##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhtslib_1.10.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhtslib.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhtslib.buildbin-libdir Rhtslib_1.10.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rhtslib’ ...
** libs
rm -f *.o *.a
cd ./htslib && make distclean-recursive && cd ..
make[1]: *** No rule to make target `distclean-recursive'. Stop.
make: [clean] Error 2 (ignored)
rm -fr ./htslib/autom4te* ./htslib/config.h ./htslib/config.log ./htslib/config.status ./htslib/libtool ./htslib/lib/Makefile ./htslib/Makefile ./htslib/test/Makefile ./htslib/stamp-h1 ./htslib/cram/.deps
running configuration...
cd ./htslib/ && ./configure --disable-dependency-tracking \
--prefix="/Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib" \
CC="`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CC`" CFLAGS="`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CPICFLAGS`" \
LDFLAGS="`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS`" CPPFLAGS="`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CPPFLAGS`" CPP="`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CPP`"
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for style of include used by make... GNU
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether clang understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking dependency style of clang... none
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether _XOPEN_SOURCE should be defined... no
checking build system type... x86_64-apple-darwin15.6.0
checking host system type... x86_64-apple-darwin15.6.0
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by clang... /usr/bin/ld
checking if the linker (/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... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin15.6.0 file names to x86_64-apple-darwin15.6.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fno-common -DPIC
checking if clang PIC flag -fno-common -DPIC works... yes
checking if clang static flag -static works... no
checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin15.6.0 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... yes
checking whether to build static libraries... yes
checking for gcc... (cached) clang
checking whether we are using the GNU C compiler... (cached) yes
checking whether clang accepts -g... (cached) yes
checking for clang option to accept ISO C89... (cached) none needed
checking whether clang understands -c and -o together... (cached) yes
checking dependency style of clang... (cached) none
checking for Minix Amsterdam compiler... no
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for arpa/inet.h... yes
checking for features.h... no
checking for sys/socket.h... yes
checking for unistd.h... (cached) yes
checking for sys/time.h... yes
checking for wchar.h... yes
checking for stdint.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for netdb.h... yes
checking for sys/select.h... yes
checking for sys/stat.h... (cached) yes
checking for sys/uio.h... yes
checking whether the preprocessor supports include_next... yes
checking whether system header files limit the line length... no
checking for _set_invalid_parameter_handler... no
checking for fcntl... yes
checking for symlink... yes
checking for fsync... yes
checking for getdtablesize... yes
checking for gettimeofday... yes
checking for complete errno.h... yes
checking for working fcntl.h... no (bad O_NOATIME)
checking for pid_t... yes
checking for mode_t... yes
checking whether fdatasync is declared... no
checking whether getdtablesize is declared... yes
checking for C/C++ restrict keyword... __restrict
checking for struct timeval... yes
checking for wide-enough struct timeval.tv_sec member... yes
checking whether gettimeofday is declared without a macro... yes
checking for unsigned long long int... yes
checking for long long int... yes
checking whether stdint.h conforms to C99... no
checking sys/inttypes.h usability... no
checking sys/inttypes.h presence... no
checking for sys/inttypes.h... no
checking sys/bitypes.h usability... no
checking sys/bitypes.h presence... no
checking for sys/bitypes.h... no
checking for bit size of ptrdiff_t... 64
checking for bit size of size_t... 64
checking for bit size of sig_atomic_t... 32
checking for bit size of wchar_t... 32
checking for bit size of wint_t... 32
checking whether sig_atomic_t is signed... yes
checking whether wchar_t is signed... yes
checking whether wint_t is signed... yes
checking for ptrdiff_t integer literal suffix... l
checking for size_t integer literal suffix... ul
checking for sig_atomic_t integer literal suffix...
checking for wchar_t integer literal suffix...
checking for wint_t integer literal suffix...
checking whether imaxabs is declared without a macro... yes
checking whether imaxdiv is declared without a macro... yes
checking whether strtoimax is declared without a macro... yes
checking whether strtoumax is declared without a macro... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking whether <sys/socket.h> is self-contained... yes
checking for shutdown... yes
checking whether <sys/socket.h> defines the SHUT_* macros... yes
checking for struct sockaddr_storage... yes
checking for sa_family_t... yes
checking for struct sockaddr_storage.ss_family... yes
checking whether socket is declared without a macro... yes
checking whether connect is declared without a macro... yes
checking whether accept is declared without a macro... yes
checking whether bind is declared without a macro... yes
checking whether getpeername is declared without a macro... yes
checking whether getsockname is declared without a macro... yes
checking whether getsockopt is declared without a macro... yes
checking whether listen is declared without a macro... yes
checking whether recv is declared without a macro... yes
checking whether send is declared without a macro... yes
checking whether recvfrom is declared without a macro... yes
checking whether sendto is declared without a macro... yes
checking whether setsockopt is declared without a macro... yes
checking whether shutdown is declared without a macro... yes
checking whether accept4 is declared without a macro... no
checking for sigset_t... yes
checking for uid_t in sys/types.h... yes
checking for library containing setsockopt... none needed
checking for wchar_t... yes
checking whether ffsl is declared without a macro... yes
checking whether ffsll is declared without a macro... yes
checking whether memmem is declared without a macro... yes
checking whether mempcpy is declared without a macro... no
checking whether memrchr is declared without a macro... no
checking whether rawmemchr is declared without a macro... no
checking whether stpcpy is declared without a macro... yes
checking whether stpncpy is declared without a macro... yes
checking whether strchrnul is declared without a macro... no
checking whether strdup is declared without a macro... yes
checking whether strncat is declared without a macro... yes
checking whether strndup is declared without a macro... yes
checking whether strnlen is declared without a macro... yes
checking whether strpbrk is declared without a macro... yes
checking whether strsep is declared without a macro... yes
checking whether strcasestr is declared without a macro... yes
checking whether strtok_r is declared without a macro... yes
checking whether strerror_r is declared without a macro... yes
checking whether strsignal is declared without a macro... yes
checking whether strverscmp is declared without a macro... no
checking whether stat file-mode macros are broken... no
checking for struct timespec in <time.h>... yes
checking for alloca as a compiler built-in... yes
checking whether inet_ntop is declared without a macro... yes
checking whether inet_pton is declared without a macro... yes
checking whether dup2 works... yes
checking whether fcntl handles F_DUPFD correctly... yes
checking whether fcntl understands F_DUPFD_CLOEXEC... yes
checking whether fcntl is declared without a macro... yes
checking whether openat is declared without a macro... yes
checking for fdatasync... yes
checking whether getdtablesize works... yes
checking for getpagesize... yes
checking whether getpagesize is declared... yes
checking whether gettimeofday clobbers localtime buffer... no
checking for gettimeofday with POSIX signature... yes
checking whether INT32_MAX < INTMAX_MAX... yes
checking whether INT64_MAX == LONG_MAX... yes
checking whether UINT32_MAX < UINTMAX_MAX... yes
checking whether UINT64_MAX == ULONG_MAX... yes
checking whether getaddrinfo is declared without a macro... yes
checking whether freeaddrinfo is declared without a macro... yes
checking whether gai_strerror is declared without a macro... yes
checking whether getnameinfo is declared without a macro... yes
checking for volatile sig_atomic_t... yes
checking for sighandler_t... no
checking whether pthread_sigmask is declared without a macro... yes
checking whether sigaction is declared without a macro... yes
checking whether sigaddset is declared without a macro... yes
checking whether sigdelset is declared without a macro... yes
checking whether sigemptyset is declared without a macro... yes
checking whether sigfillset is declared without a macro... yes
checking whether sigismember is declared without a macro... yes
checking whether sigpending is declared without a macro... yes
checking whether sigprocmask is declared without a macro... yes
checking for socklen_t... yes
checking for ssize_t... yes
checking for working stdalign.h... yes
checking for max_align_t... yes
checking whether NULL can be used in arbitrary expressions... yes
checking whether _Exit is declared without a macro... yes
checking whether atoll is declared without a macro... yes
checking whether canonicalize_file_name is declared without a macro... no
checking whether getloadavg is declared without a macro... yes
checking whether getsubopt is declared without a macro... yes
checking whether grantpt is declared without a macro... yes
checking whether initstate is declared without a macro... yes
checking whether initstate_r is declared without a macro... no
checking whether mkdtemp is declared without a macro... no
checking whether mkostemp is declared without a macro... no
checking whether mkostemps is declared without a macro... no
checking whether mkstemp is declared without a macro... yes
checking whether mkstemps is declared without a macro... no
checking whether posix_openpt is declared without a macro... yes
checking whether ptsname is declared without a macro... yes
checking whether ptsname_r is declared without a macro... no
checking whether random is declared without a macro... yes
checking whether random_r is declared without a macro... no
checking whether realpath is declared without a macro... yes
checking whether rpmatch is declared without a macro... no
checking whether secure_getenv is declared without a macro... no
checking whether setenv is declared without a macro... yes
checking whether setstate is declared without a macro... yes
checking whether setstate_r is declared without a macro... no
checking whether srandom is declared without a macro... yes
checking whether srandom_r is declared without a macro... no
checking whether strtod is declared without a macro... yes
checking whether strtoll is declared without a macro... yes
checking whether strtoull is declared without a macro... yes
checking whether unlockpt is declared without a macro... yes
checking whether unsetenv is declared without a macro... yes
checking whether <sys/select.h> is self-contained... yes
checking whether pselect is declared without a macro... yes
checking whether select is declared without a macro... yes
checking for nlink_t... yes
checking whether fchmodat is declared without a macro... yes
checking whether fstat is declared without a macro... yes
checking whether fstatat is declared without a macro... yes
checking whether futimens is declared without a macro... no
checking whether lchmod is declared without a macro... yes
checking whether lstat is declared without a macro... yes
checking whether mkdirat is declared without a macro... yes
checking whether mkfifo is declared without a macro... yes
checking whether mkfifoat is declared without a macro... no
checking whether mknod is declared without a macro... yes
checking whether mknodat is declared without a macro... no
checking whether stat is declared without a macro... yes
checking whether utimensat is declared without a macro... no
checking whether chdir is declared without a macro... yes
checking whether chown is declared without a macro... yes
checking whether dup is declared without a macro... yes
checking whether dup2 is declared without a macro... yes
checking whether dup3 is declared without a macro... no
checking whether environ is declared without a macro... no
checking whether euidaccess is declared without a macro... no
checking whether faccessat is declared without a macro... yes
checking whether fchdir is declared without a macro... yes
checking whether fchownat is declared without a macro... yes
checking whether fdatasync is declared without a macro... no
checking whether fsync is declared without a macro... yes
checking whether ftruncate is declared without a macro... yes
checking whether getcwd is declared without a macro... yes
checking whether getdomainname is declared without a macro... yes
checking whether getdtablesize is declared without a macro... yes
checking whether getgroups is declared without a macro... yes
checking whether gethostname is declared without a macro... yes
checking whether getlogin is declared without a macro... yes
checking whether getlogin_r is declared without a macro... yes
checking whether getpagesize is declared without a macro... yes
checking whether getusershell is declared without a macro... yes
checking whether setusershell is declared without a macro... yes
checking whether endusershell is declared without a macro... yes
checking whether group_member is declared without a macro... no
checking whether isatty is declared without a macro... yes
checking whether lchown is declared without a macro... yes
checking whether link is declared without a macro... yes
checking whether linkat is declared without a macro... yes
checking whether lseek is declared without a macro... yes
checking whether pipe is declared without a macro... yes
checking whether pipe2 is declared without a macro... no
checking whether pread is declared without a macro... yes
checking whether pwrite is declared without a macro... yes
checking whether readlink is declared without a macro... yes
checking whether readlinkat is declared without a macro... yes
checking whether rmdir is declared without a macro... yes
checking whether sethostname is declared without a macro... yes
checking whether sleep is declared without a macro... yes
checking whether symlink is declared without a macro... yes
checking whether symlinkat is declared without a macro... yes
checking whether ttyname_r is declared without a macro... yes
checking whether unlink is declared without a macro... yes
checking whether unlinkat is declared without a macro... yes
checking whether usleep is declared without a macro... yes
checking whether ln -s works... yes
checking for library containing pthread_create... none required
checking for cos in -lm... yes
checking for zlibVersion in -lz... yes
checking alloca.h usability... yes
checking alloca.h presence... yes
checking for alloca.h... yes
checking for arpa/inet.h... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for netdb.h... (cached) yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for sys/select.h... (cached) yes
checking for sys/socket.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for sys/time.h... (cached) yes
checking for unistd.h... (cached) yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for int8_t... yes
checking for off_t... yes
checking for size_t... (cached) yes
checking for ssize_t... yes
checking for struct stat.st_blksize... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for uint8_t... yes
checking for working alloca.h... (cached) yes
checking for alloca... (cached) yes
checking for error_at_line... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for working strtod... yes
checking for atexit... yes
checking for fdatasync... (cached) yes
checking for floor... yes
checking for ftruncate... yes
checking for getcwd... yes
checking for gethostbyaddr... yes
checking for gethostbyname... yes
checking for getpagesize... (cached) yes
checking for gettimeofday... (cached) yes
checking for memmove... yes
checking for memset... yes
checking for mkdir... yes
checking for select... yes
checking for socket... yes
checking for strcasecmp... yes
checking for strchr... yes
checking for strdup... yes
checking for strerror... yes
checking for strrchr... yes
checking for strstr... yes
checking for strtol... yes
checking for strtoul... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating test/Makefile
config.status: creating lib/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
buildling library...
cd ./htslib/ && make
make all-recursive
Making all in lib
rm -f alloca.h-t alloca.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
cat ./alloca.in.h; \
} > alloca.h-t && \
mv -f alloca.h-t alloca.h
rm -f c++defs.h-t c++defs.h && \
sed -n -e '/_GL_CXXDEFS/,$p' \
< .././snippet/c++defs.h \
> c++defs.h-t && \
mv c++defs.h-t c++defs.h
rm -f warn-on-use.h-t warn-on-use.h && \
sed -n -e '/^.ifndef/,$p' \
< .././snippet/warn-on-use.h \
> warn-on-use.h-t && \
mv warn-on-use.h-t warn-on-use.h
rm -f arg-nonnull.h-t arg-nonnull.h && \
sed -n -e '/GL_ARG_NONNULL/,$p' \
< .././snippet/arg-nonnull.h \
> arg-nonnull.h-t && \
mv arg-nonnull.h-t arg-nonnull.h
.././install-sh -c -d arpa
rm -f arpa/inet.h-t arpa/inet.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''HAVE_FEATURES_H''@|0|g' \
-e 's|@''NEXT_ARPA_INET_H''@|<arpa/inet.h>|g' \
-e 's|@''HAVE_ARPA_INET_H''@|1|g' \
-e 's/@''GNULIB_INET_NTOP''@/0/g' \
-e 's/@''GNULIB_INET_PTON''@/0/g' \
-e 's|@''HAVE_DECL_INET_NTOP''@|1|g' \
-e 's|@''HAVE_DECL_INET_PTON''@|1|g' \
-e 's|@''REPLACE_INET_NTOP''@|0|g' \
-e 's|@''REPLACE_INET_PTON''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./arpa_inet.in.h; \
} > arpa/inet.h-t && \
mv arpa/inet.h-t arpa/inet.h
rm -f fcntl.h-t fcntl.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_FCNTL_H''@|<fcntl.h>|g' \
-e 's/@''GNULIB_FCNTL''@/1/g' \
-e 's/@''GNULIB_NONBLOCKING''@/0/g' \
-e 's/@''GNULIB_OPEN''@/0/g' \
-e 's/@''GNULIB_OPENAT''@/0/g' \
-e 's|@''HAVE_FCNTL''@|1|g' \
-e 's|@''HAVE_OPENAT''@|1|g' \
-e 's|@''REPLACE_FCNTL''@|0|g' \
-e 's|@''REPLACE_OPEN''@|0|g' \
-e 's|@''REPLACE_OPENAT''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./fcntl.in.h; \
} > fcntl.h-t && \
mv fcntl.h-t fcntl.h
rm -f inttypes.h-t inttypes.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's/@''HAVE_INTTYPES_H''@/1/g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_INTTYPES_H''@|<inttypes.h>|g' \
-e 's/@''PRI_MACROS_BROKEN''@/0/g' \
-e 's/@''APPLE_UNIVERSAL_BUILD''@/0/g' \
-e 's/@''HAVE_LONG_LONG_INT''@/1/g' \
-e 's/@''HAVE_UNSIGNED_LONG_LONG_INT''@/1/g' \
-e 's/@''PRIPTR_PREFIX''@/"l"/g' \
-e 's/@''GNULIB_IMAXABS''@/0/g' \
-e 's/@''GNULIB_IMAXDIV''@/0/g' \
-e 's/@''GNULIB_STRTOIMAX''@/0/g' \
-e 's/@''GNULIB_STRTOUMAX''@/0/g' \
-e 's/@''HAVE_DECL_IMAXABS''@/1/g' \
-e 's/@''HAVE_DECL_IMAXDIV''@/1/g' \
-e 's/@''HAVE_DECL_STRTOIMAX''@/1/g' \
-e 's/@''HAVE_DECL_STRTOUMAX''@/1/g' \
-e 's/@''REPLACE_STRTOIMAX''@/0/g' \
-e 's/@''REPLACE_STRTOUMAX''@/0/g' \
-e 's/@''INT32_MAX_LT_INTMAX_MAX''@/1/g' \
-e 's/@''INT64_MAX_EQ_LONG_MAX''@/1/g' \
-e 's/@''UINT32_MAX_LT_UINTMAX_MAX''@/1/g' \
-e 's/@''UINT64_MAX_EQ_ULONG_MAX''@/1/g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./inttypes.in.h; \
} > inttypes.h-t && \
mv inttypes.h-t inttypes.h
rm -f netdb.h-t netdb.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_NETDB_H''@|<netdb.h>|g' \
-e 's|@''HAVE_NETDB_H''@|1|g' \
-e 's/@''GNULIB_GETADDRINFO''@/0/g' \
-e 's|@''HAVE_STRUCT_ADDRINFO''@|1|g' \
-e 's|@''HAVE_DECL_FREEADDRINFO''@|1|g' \
-e 's|@''HAVE_DECL_GAI_STRERROR''@|1|g' \
-e 's|@''HAVE_DECL_GETADDRINFO''@|1|g' \
-e 's|@''HAVE_DECL_GETNAMEINFO''@|1|g' \
-e 's|@''REPLACE_GAI_STRERROR''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./netdb.in.h; \
} > netdb.h-t && \
mv netdb.h-t netdb.h
rm -f signal.h-t signal.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */' && \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_SIGNAL_H''@|<signal.h>|g' \
-e 's|@''GNULIB_PTHREAD_SIGMASK''@|0|g' \
-e 's|@''GNULIB_RAISE''@|0|g' \
-e 's/@''GNULIB_SIGNAL_H_SIGPIPE''@/0/g' \
-e 's/@''GNULIB_SIGPROCMASK''@/0/g' \
-e 's/@''GNULIB_SIGACTION''@/0/g' \
-e 's|@''HAVE_POSIX_SIGNALBLOCKING''@|1|g' \
-e 's|@''HAVE_PTHREAD_SIGMASK''@|1|g' \
-e 's|@''HAVE_RAISE''@|1|g' \
-e 's|@''HAVE_SIGSET_T''@|1|g' \
-e 's|@''HAVE_SIGINFO_T''@|1|g' \
-e 's|@''HAVE_SIGACTION''@|1|g' \
-e 's|@''HAVE_STRUCT_SIGACTION_SA_SIGACTION''@|1|g' \
-e 's|@''HAVE_TYPE_VOLATILE_SIG_ATOMIC_T''@|1|g' \
-e 's|@''HAVE_SIGHANDLER_T''@|0|g' \
-e 's|@''REPLACE_PTHREAD_SIGMASK''@|0|g' \
-e 's|@''REPLACE_RAISE''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./signal.in.h; \
} > signal.h-t && \
mv signal.h-t signal.h
rm -f stdint.h-t stdint.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's/@''HAVE_STDINT_H''@/1/g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_STDINT_H''@|<stdint.h>|g' \
-e 's/@''HAVE_SYS_TYPES_H''@/1/g' \
-e 's/@''HAVE_INTTYPES_H''@/1/g' \
-e 's/@''HAVE_SYS_INTTYPES_H''@/0/g' \
-e 's/@''HAVE_SYS_BITYPES_H''@/0/g' \
-e 's/@''HAVE_WCHAR_H''@/1/g' \
-e 's/@''HAVE_LONG_LONG_INT''@/1/g' \
-e 's/@''HAVE_UNSIGNED_LONG_LONG_INT''@/1/g' \
-e 's/@''APPLE_UNIVERSAL_BUILD''@/0/g' \
-e 's/@''BITSIZEOF_PTRDIFF_T''@/64/g' \
-e 's/@''PTRDIFF_T_SUFFIX''@/l/g' \
-e 's/@''BITSIZEOF_SIG_ATOMIC_T''@/32/g' \
-e 's/@''HAVE_SIGNED_SIG_ATOMIC_T''@/1/g' \
-e 's/@''SIG_ATOMIC_T_SUFFIX''@//g' \
-e 's/@''BITSIZEOF_SIZE_T''@/64/g' \
-e 's/@''SIZE_T_SUFFIX''@/ul/g' \
-e 's/@''BITSIZEOF_WCHAR_T''@/32/g' \
-e 's/@''HAVE_SIGNED_WCHAR_T''@/1/g' \
-e 's/@''WCHAR_T_SUFFIX''@//g' \
-e 's/@''BITSIZEOF_WINT_T''@/32/g' \
-e 's/@''HAVE_SIGNED_WINT_T''@/1/g' \
-e 's/@''WINT_T_SUFFIX''@//g' \
< ./stdint.in.h; \
} > stdint.h-t && \
mv stdint.h-t stdint.h
rm -f stdlib.h-t stdlib.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */' && \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_STDLIB_H''@|<stdlib.h>|g' \
-e 's/@''GNULIB__EXIT''@/0/g' \
-e 's/@''GNULIB_ATOLL''@/0/g' \
-e 's/@''GNULIB_CALLOC_POSIX''@/0/g' \
-e 's/@''GNULIB_CANONICALIZE_FILE_NAME''@/0/g' \
-e 's/@''GNULIB_GETLOADAVG''@/0/g' \
-e 's/@''GNULIB_GETSUBOPT''@/0/g' \
-e 's/@''GNULIB_GRANTPT''@/0/g' \
-e 's/@''GNULIB_MALLOC_POSIX''@/0/g' \
-e 's/@''GNULIB_MBTOWC''@/0/g' \
-e 's/@''GNULIB_MKDTEMP''@/0/g' \
-e 's/@''GNULIB_MKOSTEMP''@/0/g' \
-e 's/@''GNULIB_MKOSTEMPS''@/0/g' \
-e 's/@''GNULIB_MKSTEMP''@/0/g' \
-e 's/@''GNULIB_MKSTEMPS''@/0/g' \
-e 's/@''GNULIB_POSIX_OPENPT''@/0/g' \
-e 's/@''GNULIB_PTSNAME''@/0/g' \
-e 's/@''GNULIB_PTSNAME_R''@/0/g' \
-e 's/@''GNULIB_PUTENV''@/0/g' \
-e 's/@''GNULIB_QSORT_R''@/0/g' \
-e 's/@''GNULIB_RANDOM''@/0/g' \
-e 's/@''GNULIB_RANDOM_R''@/0/g' \
-e 's/@''GNULIB_REALLOC_POSIX''@/0/g' \
-e 's/@''GNULIB_REALPATH''@/0/g' \
-e 's/@''GNULIB_RPMATCH''@/0/g' \
-e 's/@''GNULIB_SECURE_GETENV''@/0/g' \
-e 's/@''GNULIB_SETENV''@/0/g' \
-e 's/@''GNULIB_STRTOD''@/0/g' \
-e 's/@''GNULIB_STRTOLL''@/0/g' \
-e 's/@''GNULIB_STRTOULL''@/0/g' \
-e 's/@''GNULIB_SYSTEM_POSIX''@/0/g' \
-e 's/@''GNULIB_UNLOCKPT''@/0/g' \
-e 's/@''GNULIB_UNSETENV''@/0/g' \
-e 's/@''GNULIB_WCTOMB''@/0/g' \
< ./stdlib.in.h | \
sed -e 's|@''HAVE__EXIT''@|1|g' \
-e 's|@''HAVE_ATOLL''@|1|g' \
-e 's|@''HAVE_CANONICALIZE_FILE_NAME''@|1|g' \
-e 's|@''HAVE_DECL_GETLOADAVG''@|1|g' \
-e 's|@''HAVE_GETSUBOPT''@|1|g' \
-e 's|@''HAVE_GRANTPT''@|1|g' \
-e 's|@''HAVE_MKDTEMP''@|1|g' \
-e 's|@''HAVE_MKOSTEMP''@|1|g' \
-e 's|@''HAVE_MKOSTEMPS''@|1|g' \
-e 's|@''HAVE_MKSTEMP''@|1|g' \
-e 's|@''HAVE_MKSTEMPS''@|1|g' \
-e 's|@''HAVE_POSIX_OPENPT''@|1|g' \
-e 's|@''HAVE_PTSNAME''@|1|g' \
-e 's|@''HAVE_PTSNAME_R''@|1|g' \
-e 's|@''HAVE_RANDOM''@|1|g' \
-e 's|@''HAVE_RANDOM_H''@|1|g' \
-e 's|@''HAVE_RANDOM_R''@|1|g' \
-e 's|@''HAVE_REALPATH''@|1|g' \
-e 's|@''HAVE_RPMATCH''@|1|g' \
-e 's|@''HAVE_SECURE_GETENV''@|1|g' \
-e 's|@''HAVE_DECL_SETENV''@|1|g' \
-e 's|@''HAVE_STRTOD''@|1|g' \
-e 's|@''HAVE_STRTOLL''@|1|g' \
-e 's|@''HAVE_STRTOULL''@|1|g' \
-e 's|@''HAVE_STRUCT_RANDOM_DATA''@|1|g' \
-e 's|@''HAVE_SYS_LOADAVG_H''@|0|g' \
-e 's|@''HAVE_UNLOCKPT''@|1|g' \
-e 's|@''HAVE_DECL_UNSETENV''@|1|g' \
-e 's|@''REPLACE_CALLOC''@|0|g' \
-e 's|@''REPLACE_CANONICALIZE_FILE_NAME''@|0|g' \
-e 's|@''REPLACE_MALLOC''@|0|g' \
-e 's|@''REPLACE_MBTOWC''@|0|g' \
-e 's|@''REPLACE_MKSTEMP''@|0|g' \
-e 's|@''REPLACE_PTSNAME''@|0|g' \
-e 's|@''REPLACE_PTSNAME_R''@|0|g' \
-e 's|@''REPLACE_PUTENV''@|0|g' \
-e 's|@''REPLACE_QSORT_R''@|0|g' \
-e 's|@''REPLACE_RANDOM_R''@|0|g' \
-e 's|@''REPLACE_REALLOC''@|0|g' \
-e 's|@''REPLACE_REALPATH''@|0|g' \
-e 's|@''REPLACE_SETENV''@|0|g' \
-e 's|@''REPLACE_STRTOD''@|0|g' \
-e 's|@''REPLACE_UNSETENV''@|0|g' \
-e 's|@''REPLACE_WCTOMB''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _Noreturn/r .././snippet/_Noreturn.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h'; \
} > stdlib.h-t && \
mv stdlib.h-t stdlib.h
rm -f string.h-t string.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */' && \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_STRING_H''@|<string.h>|g' \
-e 's/@''GNULIB_FFSL''@/0/g' \
-e 's/@''GNULIB_FFSLL''@/0/g' \
-e 's/@''GNULIB_MBSLEN''@/0/g' \
-e 's/@''GNULIB_MBSNLEN''@/0/g' \
-e 's/@''GNULIB_MBSCHR''@/0/g' \
-e 's/@''GNULIB_MBSRCHR''@/0/g' \
-e 's/@''GNULIB_MBSSTR''@/0/g' \
-e 's/@''GNULIB_MBSCASECMP''@/0/g' \
-e 's/@''GNULIB_MBSNCASECMP''@/0/g' \
-e 's/@''GNULIB_MBSPCASECMP''@/0/g' \
-e 's/@''GNULIB_MBSCASESTR''@/0/g' \
-e 's/@''GNULIB_MBSCSPN''@/0/g' \
-e 's/@''GNULIB_MBSPBRK''@/0/g' \
-e 's/@''GNULIB_MBSSPN''@/0/g' \
-e 's/@''GNULIB_MBSSEP''@/0/g' \
-e 's/@''GNULIB_MBSTOK_R''@/0/g' \
-e 's/@''GNULIB_MEMCHR''@/0/g' \
-e 's/@''GNULIB_MEMMEM''@/0/g' \
-e 's/@''GNULIB_MEMPCPY''@/0/g' \
-e 's/@''GNULIB_MEMRCHR''@/0/g' \
-e 's/@''GNULIB_RAWMEMCHR''@/0/g' \
-e 's/@''GNULIB_STPCPY''@/0/g' \
-e 's/@''GNULIB_STPNCPY''@/0/g' \
-e 's/@''GNULIB_STRCHRNUL''@/0/g' \
-e 's/@''GNULIB_STRDUP''@/0/g' \
-e 's/@''GNULIB_STRNCAT''@/0/g' \
-e 's/@''GNULIB_STRNDUP''@/0/g' \
-e 's/@''GNULIB_STRNLEN''@/0/g' \
-e 's/@''GNULIB_STRPBRK''@/0/g' \
-e 's/@''GNULIB_STRSEP''@/0/g' \
-e 's/@''GNULIB_STRSTR''@/0/g' \
-e 's/@''GNULIB_STRCASESTR''@/0/g' \
-e 's/@''GNULIB_STRTOK_R''@/0/g' \
-e 's/@''GNULIB_STRERROR''@/0/g' \
-e 's/@''GNULIB_STRERROR_R''@/0/g' \
-e 's/@''GNULIB_STRSIGNAL''@/0/g' \
-e 's/@''GNULIB_STRVERSCMP''@/0/g' \
< ./string.in.h | \
sed -e 's|@''HAVE_FFSL''@|1|g' \
-e 's|@''HAVE_FFSLL''@|1|g' \
-e 's|@''HAVE_MBSLEN''@|0|g' \
-e 's|@''HAVE_MEMCHR''@|1|g' \
-e 's|@''HAVE_DECL_MEMMEM''@|1|g' \
-e 's|@''HAVE_MEMPCPY''@|1|g' \
-e 's|@''HAVE_DECL_MEMRCHR''@|1|g' \
-e 's|@''HAVE_RAWMEMCHR''@|1|g' \
-e 's|@''HAVE_STPCPY''@|1|g' \
-e 's|@''HAVE_STPNCPY''@|1|g' \
-e 's|@''HAVE_STRCHRNUL''@|1|g' \
-e 's|@''HAVE_DECL_STRDUP''@|1|g' \
-e 's|@''HAVE_DECL_STRNDUP''@|1|g' \
-e 's|@''HAVE_DECL_STRNLEN''@|1|g' \
-e 's|@''HAVE_STRPBRK''@|1|g' \
-e 's|@''HAVE_STRSEP''@|1|g' \
-e 's|@''HAVE_STRCASESTR''@|1|g' \
-e 's|@''HAVE_DECL_STRTOK_R''@|1|g' \
-e 's|@''HAVE_DECL_STRERROR_R''@|1|g' \
-e 's|@''HAVE_DECL_STRSIGNAL''@|1|g' \
-e 's|@''HAVE_STRVERSCMP''@|1|g' \
-e 's|@''REPLACE_STPNCPY''@|0|g' \
-e 's|@''REPLACE_MEMCHR''@|0|g' \
-e 's|@''REPLACE_MEMMEM''@|0|g' \
-e 's|@''REPLACE_STRCASESTR''@|0|g' \
-e 's|@''REPLACE_STRCHRNUL''@|0|g' \
-e 's|@''REPLACE_STRDUP''@|0|g' \
-e 's|@''REPLACE_STRSTR''@|0|g' \
-e 's|@''REPLACE_STRERROR''@|0|g' \
-e 's|@''REPLACE_STRERROR_R''@|0|g' \
-e 's|@''REPLACE_STRNCAT''@|0|g' \
-e 's|@''REPLACE_STRNDUP''@|0|g' \
-e 's|@''REPLACE_STRNLEN''@|0|g' \
-e 's|@''REPLACE_STRSIGNAL''@|0|g' \
-e 's|@''REPLACE_STRTOK_R''@|0|g' \
-e 's|@''UNDEFINE_STRTOK_R''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h'; \
< ./string.in.h; \
} > string.h-t && \
mv string.h-t string.h
.././install-sh -c -d sys
rm -f sys/select.h-t sys/select.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_SYS_SELECT_H''@|<sys/select.h>|g' \
-e 's|@''HAVE_SYS_SELECT_H''@|1|g' \
-e 's/@''GNULIB_PSELECT''@/0/g' \
-e 's/@''GNULIB_SELECT''@/0/g' \
-e 's|@''HAVE_WINSOCK2_H''@|0|g' \
-e 's|@''HAVE_PSELECT''@|1|g' \
-e 's|@''REPLACE_PSELECT''@|0|g' \
-e 's|@''REPLACE_SELECT''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./sys_select.in.h; \
} > sys/select.h-t && \
mv sys/select.h-t sys/select.h
.././install-sh -c -d sys
rm -f sys/socket.h-t sys/socket.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_SYS_SOCKET_H''@|<sys/socket.h>|g' \
-e 's|@''HAVE_SYS_SOCKET_H''@|1|g' \
-e 's/@''GNULIB_CLOSE''@/1/g' \
-e 's/@''GNULIB_SOCKET''@/0/g' \
-e 's/@''GNULIB_CONNECT''@/0/g' \
-e 's/@''GNULIB_ACCEPT''@/0/g' \
-e 's/@''GNULIB_BIND''@/0/g' \
-e 's/@''GNULIB_GETPEERNAME''@/0/g' \
-e 's/@''GNULIB_GETSOCKNAME''@/0/g' \
-e 's/@''GNULIB_GETSOCKOPT''@/0/g' \
-e 's/@''GNULIB_LISTEN''@/0/g' \
-e 's/@''GNULIB_RECV''@/1/g' \
-e 's/@''GNULIB_SEND''@/1/g' \
-e 's/@''GNULIB_RECVFROM''@/0/g' \
-e 's/@''GNULIB_SENDTO''@/0/g' \
-e 's/@''GNULIB_SETSOCKOPT''@/0/g' \
-e 's/@''GNULIB_SHUTDOWN''@/0/g' \
-e 's/@''GNULIB_ACCEPT4''@/0/g' \
-e 's|@''HAVE_WINSOCK2_H''@|0|g' \
-e 's|@''HAVE_WS2TCPIP_H''@|0|g' \
-e 's|@''HAVE_STRUCT_SOCKADDR_STORAGE''@|1|g' \
-e 's|@''HAVE_STRUCT_SOCKADDR_STORAGE_SS_FAMILY''@|1|g' \
-e 's|@''HAVE_SA_FAMILY_T''@|1|g' \
-e 's|@''HAVE_ACCEPT4''@|1|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./sys_socket.in.h; \
} > sys/socket.h-t && \
mv -f sys/socket.h-t sys/socket.h
.././install-sh -c -d sys
rm -f sys/stat.h-t sys/stat.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_SYS_STAT_H''@|<sys/stat.h>|g' \
-e 's|@''WINDOWS_64_BIT_ST_SIZE''@|0|g' \
-e 's/@''GNULIB_FCHMODAT''@/0/g' \
-e 's/@''GNULIB_FSTAT''@/0/g' \
-e 's/@''GNULIB_FSTATAT''@/0/g' \
-e 's/@''GNULIB_FUTIMENS''@/0/g' \
-e 's/@''GNULIB_LCHMOD''@/0/g' \
-e 's/@''GNULIB_LSTAT''@/0/g' \
-e 's/@''GNULIB_MKDIRAT''@/0/g' \
-e 's/@''GNULIB_MKFIFO''@/0/g' \
-e 's/@''GNULIB_MKFIFOAT''@/0/g' \
-e 's/@''GNULIB_MKNOD''@/0/g' \
-e 's/@''GNULIB_MKNODAT''@/0/g' \
-e 's/@''GNULIB_STAT''@/0/g' \
-e 's/@''GNULIB_UTIMENSAT''@/0/g' \
-e 's|@''HAVE_FCHMODAT''@|1|g' \
-e 's|@''HAVE_FSTATAT''@|1|g' \
-e 's|@''HAVE_FUTIMENS''@|1|g' \
-e 's|@''HAVE_LCHMOD''@|1|g' \
-e 's|@''HAVE_LSTAT''@|1|g' \
-e 's|@''HAVE_MKDIRAT''@|1|g' \
-e 's|@''HAVE_MKFIFO''@|1|g' \
-e 's|@''HAVE_MKFIFOAT''@|1|g' \
-e 's|@''HAVE_MKNOD''@|1|g' \
-e 's|@''HAVE_MKNODAT''@|1|g' \
-e 's|@''HAVE_UTIMENSAT''@|1|g' \
-e 's|@''REPLACE_FSTAT''@|0|g' \
-e 's|@''REPLACE_FSTATAT''@|0|g' \
-e 's|@''REPLACE_FUTIMENS''@|0|g' \
-e 's|@''REPLACE_LSTAT''@|0|g' \
-e 's|@''REPLACE_MKDIR''@|0|g' \
-e 's|@''REPLACE_MKFIFO''@|0|g' \
-e 's|@''REPLACE_MKNOD''@|0|g' \
-e 's|@''REPLACE_STAT''@|0|g' \
-e 's|@''REPLACE_UTIMENSAT''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./sys_stat.in.h; \
} > sys/stat.h-t && \
mv sys/stat.h-t sys/stat.h
.././install-sh -c -d sys
rm -f sys/time.h-t sys/time.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's/@''HAVE_SYS_TIME_H''@/1/g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_SYS_TIME_H''@|<sys/time.h>|g' \
-e 's/@''GNULIB_GETTIMEOFDAY''@/1/g' \
-e 's|@''HAVE_WINSOCK2_H''@|0|g' \
-e 's/@''HAVE_GETTIMEOFDAY''@/1/g' \
-e 's/@''HAVE_STRUCT_TIMEVAL''@/1/g' \
-e 's/@''REPLACE_GETTIMEOFDAY''@/0/g' \
-e 's/@''REPLACE_STRUCT_TIMEVAL''@/0/g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./sys_time.in.h; \
} > sys/time.h-t && \
mv sys/time.h-t sys/time.h
.././install-sh -c -d sys
rm -f sys/types.h-t sys/types.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_SYS_TYPES_H''@|<sys/types.h>|g' \
-e 's|@''WINDOWS_64_BIT_OFF_T''@|0|g' \
< ./sys_types.in.h; \
} > sys/types.h-t && \
mv sys/types.h-t sys/types.h
.././install-sh -c -d sys
rm -f sys/uio.h-t sys/uio.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_SYS_UIO_H''@|<sys/uio.h>|g' \
-e 's|@''HAVE_SYS_UIO_H''@|1|g' \
< ./sys_uio.in.h; \
} > sys/uio.h-t && \
mv -f sys/uio.h-t sys/uio.h
rm -f time.h-t time.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */' && \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_TIME_H''@|<time.h>|g' \
-e 's/@''GNULIB_GETTIMEOFDAY''@/1/g' \
-e 's/@''GNULIB_MKTIME''@/0/g' \
-e 's/@''GNULIB_NANOSLEEP''@/0/g' \
-e 's/@''GNULIB_STRPTIME''@/0/g' \
-e 's/@''GNULIB_TIMEGM''@/0/g' \
-e 's/@''GNULIB_TIME_R''@/0/g' \
-e 's|@''HAVE_DECL_LOCALTIME_R''@|1|g' \
-e 's|@''HAVE_NANOSLEEP''@|1|g' \
-e 's|@''HAVE_STRPTIME''@|1|g' \
-e 's|@''HAVE_TIMEGM''@|1|g' \
-e 's|@''REPLACE_GMTIME''@|0|g' \
-e 's|@''REPLACE_LOCALTIME''@|0|g' \
-e 's|@''REPLACE_LOCALTIME_R''@|GNULIB_PORTCHECK|g' \
-e 's|@''REPLACE_MKTIME''@|GNULIB_PORTCHECK|g' \
-e 's|@''REPLACE_NANOSLEEP''@|GNULIB_PORTCHECK|g' \
-e 's|@''REPLACE_TIMEGM''@|GNULIB_PORTCHECK|g' \
-e 's|@''PTHREAD_H_DEFINES_STRUCT_TIMESPEC''@|0|g' \
-e 's|@''SYS_TIME_H_DEFINES_STRUCT_TIMESPEC''@|0|g' \
-e 's|@''TIME_H_DEFINES_STRUCT_TIMESPEC''@|1|g' \
-e 's|@''UNISTD_H_DEFINES_STRUCT_TIMESPEC''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h' \
< ./time.in.h; \
} > time.h-t && \
mv time.h-t time.h
rm -f unistd.h-t unistd.h && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */'; \
sed -e 's|@''GUARD_PREFIX''@|GL|g' \
-e 's|@''HAVE_UNISTD_H''@|1|g' \
-e 's|@''INCLUDE_NEXT''@|include_next|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|#pragma GCC system_header|g' \
-e 's|@''PRAGMA_COLUMNS''@||g' \
-e 's|@''NEXT_UNISTD_H''@|<unistd.h>|g' \
-e 's|@''WINDOWS_64_BIT_OFF_T''@|0|g' \
-e 's/@''GNULIB_CHDIR''@/0/g' \
-e 's/@''GNULIB_CHOWN''@/0/g' \
-e 's/@''GNULIB_CLOSE''@/1/g' \
-e 's/@''GNULIB_DUP''@/0/g' \
-e 's/@''GNULIB_DUP2''@/1/g' \
-e 's/@''GNULIB_DUP3''@/0/g' \
-e 's/@''GNULIB_ENVIRON''@/0/g' \
-e 's/@''GNULIB_EUIDACCESS''@/0/g' \
-e 's/@''GNULIB_FACCESSAT''@/0/g' \
-e 's/@''GNULIB_FCHDIR''@/0/g' \
-e 's/@''GNULIB_FCHOWNAT''@/0/g' \
-e 's/@''GNULIB_FDATASYNC''@/1/g' \
-e 's/@''GNULIB_FSYNC''@/1/g' \
-e 's/@''GNULIB_FTRUNCATE''@/0/g' \
-e 's/@''GNULIB_GETCWD''@/0/g' \
-e 's/@''GNULIB_GETDOMAINNAME''@/0/g' \
-e 's/@''GNULIB_GETDTABLESIZE''@/1/g' \
-e 's/@''GNULIB_GETGROUPS''@/0/g' \
-e 's/@''GNULIB_GETHOSTNAME''@/0/g' \
-e 's/@''GNULIB_GETLOGIN''@/0/g' \
-e 's/@''GNULIB_GETLOGIN_R''@/0/g' \
-e 's/@''GNULIB_GETPAGESIZE''@/1/g' \
-e 's/@''GNULIB_GETUSERSHELL''@/0/g' \
-e 's/@''GNULIB_GROUP_MEMBER''@/0/g' \
-e 's/@''GNULIB_ISATTY''@/0/g' \
-e 's/@''GNULIB_LCHOWN''@/0/g' \
-e 's/@''GNULIB_LINK''@/0/g' \
-e 's/@''GNULIB_LINKAT''@/0/g' \
-e 's/@''GNULIB_LSEEK''@/0/g' \
-e 's/@''GNULIB_PIPE''@/0/g' \
-e 's/@''GNULIB_PIPE2''@/0/g' \
-e 's/@''GNULIB_PREAD''@/0/g' \
-e 's/@''GNULIB_PWRITE''@/0/g' \
-e 's/@''GNULIB_READ''@/0/g' \
-e 's/@''GNULIB_READLINK''@/0/g' \
-e 's/@''GNULIB_READLINKAT''@/0/g' \
-e 's/@''GNULIB_RMDIR''@/0/g' \
-e 's/@''GNULIB_SETHOSTNAME''@/0/g' \
-e 's/@''GNULIB_SLEEP''@/0/g' \
-e 's/@''GNULIB_SYMLINK''@/0/g' \
-e 's/@''GNULIB_SYMLINKAT''@/0/g' \
-e 's/@''GNULIB_TTYNAME_R''@/0/g' \
-e 's/@''GNULIB_UNISTD_H_GETOPT''@/0/g' \
-e 's/@''GNULIB_UNISTD_H_NONBLOCKING''@/0/g' \
-e 's/@''GNULIB_UNISTD_H_SIGPIPE''@/0/g' \
-e 's/@''GNULIB_UNLINK''@/0/g' \
-e 's/@''GNULIB_UNLINKAT''@/0/g' \
-e 's/@''GNULIB_USLEEP''@/0/g' \
-e 's/@''GNULIB_WRITE''@/0/g' \
< ./unistd.in.h | \
sed -e 's|@''HAVE_CHOWN''@|1|g' \
-e 's|@''HAVE_DUP2''@|1|g' \
-e 's|@''HAVE_DUP3''@|1|g' \
-e 's|@''HAVE_EUIDACCESS''@|1|g' \
-e 's|@''HAVE_FACCESSAT''@|1|g' \
-e 's|@''HAVE_FCHDIR''@|1|g' \
-e 's|@''HAVE_FCHOWNAT''@|1|g' \
-e 's|@''HAVE_FDATASYNC''@|1|g' \
-e 's|@''HAVE_FSYNC''@|1|g' \
-e 's|@''HAVE_FTRUNCATE''@|1|g' \
-e 's|@''HAVE_GETDTABLESIZE''@|1|g' \
-e 's|@''HAVE_GETGROUPS''@|1|g' \
-e 's|@''HAVE_GETHOSTNAME''@|1|g' \
-e 's|@''HAVE_GETLOGIN''@|1|g' \
-e 's|@''HAVE_GETPAGESIZE''@|1|g' \
-e 's|@''HAVE_GROUP_MEMBER''@|1|g' \
-e 's|@''HAVE_LCHOWN''@|1|g' \
-e 's|@''HAVE_LINK''@|1|g' \
-e 's|@''HAVE_LINKAT''@|1|g' \
-e 's|@''HAVE_PIPE''@|1|g' \
-e 's|@''HAVE_PIPE2''@|1|g' \
-e 's|@''HAVE_PREAD''@|1|g' \
-e 's|@''HAVE_PWRITE''@|1|g' \
-e 's|@''HAVE_READLINK''@|1|g' \
-e 's|@''HAVE_READLINKAT''@|1|g' \
-e 's|@''HAVE_SETHOSTNAME''@|1|g' \
-e 's|@''HAVE_SLEEP''@|1|g' \
-e 's|@''HAVE_SYMLINK''@|1|g' \
-e 's|@''HAVE_SYMLINKAT''@|1|g' \
-e 's|@''HAVE_UNLINKAT''@|1|g' \
-e 's|@''HAVE_USLEEP''@|1|g' \
-e 's|@''HAVE_DECL_ENVIRON''@|1|g' \
-e 's|@''HAVE_DECL_FCHDIR''@|1|g' \
-e 's|@''HAVE_DECL_FDATASYNC''@|0|g' \
-e 's|@''HAVE_DECL_GETDOMAINNAME''@|1|g' \
-e 's|@''HAVE_DECL_GETLOGIN_R''@|1|g' \
-e 's|@''HAVE_DECL_GETPAGESIZE''@|1|g' \
-e 's|@''HAVE_DECL_GETUSERSHELL''@|1|g' \
-e 's|@''HAVE_DECL_SETHOSTNAME''@|1|g' \
-e 's|@''HAVE_DECL_TTYNAME_R''@|1|g' \
-e 's|@''HAVE_OS_H''@|0|g' \
-e 's|@''HAVE_SYS_PARAM_H''@|0|g' \
| \
sed -e 's|@''REPLACE_CHOWN''@|0|g' \
-e 's|@''REPLACE_CLOSE''@|0|g' \
-e 's|@''REPLACE_DUP''@|0|g' \
-e 's|@''REPLACE_DUP2''@|0|g' \
-e 's|@''REPLACE_FCHOWNAT''@|0|g' \
-e 's|@''REPLACE_FTRUNCATE''@|0|g' \
-e 's|@''REPLACE_GETCWD''@|0|g' \
-e 's|@''REPLACE_GETDOMAINNAME''@|0|g' \
-e 's|@''REPLACE_GETDTABLESIZE''@|0|g' \
-e 's|@''REPLACE_GETLOGIN_R''@|0|g' \
-e 's|@''REPLACE_GETGROUPS''@|0|g' \
-e 's|@''REPLACE_GETPAGESIZE''@|0|g' \
-e 's|@''REPLACE_ISATTY''@|0|g' \
-e 's|@''REPLACE_LCHOWN''@|0|g' \
-e 's|@''REPLACE_LINK''@|0|g' \
-e 's|@''REPLACE_LINKAT''@|0|g' \
-e 's|@''REPLACE_LSEEK''@|0|g' \
-e 's|@''REPLACE_PREAD''@|0|g' \
-e 's|@''REPLACE_PWRITE''@|0|g' \
-e 's|@''REPLACE_READ''@|0|g' \
-e 's|@''REPLACE_READLINK''@|0|g' \
-e 's|@''REPLACE_READLINKAT''@|0|g' \
-e 's|@''REPLACE_RMDIR''@|0|g' \
-e 's|@''REPLACE_SLEEP''@|0|g' \
-e 's|@''REPLACE_SYMLINK''@|0|g' \
-e 's|@''REPLACE_SYMLINKAT''@|0|g' \
-e 's|@''REPLACE_TTYNAME_R''@|0|g' \
-e 's|@''REPLACE_UNLINK''@|0|g' \
-e 's|@''REPLACE_UNLINKAT''@|0|g' \
-e 's|@''REPLACE_USLEEP''@|0|g' \
-e 's|@''REPLACE_WRITE''@|0|g' \
-e 's|@''UNISTD_H_HAVE_WINSOCK2_H''@|0|g' \
-e 's|@''UNISTD_H_HAVE_WINSOCK2_H_AND_USE_SOCKETS''@|0|g' \
-e '/definitions of _GL_FUNCDECL_RPL/r c++defs.h' \
-e '/definition of _GL_ARG_NONNULL/r arg-nonnull.h' \
-e '/definition of _GL_WARN_ON_USE/r warn-on-use.h'; \
} > unistd.h-t && \
mv unistd.h-t unistd.h
make all-recursive
/bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -Wall -g -O2 -fPIC -c -o fd-hook.lo fd-hook.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -Wall -g -O2 -fPIC -c fd-hook.c -fno-common -DPIC -o .libs/fd-hook.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -Wall -g -O2 -fPIC -c fd-hook.c -o fd-hook.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -Wall -g -O2 -fPIC -c -o sys_socket.lo sys_socket.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -Wall -g -O2 -fPIC -c sys_socket.c -fno-common -DPIC -o .libs/sys_socket.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -Wall -g -O2 -fPIC -c sys_socket.c -o sys_socket.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -Wall -g -O2 -fPIC -c -o unistd.lo unistd.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -Wall -g -O2 -fPIC -c unistd.c -fno-common -DPIC -o .libs/unistd.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -Wall -g -O2 -fPIC -c unistd.c -o unistd.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CC --mode=link clang -Wall -g -O2 -fPIC -no-undefined -L/usr/local/lib -o libgnu.la fd-hook.lo sys_socket.lo unistd.lo -lz -lm
libtool: link: ar cru .libs/libgnu.a .libs/fd-hook.o .libs/sys_socket.o .libs/unistd.o
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgnu.a(fd-hook.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgnu.a(sys_socket.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgnu.a(unistd.o) has no symbols
libtool: link: ranlib .libs/libgnu.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgnu.a(fd-hook.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgnu.a(sys_socket.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgnu.a(unistd.o) has no symbols
warning: /Library/Developer/CommandLineTools/usr/bin/ranlib: warning for library: .libs/libgnu.a the table of contents is empty (no object file members in the library define global symbols)
libtool: link: ( cd ".libs" && rm -f "libgnu.la" && ln -s "../libgnu.la" "libgnu.la" )
Making all in test
make[3]: Nothing to be done for `all'.
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-kfunc.lo `test -f 'kfunc.c' || echo './'`kfunc.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c kfunc.c -fno-common -DPIC -o .libs/libhts_la-kfunc.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c kfunc.c -o libhts_la-kfunc.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-knetfile.lo `test -f 'knetfile.c' || echo './'`knetfile.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c knetfile.c -fno-common -DPIC -o .libs/libhts_la-knetfile.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c knetfile.c -o libhts_la-knetfile.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-kstring.lo `test -f 'kstring.c' || echo './'`kstring.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c kstring.c -fno-common -DPIC -o .libs/libhts_la-kstring.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c kstring.c -o libhts_la-kstring.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-bgzf.lo `test -f 'bgzf.c' || echo './'`bgzf.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c bgzf.c -fno-common -DPIC -o .libs/libhts_la-bgzf.o
bgzf.c:70:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
./htslib/khash.h:601:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./htslib/khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:215:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:27:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c bgzf.c -o libhts_la-bgzf.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-faidx.lo `test -f 'faidx.c' || echo './'`faidx.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c faidx.c -fno-common -DPIC -o .libs/libhts_la-faidx.o
faidx.c:47:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, faidx1_t)
^
./htslib/khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:215:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:64:1: note: expanded from here
kh_clear_s
^
faidx.c:47:1: warning: unused function 'kh_del_s' [-Wunused-function]
./htslib/khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:341:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:78:1: note: expanded from here
kh_del_s
^
2 warnings generated.
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c faidx.c -o libhts_la-faidx.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-hfile.lo `test -f 'hfile.c' || echo './'`hfile.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c hfile.c -fno-common -DPIC -o .libs/libhts_la-hfile.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c hfile.c -o libhts_la-hfile.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-hfile_net.lo `test -f 'hfile_net.c' || echo './'`hfile_net.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c hfile_net.c -fno-common -DPIC -o .libs/libhts_la-hfile_net.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c hfile_net.c -o libhts_la-hfile_net.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-hts.lo `test -f 'hts.c' || echo './'`hts.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c hts.c -fno-common -DPIC -o .libs/libhts_la-hts.o
hts.c:48:5: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT2(, BGZF*, bgzf_read, 65536)
^
./htslib/kseq.h:152:2: note: expanded from macro 'KSTREAM_INIT2'
__KS_INLINED(__read)
^
./htslib/kseq.h:68:20: note: expanded from macro '__KS_INLINED'
static inline int ks_getc(kstream_t *ks) \
^
hts.c:638:1: warning: unused function 'kh_clear_bin' [-Wunused-function]
KHASH_MAP_INIT_INT(bin, bins_t)
^
./htslib/khash.h:586:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./htslib/khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:215:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:67:1: note: expanded from here
kh_clear_bin
^
2 warnings generated.
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c hts.c -o libhts_la-hts.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-regidx.lo `test -f 'regidx.c' || echo './'`regidx.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c regidx.c -fno-common -DPIC -o .libs/libhts_la-regidx.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c regidx.c -o libhts_la-regidx.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-sam.lo `test -f 'sam.c' || echo './'`sam.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c sam.c -fno-common -DPIC -o .libs/libhts_la-sam.o
sam.c:1427:1: warning: unused function 'kh_clear_olap_hash' [-Wunused-function]
KHASH_MAP_INIT_STR(olap_hash, lbnode_t *)
^
./htslib/khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:215:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:236:1: note: expanded from here
kh_clear_olap_hash
^
1 warning generated.
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c sam.c -o libhts_la-sam.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-synced_bcf_reader.lo `test -f 'synced_bcf_reader.c' || echo './'`synced_bcf_reader.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c synced_bcf_reader.c -fno-common -DPIC -o .libs/libhts_la-synced_bcf_reader.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c synced_bcf_reader.c -o libhts_la-synced_bcf_reader.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-vcf_sweep.lo `test -f 'vcf_sweep.c' || echo './'`vcf_sweep.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c vcf_sweep.c -fno-common -DPIC -o .libs/libhts_la-vcf_sweep.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c vcf_sweep.c -o libhts_la-vcf_sweep.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-tbx.lo `test -f 'tbx.c' || echo './'`tbx.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c tbx.c -fno-common -DPIC -o .libs/libhts_la-tbx.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c tbx.c -o libhts_la-tbx.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-vcf.lo `test -f 'vcf.c' || echo './'`vcf.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c vcf.c -fno-common -DPIC -o .libs/libhts_la-vcf.o
vcf.c:45:1: warning: unused function 'kh_clear_vdict' [-Wunused-function]
KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
^
./htslib/khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:215:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:100:1: note: expanded from here
kh_clear_vdict
^
vcf.c:45:1: warning: unused function 'kh_del_vdict' [-Wunused-function]
./htslib/khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:341:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:114:1: note: expanded from here
kh_del_vdict
^
2 warnings generated.
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c vcf.c -o libhts_la-vcf.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o libhts_la-vcfutils.lo `test -f 'vcfutils.c' || echo './'`vcfutils.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c vcfutils.c -fno-common -DPIC -o .libs/libhts_la-vcfutils.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c vcfutils.c -o libhts_la-vcfutils.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-cram_codecs.lo `test -f 'cram/cram_codecs.c' || echo './'`cram/cram_codecs.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_codecs.c -fno-common -DPIC -o cram/.libs/libhts_la-cram_codecs.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_codecs.c -o cram/libhts_la-cram_codecs.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-cram_decode.lo `test -f 'cram/cram_decode.c' || echo './'`cram/cram_decode.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_decode.c -fno-common -DPIC -o cram/.libs/libhts_la-cram_decode.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_decode.c -o cram/libhts_la-cram_decode.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-cram_encode.lo `test -f 'cram/cram_encode.c' || echo './'`cram/cram_encode.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_encode.c -fno-common -DPIC -o cram/.libs/libhts_la-cram_encode.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_encode.c -o cram/libhts_la-cram_encode.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-cram_index.lo `test -f 'cram/cram_index.c' || echo './'`cram/cram_index.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_index.c -fno-common -DPIC -o cram/.libs/libhts_la-cram_index.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_index.c -o cram/libhts_la-cram_index.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-cram_io.lo `test -f 'cram/cram_io.c' || echo './'`cram/cram_io.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_io.c -fno-common -DPIC -o cram/.libs/libhts_la-cram_io.o
cram/cram_io.c:2728:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
cp += itf8_put(cp, -2);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cram/cram_io.h:97:311: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&˜0x7f))?((c)[0]=(v),1):(!((v)&˜0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&˜0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&˜0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cram/cram_io.c:2728:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
cp += itf8_put(cp, -2);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cram/cram_io.h:97:345: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&˜0x7f))?((c)[0]=(v),1):(!((v)&˜0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&˜0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&˜0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
cram/cram_io.c:2728:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
cp += itf8_put(cp, -2);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cram/cram_io.h:97:367: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&˜0x7f))?((c)[0]=(v),1):(!((v)&˜0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&˜0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&˜0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
cram/cram_io.c:2728:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
cp += itf8_put(cp, -2);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cram/cram_io.h:97:388: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&˜0x7f))?((c)[0]=(v),1):(!((v)&˜0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&˜0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&˜0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
˜˜˜˜˜˜˜˜˜^˜˜˜˜
4 warnings generated.
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_io.c -o cram/libhts_la-cram_io.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-cram_samtools.lo `test -f 'cram/cram_samtools.c' || echo './'`cram/cram_samtools.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_samtools.c -fno-common -DPIC -o cram/.libs/libhts_la-cram_samtools.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_samtools.c -o cram/libhts_la-cram_samtools.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-cram_stats.lo `test -f 'cram/cram_stats.c' || echo './'`cram/cram_stats.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_stats.c -fno-common -DPIC -o cram/.libs/libhts_la-cram_stats.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/cram_stats.c -o cram/libhts_la-cram_stats.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-files.lo `test -f 'cram/files.c' || echo './'`cram/files.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/files.c -fno-common -DPIC -o cram/.libs/libhts_la-files.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/files.c -o cram/libhts_la-files.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-mFILE.lo `test -f 'cram/mFILE.c' || echo './'`cram/mFILE.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/mFILE.c -fno-common -DPIC -o cram/.libs/libhts_la-mFILE.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/mFILE.c -o cram/libhts_la-mFILE.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-md5.lo `test -f 'cram/md5.c' || echo './'`cram/md5.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/md5.c -fno-common -DPIC -o cram/.libs/libhts_la-md5.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/md5.c -o cram/libhts_la-md5.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-open_trace_file.lo `test -f 'cram/open_trace_file.c' || echo './'`cram/open_trace_file.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/open_trace_file.c -fno-common -DPIC -o cram/.libs/libhts_la-open_trace_file.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/open_trace_file.c -o cram/libhts_la-open_trace_file.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-pooled_alloc.lo `test -f 'cram/pooled_alloc.c' || echo './'`cram/pooled_alloc.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/pooled_alloc.c -fno-common -DPIC -o cram/.libs/libhts_la-pooled_alloc.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/pooled_alloc.c -o cram/libhts_la-pooled_alloc.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-rANS_static.lo `test -f 'cram/rANS_static.c' || echo './'`cram/rANS_static.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/rANS_static.c -fno-common -DPIC -o cram/.libs/libhts_la-rANS_static.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/rANS_static.c -o cram/libhts_la-rANS_static.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-sam_header.lo `test -f 'cram/sam_header.c' || echo './'`cram/sam_header.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/sam_header.c -fno-common -DPIC -o cram/.libs/libhts_la-sam_header.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/sam_header.c -o cram/libhts_la-sam_header.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-string_alloc.lo `test -f 'cram/string_alloc.c' || echo './'`cram/string_alloc.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/string_alloc.c -fno-common -DPIC -o cram/.libs/libhts_la-string_alloc.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/string_alloc.c -o cram/libhts_la-string_alloc.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-thread_pool.lo `test -f 'cram/thread_pool.c' || echo './'`cram/thread_pool.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/thread_pool.c -fno-common -DPIC -o cram/.libs/libhts_la-thread_pool.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/thread_pool.c -o cram/libhts_la-thread_pool.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-vlen.lo `test -f 'cram/vlen.c' || echo './'`cram/vlen.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/vlen.c -fno-common -DPIC -o cram/.libs/libhts_la-vlen.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/vlen.c -o cram/libhts_la-vlen.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o cram/libhts_la-zfio.lo `test -f 'cram/zfio.c' || echo './'`cram/zfio.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/zfio.c -fno-common -DPIC -o cram/.libs/libhts_la-zfio.o
libtool: compile: clang -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c cram/zfio.c -o cram/libhts_la-zfio.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CC --mode=link clang -Wall -g -O2 -fPIC -no-undefined -L/usr/local/lib -o libhts.la -rpath /Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/lib libhts_la-kfunc.lo libhts_la-knetfile.lo libhts_la-kstring.lo libhts_la-bgzf.lo libhts_la-faidx.lo libhts_la-hfile.lo libhts_la-hfile_net.lo libhts_la-hts.lo libhts_la-regidx.lo libhts_la-sam.lo libhts_la-synced_bcf_reader.lo libhts_la-vcf_sweep.lo libhts_la-tbx.lo libhts_la-vcf.lo libhts_la-vcfutils.lo cram/libhts_la-cram_codecs.lo cram/libhts_la-cram_decode.lo cram/libhts_la-cram_encode.lo cram/libhts_la-cram_index.lo cram/libhts_la-cram_io.lo cram/libhts_la-cram_samtools.lo cram/libhts_la-cram_stats.lo cram/libhts_la-files.lo cram/libhts_la-mFILE.lo cram/libhts_la-md5.lo cram/libhts_la-open_trace_file.lo cram/libhts_la-pooled_alloc.lo cram/libhts_la-rANS_static.lo cram/libhts_la-sam_header.lo cram/libhts_la-string_alloc.lo cram/libhts_la-thread_pool.lo cram/libhts_la-vlen.lo cram/libhts_la-zfio.lo lib/libgnu.la -lz -lm
libtool: link: clang -dynamiclib -o .libs/libhts.0.dylib .libs/libhts_la-kfunc.o .libs/libhts_la-knetfile.o .libs/libhts_la-kstring.o .libs/libhts_la-bgzf.o .libs/libhts_la-faidx.o .libs/libhts_la-hfile.o .libs/libhts_la-hfile_net.o .libs/libhts_la-hts.o .libs/libhts_la-regidx.o .libs/libhts_la-sam.o .libs/libhts_la-synced_bcf_reader.o .libs/libhts_la-vcf_sweep.o .libs/libhts_la-tbx.o .libs/libhts_la-vcf.o .libs/libhts_la-vcfutils.o cram/.libs/libhts_la-cram_codecs.o cram/.libs/libhts_la-cram_decode.o cram/.libs/libhts_la-cram_encode.o cram/.libs/libhts_la-cram_index.o cram/.libs/libhts_la-cram_io.o cram/.libs/libhts_la-cram_samtools.o cram/.libs/libhts_la-cram_stats.o cram/.libs/libhts_la-files.o cram/.libs/libhts_la-mFILE.o cram/.libs/libhts_la-md5.o cram/.libs/libhts_la-open_trace_file.o cram/.libs/libhts_la-pooled_alloc.o cram/.libs/libhts_la-rANS_static.o cram/.libs/libhts_la-sam_header.o cram/.libs/libhts_la-string_alloc.o cram/.libs/libhts_la-thread_pool.o cram/.libs/libhts_la-vlen.o cram/.libs/libhts_la-zfio.o -Wl,-force_load,lib/.libs/libgnu.a -L/usr/local/lib -lz -lm -O2 -install_name /Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/lib/libhts.0.dylib -compatibility_version 1 -current_version 1.0 -Wl,-single_module
libtool: link: (cd ".libs" && rm -f "libhts.dylib" && ln -s "libhts.0.dylib" "libhts.dylib")
libtool: link: (cd .libs/libhts.lax/libgnu.a && ar x "/private/tmp/Rtmps4BPel/R.INSTALL5e5b369e1f97/Rhtslib/src/htslib/lib/.libs/libgnu.a")
libtool: link: ar cru .libs/libhts.a libhts_la-kfunc.o libhts_la-knetfile.o libhts_la-kstring.o libhts_la-bgzf.o libhts_la-faidx.o libhts_la-hfile.o libhts_la-hfile_net.o libhts_la-hts.o libhts_la-regidx.o libhts_la-sam.o libhts_la-synced_bcf_reader.o libhts_la-vcf_sweep.o libhts_la-tbx.o libhts_la-vcf.o libhts_la-vcfutils.o cram/libhts_la-cram_codecs.o cram/libhts_la-cram_decode.o cram/libhts_la-cram_encode.o cram/libhts_la-cram_index.o cram/libhts_la-cram_io.o cram/libhts_la-cram_samtools.o cram/libhts_la-cram_stats.o cram/libhts_la-files.o cram/libhts_la-mFILE.o cram/libhts_la-md5.o cram/libhts_la-open_trace_file.o cram/libhts_la-pooled_alloc.o cram/libhts_la-rANS_static.o cram/libhts_la-sam_header.o cram/libhts_la-string_alloc.o cram/libhts_la-thread_pool.o cram/libhts_la-vlen.o cram/libhts_la-zfio.o .libs/libhts.lax/libgnu.a/fd-hook.o .libs/libhts.lax/libgnu.a/sys_socket.o .libs/libhts.lax/libgnu.a/unistd.o
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhts.a(fd-hook.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhts.a(sys_socket.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhts.a(unistd.o) has no symbols
libtool: link: ranlib .libs/libhts.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhts.a(fd-hook.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhts.a(sys_socket.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhts.a(unistd.o) has no symbols
libtool: link: rm -fr .libs/libhts.lax
libtool: link: ( cd ".libs" && rm -f "libhts.la" && ln -s "../libhts.la" "libhts.la" )
clang -DHAVE_CONFIG_H -I. -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o bgzip.o bgzip.c
/bin/sh ./libtool --tag=CC --mode=link clang -Wall -g -O2 -fPIC -L/usr/local/lib -o bgzip bgzip.o ./libhts.la ./lib/libgnu.la -lz -lm
libtool: link: clang -Wall -g -O2 -fPIC -o .libs/bgzip bgzip.o -L/usr/local/lib ./.libs/libhts.dylib ./lib/.libs/libgnu.a -lz -lm
clang -DHAVE_CONFIG_H -I. -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o htsfile.o htsfile.c
/bin/sh ./libtool --tag=CC --mode=link clang -Wall -g -O2 -fPIC -L/usr/local/lib -o htsfile htsfile.o ./libhts.la ./lib/libgnu.la -lz -lm
libtool: link: clang -Wall -g -O2 -fPIC -o .libs/htsfile htsfile.o -L/usr/local/lib ./.libs/libhts.dylib ./lib/.libs/libgnu.a -lz -lm
clang -DHAVE_CONFIG_H -I. -I./lib -I./htslib -I/usr/local/include -Wall -g -O2 -fPIC -c -o tabix.o tabix.c
/bin/sh ./libtool --tag=CC --mode=link clang -Wall -g -O2 -fPIC -L/usr/local/lib -o tabix tabix.o ./libhts.la ./lib/libgnu.la -lz -lm
libtool: link: clang -Wall -g -O2 -fPIC -o .libs/tabix tabix.o -L/usr/local/lib ./.libs/libhts.dylib ./lib/.libs/libgnu.a -lz -lm
installing libraries and headers...
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/lib/libhts.a(fd-hook.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/lib/libhts.a(sys_socket.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/lib/libhts.a(unistd.o) has no symbols
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Rhtslib.c -o Rhtslib.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rhtslib.so Rhtslib.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rhtslib)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "Rhtslib.buildbin-libdir/Rhtslib/libs//Rhtslib.so"
