THREAD_SAFE -I. -fPIC -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -version-info 1:0:0 -o libgstruct-1.0.la -rpath /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib libgstruct_1.0_la-except.lo libgstruct_1.0_la-assert.lo libgstruct_1.0_la-mem.lo libgstruct_1.0_la-intlist.lo libgstruct_1.0_la-list.lo libgstruct_1.0_la-littleendian.lo libgstruct_1.0_la-bigendian.lo libgstruct_1.0_la-interval.lo libgstruct_1.0_la-uintlist.lo libgstruct_1.0_la-stopwatch.lo libgstruct_1.0_la-access.lo libgstruct_1.0_la-iit-read.lo libgstruct_1.0_la-chrom.lo libgstruct_1.0_la-genomicpos.lo libgstruct_1.0_la-md5.lo libgstruct_1.0_la-sequence.lo libgstruct_1.0_la-genome.lo libgstruct_1.0_la-uinttable.lo libgstruct_1.0_la-table.lo libgstruct_1.0_la-chrnum.lo libgstruct_1.0_la-bamread.lo libgstruct_1.0_la-samread.lo libgstruct_1.0_la-parserange.lo libgstruct_1.0_la-tableuint.lo libgstruct_1.0_la-iit-write.lo libgstruct_1.0_la-ucharlist.lo libgstruct_1.0_la-matchpool.lo libgstruct_1.0_la-mismatchpool.lo libgstruct_1.0_la-tally.lo libgstruct_1.0_la-translation.lo libgstruct_1.0_la-expr.lo libgstruct_1.0_la-bamtally.lo libgstruct_1.0_la-datadir.lo -lz -lm libtool: link: ar cr .libs/libgstruct-1.0.a libgstruct_1.0_la-except.o libgstruct_1.0_la-assert.o libgstruct_1.0_la-mem.o libgstruct_1.0_la-intlist.o libgstruct_1.0_la-list.o libgstruct_1.0_la-littleendian.o libgstruct_1.0_la-bigendian.o libgstruct_1.0_la-interval.o libgstruct_1.0_la-uintlist.o libgstruct_1.0_la-stopwatch.o libgstruct_1.0_la-access.o libgstruct_1.0_la-iit-read.o libgstruct_1.0_la-chrom.o libgstruct_1.0_la-genomicpos.o libgstruct_1.0_la-md5.o libgstruct_1.0_la-sequence.o libgstruct_1.0_la-genome.o libgstruct_1.0_la-uinttable.o libgstruct_1.0_la-table.o libgstruct_1.0_la-chrnum.o libgstruct_1.0_la-bamread.o libgstruct_1.0_la-samread.o libgstruct_1.0_la-parserange.o libgstruct_1.0_la-tableuint.o libgstruct_1.0_la-iit-write.o libgstruct_1.0_la-ucharlist.o libgstruct_1.0_la-matchpool.o libgstruct_1.0_la-mismatchpool.o libgstruct_1.0_la-tally.o libgstruct_1.0_la-translation.o libgstruct_1.0_la-expr.o libgstruct_1.0_la-bamtally.o libgstruct_1.0_la-datadir.o libtool: link: ranlib .libs/libgstruct-1.0.a libtool: link: ( cd ".libs" && rm -f "libgstruct-1.0.la" && ln -s "../libgstruct-1.0.la" "libgstruct-1.0.la" ) mkdir -p '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libgstruct-1.0.la '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib' libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib/libgstruct-1.0.la libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: chmod 644 /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: ranlib /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib/libgstruct-1.0.a mkdir -p '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include/gstruct' /usr/bin/install -c -m 644 config.h fopen.h bool.h types.h except.h assert.h mem.h intlistdef.h intlist.h listdef.h list.h littleendian.h bigendian.h interval.h uintlist.h stopwatch.h access.h iitdef.h iit-read.h chrom.h genomicpos.h md5.h complement.h sequence.h genome.h uinttable.h table.h chrnum.h bamread.h samread.h parserange.h dynprog.h dynprog_nogap.h dynprog_simd.h dynprog_cigar.h dynprog_single.h tableuint.h iit-write.h ucharlist.h matchdef.h '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include/gstruct' /usr/bin/install -c -m 644 matchpool.h mismatchdef.h mismatchpool.h tally.h translation.h bamtally.h datadir.h '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include/gstruct' mkdir -p '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib/pkgconfig' /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib/pkgconfig' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bamreader.c -o bamreader.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bamtally.c -o bamtally.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c iit.c -o iit.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c variantsummary.c -o variantsummary.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genome.c -o genome.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/include -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_gmapR.c -o R_init_gmapR.o clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz -F/Library/Frameworks/R.framework/.. -framework R cd gmap/; \ ./configure --with-gmapdb= --prefix=/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr \ --libdir=/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/lib --disable-maintainer-mode checking package version... 2013-11-01 checking whether to enable maintainer-specific portions of Makefiles... no checking CONFIG_SITE... ./config.site loading script ./config.site checking CFLAGS... not set by user so using default -O3 checking build system type... aarch64-apple-darwin22.6.0 checking host system type... aarch64-apple-darwin22.6.0 checking target system type... 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default checking whether simd is enabled... not specified so enabled by default checking gmapdb... /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share checking MAX_READLENGTH... 250 checking for zlib support... enabled 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 bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking for goby library... disabled 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 util/Makefile config.status: creating util/gmap_compress.pl config.status: creating util/gmap_uncompress.pl config.status: creating util/gmap_process.pl config.status: creating util/gmap_setup.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_reassemble.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands cd gmap; \ make CC="clang -arch arm64 -std=gnu2x" install Making install in src clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-except.o -MD -MP -MF .deps/gmap-except.Tpo -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmap-except.Tpo .deps/gmap-except.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-assert.o -MD -MP -MF .deps/gmap-assert.Tpo -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmap-assert.Tpo .deps/gmap-assert.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-mem.o -MD -MP -MF .deps/gmap-mem.Tpo -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmap-mem.Tpo .deps/gmap-mem.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intlist.o -MD -MP -MF .deps/gmap-intlist.Tpo -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmap-intlist.Tpo .deps/gmap-intlist.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-list.o -MD -MP -MF .deps/gmap-list.Tpo -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmap-list.Tpo .deps/gmap-list.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-littleendian.o -MD -MP -MF .deps/gmap-littleendian.Tpo -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gmap-littleendian.Tpo .deps/gmap-littleendian.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bigendian.o -MD -MP -MF .deps/gmap-bigendian.Tpo -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gmap-bigendian.Tpo .deps/gmap-bigendian.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-univinterval.o -MD -MP -MF .deps/gmap-univinterval.Tpo -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~ %u univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu %lu %d",this->low,this->high,this->type); ~~~ ^~~~~~~~~~ %u 2 warnings generated. mv -f .deps/gmap-univinterval.Tpo .deps/gmap-univinterval.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-interval.o -MD -MP -MF .deps/gmap-interval.Tpo -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmap-interval.Tpo .deps/gmap-interval.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uintlist.o -MD -MP -MF .deps/gmap-uintlist.Tpo -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmap-uintlist.Tpo .deps/gmap-uintlist.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stopwatch.o -MD -MP -MF .deps/gmap-stopwatch.Tpo -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmap-stopwatch.Tpo .deps/gmap-stopwatch.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-access.o -MD -MP -MF .deps/gmap-access.Tpo -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c access.c:338:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:338:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] length,length,errno,strerror(errno)); ^~~~~~ access.c:403:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:473:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ access.c:536:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:621:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat] *len,length,errno,strerror(errno)); ^~~~~~ 6 warnings generated. mv -f .deps/gmap-access.Tpo .deps/gmap-access.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read-univ.o -MD -MP -MF .deps/gmap-iit-read-univ.Tpo -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf(" %lu..%lu",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~~~ %u iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("%lu..%lu\t",startpos,endpos); ~~~ ^~~~~~ %u iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~ %u iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",endpos+1U,startpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~~~ %u iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] printf("%lu..%lu\t",startpos+1U,endpos+1U); ~~~ ^~~~~~~~~ %u 10 warnings generated. mv -f .deps/gmap-iit-read-univ.Tpo .deps/gmap-iit-read-univ.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read.o -MD -MP -MF .deps/gmap-iit-read.Tpo -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c iit-read.c:1683:25: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] if (new->version >= 2 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)+sizeof(int)) { ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1683:25: note: use '&' for a bitwise operation if (new->version >= 2 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)+sizeof(int)) { ^~ & iit-read.c:1683:25: note: remove constant to silence this warning if (new->version >= 2 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)+sizeof(int)) { ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1685:32: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand] } else if (new->version <= 1 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)) { ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1685:32: note: use '&' for a bitwise operation } else if (new->version <= 1 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)) { ^~ & iit-read.c:1685:32: note: remove constant to silence this warning } else if (new->version <= 1 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)) { ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. mv -f .deps/gmap-iit-read.Tpo .deps/gmap-iit-read.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-md5.o -MD -MP -MF .deps/gmap-md5.Tpo -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gmap-md5.Tpo .deps/gmap-md5.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bzip2.o -MD -MP -MF .deps/gmap-bzip2.Tpo -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmap-bzip2.Tpo .deps/gmap-bzip2.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-sequence.o -MD -MP -MF .deps/gmap-sequence.Tpo -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmap-sequence.Tpo .deps/gmap-sequence.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-reader.o -MD -MP -MF .deps/gmap-reader.Tpo -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gmap-reader.Tpo .deps/gmap-reader.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genomicpos.o -MD -MP -MF .deps/gmap-genomicpos.Tpo -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmap-genomicpos.Tpo .deps/gmap-genomicpos.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress.o -MD -MP -MF .deps/gmap-compress.Tpo -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmap-compress.Tpo .deps/gmap-compress.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress-write.o -MD -MP -MF .deps/gmap-compress-write.Tpo -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ~~~ ^~~~~~~~~~ %u compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] Buffer[i],position+i); ^~~~~~~~~~ 3 warnings generated. mv -f .deps/gmap-compress-write.Tpo .deps/gmap-compress-write.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gbuffer.o -MD -MP -MF .deps/gmap-gbuffer.Tpo -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gmap-gbuffer.Tpo .deps/gmap-gbuffer.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome.o -MD -MP -MF .deps/gmap-genome.Tpo -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ~~~ ^~~~ %u 4 warnings generated. mv -f .deps/gmap-genome.Tpo .deps/gmap-genome.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_hr.o -MD -MP -MF .deps/gmap-genome_hr.Tpo -c -o gmap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmap-genome_hr.Tpo .deps/gmap-genome_hr.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_sites.o -MD -MP -MF .deps/gmap-genome_sites.Tpo -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/gmap-genome_sites.Tpo .deps/gmap-genome_sites.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome-write.o -MD -MP -MF .deps/gmap-genome-write.Tpo -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~~ %u genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~ %u genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~~~ %u genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ~~~ ^~~~~~~~~~~~~~~ %u genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~~~ genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] accession,startposition,endposition,fileroot); ^~~~~~~~~~~ genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~~~ genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] accession,startposition+1U,endposition+1U,fileroot); ^~~~~~~~~~~~~~ genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ~~~ ^~~~~~~~~~~~ %u 17 warnings generated. mv -f .deps/gmap-genome-write.Tpo .deps/gmap-genome-write.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bitpack64-read.o -MD -MP -MF .deps/gmap-bitpack64-read.Tpo -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmap-bitpack64-read.Tpo .deps/gmap-bitpack64-read.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb.o -MD -MP -MF .deps/gmap-indexdb.Tpo -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] filenames->positions_filename,end0*sizeof(Univcoord_T),filesize); ^~~~~~~~ indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~ indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat] ptr,sizeof(Univcoord_T),offset); ^~~~~~ indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL, ~~~ ^~~~~~~~~~~~~~ %llu 7 warnings generated. mv -f .deps/gmap-indexdb.Tpo .deps/gmap-indexdb.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb_hr.o -MD -MP -MF .deps/gmap-indexdb_hr.Tpo -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/gmap-indexdb_hr.Tpo .deps/gmap-indexdb_hr.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligo.o -MD -MP -MF .deps/gmap-oligo.Tpo -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gmap-oligo.Tpo .deps/gmap-oligo.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-block.o -MD -MP -MF .deps/gmap-block.Tpo -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c mv -f .deps/gmap-block.Tpo .deps/gmap-block.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrom.o -MD -MP -MF .deps/gmap-chrom.Tpo -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c:116:15: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while (p != '\0' && *p >= '0' && *p <= '9') { ^~~~ (void *)0 1 warning generated. mv -f .deps/gmap-chrom.Tpo .deps/gmap-chrom.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-segmentpos.o -MD -MP -MF .deps/gmap-segmentpos.Tpo -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gmap-segmentpos.Tpo .deps/gmap-segmentpos.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrnum.o -MD -MP -MF .deps/gmap-chrnum.Tpo -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gmap-chrnum.Tpo .deps/gmap-chrnum.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrsubset.o -MD -MP -MF .deps/gmap-chrsubset.Tpo -c -o gmap-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/gmap-chrsubset.Tpo .deps/gmap-chrsubset.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uinttable.o -MD -MP -MF .deps/gmap-uinttable.Tpo -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c mv -f .deps/gmap-uinttable.Tpo .deps/gmap-uinttable.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gregion.o -MD -MP -MF .deps/gmap-gregion.Tpo -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c mv -f .deps/gmap-gregion.Tpo .deps/gmap-gregion.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-match.o -MD -MP -MF .deps/gmap-match.Tpo -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c mv -f .deps/gmap-match.Tpo .deps/gmap-match.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-matchpool.o -MD -MP -MF .deps/gmap-matchpool.Tpo -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c mv -f .deps/gmap-matchpool.Tpo .deps/gmap-matchpool.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagnostic.o -MD -MP -MF .deps/gmap-diagnostic.Tpo -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c mv -f .deps/gmap-diagnostic.Tpo .deps/gmap-diagnostic.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage1.o -MD -MP -MF .deps/gmap-stage1.Tpo -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c mv -f .deps/gmap-stage1.Tpo .deps/gmap-stage1.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diag.o -MD -MP -MF .deps/gmap-diag.Tpo -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gmap-diag.Tpo .deps/gmap-diag.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagpool.o -MD -MP -MF .deps/gmap-diagpool.Tpo -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gmap-diagpool.Tpo .deps/gmap-diagpool.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cmet.o -MD -MP -MF .deps/gmap-cmet.Tpo -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gmap-cmet.Tpo .deps/gmap-cmet.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-atoi.o -MD -MP -MF .deps/gmap-atoi.Tpo -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gmap-atoi.Tpo .deps/gmap-atoi.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-orderstat.o -MD -MP -MF .deps/gmap-orderstat.Tpo -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gmap-orderstat.Tpo .deps/gmap-orderstat.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligoindex_hr.o -MD -MP -MF .deps/gmap-oligoindex_hr.Tpo -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gmap-oligoindex_hr.Tpo .deps/gmap-oligoindex_hr.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intron.o -MD -MP -MF .deps/gmap-intron.Tpo -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gmap-intron.Tpo .deps/gmap-intron.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent.o -MD -MP -MF .deps/gmap-maxent.Tpo -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gmap-maxent.Tpo .deps/gmap-maxent.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent_hr.o -MD -MP -MF .deps/gmap-maxent_hr.Tpo -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gmap-maxent_hr.Tpo .deps/gmap-maxent_hr.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pair.o -MD -MP -MF .deps/gmap-pair.Tpo -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c:2419:24: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^ pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative sprintf(token,"N%u",abs(intron_end - intron_start) + 1); ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ pair.c:4651:17: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] genome_gap = abs(intron_end - intron_start) + 1; ^ pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative genome_gap = abs(intron_end - intron_start) + 1; ^~~ 2 warnings generated. mv -f .deps/gmap-pair.Tpo .deps/gmap-pair.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pairpool.o -MD -MP -MF .deps/gmap-pairpool.Tpo -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gmap-pairpool.Tpo .deps/gmap-pairpool.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cellpool.o -MD -MP -MF .deps/gmap-cellpool.Tpo -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gmap-cellpool.Tpo .deps/gmap-cellpool.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage2.o -MD -MP -MF .deps/gmap-stage2.Tpo -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c stage2.c:1329:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ stage2.c:1812:19: warning: taking the absolute value of unsigned type 'Chrpos_T' (aka 'unsigned int') has no effect [-Wabsolute-value] diffdistance = abs(gendistance - querydistance); ^ stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative diffdistance = abs(gendistance - querydistance); ^~~ 2 warnings generated. mv -f .deps/gmap-stage2.Tpo .deps/gmap-stage2.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-doublelist.o -MD -MP -MF .deps/gmap-doublelist.Tpo -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gmap-doublelist.Tpo .deps/gmap-doublelist.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-smooth.o -MD -MP -MF .deps/gmap-smooth.Tpo -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gmap-smooth.Tpo .deps/gmap-smooth.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicestringpool.o -MD -MP -MF .deps/gmap-splicestringpool.Tpo -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gmap-splicestringpool.Tpo .deps/gmap-splicestringpool.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie_build.o -MD -MP -MF .deps/gmap-splicetrie_build.Tpo -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/gmap-splicetrie_build.Tpo .deps/gmap-splicetrie_build.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie.o -MD -MP -MF .deps/gmap-splicetrie.Tpo -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gmap-splicetrie.Tpo .deps/gmap-splicetrie.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-boyer-moore.o -MD -MP -MF .deps/gmap-boyer-moore.Tpo -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gmap-boyer-moore.Tpo .deps/gmap-boyer-moore.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-dynprog.o -MD -MP -MF .deps/gmap-dynprog.Tpo -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gmap-dynprog.Tpo .deps/gmap-dynprog.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-translation.o -MD -MP -MF .deps/gmap-translation.Tpo -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gmap-translation.Tpo .deps/gmap-translation.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pbinom.o -MD -MP -MF .deps/gmap-pbinom.Tpo -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gmap-pbinom.Tpo .deps/gmap-pbinom.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-changepoint.o -MD -MP -MF .deps/gmap-changepoint.Tpo -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gmap-changepoint.Tpo .deps/gmap-changepoint.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage3.o -MD -MP -MF .deps/gmap-stage3.Tpo -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gmap-stage3.Tpo .deps/gmap-stage3.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-request.o -MD -MP -MF .deps/gmap-request.Tpo -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gmap-request.Tpo .deps/gmap-request.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-result.o -MD -MP -MF .deps/gmap-result.Tpo -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c mv -f .deps/gmap-result.Tpo .deps/gmap-result.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-inbuffer.o -MD -MP -MF .deps/gmap-inbuffer.Tpo -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gmap-inbuffer.Tpo .deps/gmap-inbuffer.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-samheader.o -MD -MP -MF .deps/gmap-samheader.Tpo -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gmap-samheader.Tpo .deps/gmap-samheader.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-outbuffer.o -MD -MP -MF .deps/gmap-outbuffer.Tpo -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gmap-outbuffer.Tpo .deps/gmap-outbuffer.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chimera.o -MD -MP -MF .deps/gmap-chimera.Tpo -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gmap-chimera.Tpo .deps/gmap-chimera.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-datadir.o -MD -MP -MF .deps/gmap-datadir.Tpo -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gmap-datadir.Tpo .deps/gmap-datadir.Po clang -arch arm64 -std=gnu2x -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"aarch64-apple-darwin22.6.0\" -DGMAPDB=\"/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rbuild14f567914980b/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt.o -MD -MP -MF .deps/gmap-getopt.Tpo -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c getopt.c:208:11: error: unknown type name 'str' my_index (str, chr) ^ getopt.c:208:16: error: unknown type name 'chr'; did you mean 'char'? my_index (str, chr) ^~~ char getopt.c:208:20: error: expected ';' after top level declarator my_index (str, chr) ^ ; getopt.c:211:1: error: expected identifier or '(' { ^ getopt.c:291:11: error: unknown type name 'argv' exchange (argv) ^ getopt.c:291:16: error: expected ';' after top level declarator exchange (argv) ^ ; getopt.c:293:1: error: expected identifier or '(' { ^ getopt.c:376:21: error: unknown type name 'argc' _getopt_initialize (argc, argv, optstring) ^ getopt.c:376:27: error: unknown type name 'argv' _getopt_initialize (argc, argv, optstring) ^ getopt.c:376:33: error: unknown type name 'optstring' _getopt_initialize (argc, argv, optstring) ^ getopt.c:376:43: error: expected ';' after top level declarator _getopt_initialize (argc, argv, optstring) ^ ; getopt.c:378:19: error: redefinition of 'argv' with a different type: 'char *const *' vs 'char **' char *const *argv; ^ getopt.c:292:13: note: previous definition is here char **argv; ^ getopt.c:380:1: error: expected identifier or '(' { ^ getopt.c:498:19: error: unknown type name 'argc' _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:498:25: error: unknown type name 'argv' _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:498:31: error: unknown type name 'optstring' _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:498:42: error: unknown type name 'longopts' _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:498:52: error: unknown type name 'longind' _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ getopt.c:498:61: error: unknown type name 'long_only' _getopt_internal (argc, argv, optstring, longopts, longind, long_only) ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[2]: *** [gmap-getopt.o] Error 1 make[1]: *** [install-recursive] Error 1 make: *** [gmap] Error 2 ERROR: compilation failed for package ‘gmapR’ * removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpU1uxaI/Rinst14f56370a3847/gmapR’ ----------------------------------- ERROR: package installation failed