Package: Rhtslib

Version: 1.10.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Rhtslib_1.10.0.tar.gz

StartedAt: 2018-04-12 02:25:32 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:27:06 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 93.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rhtslib.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Rhtslib_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhtslib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhtslib’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/winlib/i386/libhts.a src/winlib/x64/libhts.a
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  src/htslib/.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
  src/htslib/m4/lt˜obsolete.m4
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rhtslib’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    lib   5.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00check.log’
for details.

* installing *source* package ‘Rhtslib’ ...
** libs
running configuration...
cd ./htslib/ && ./configure --disable-dependency-tracking \
--prefix="/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/Rhtslib" \
CC="`"/home/biocbuild/bbs-3.6-bioc/R/bin/R" CMD config CC`" CFLAGS="`"/home/biocbuild/bbs-3.6-bioc/R/bin/R" CMD config CFLAGS` `"/home/biocbuild/bbs-3.6-bioc/R/bin/R" CMD config CPICFLAGS`" \
LDFLAGS="`"/home/biocbuild/bbs-3.6-bioc/R/bin/R" CMD config LDFLAGS`" CPPFLAGS="`"/home/biocbuild/bbs-3.6-bioc/R/bin/R" CMD config CPPFLAGS`" CPP="`"/home/biocbuild/bbs-3.6-bioc/R/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... /bin/mkdir -p
checking for gawk... gawk
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... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
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checking for sys/stat.h... yes
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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-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
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checking if the linker (/usr/bin/ld) is GNU ld... yes
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... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
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checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking if gcc PIC flag -fPIC -DPIC works... yes
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checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
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checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
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checking for alloca... yes
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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
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checking whether usleep is declared without a macro... yes
checking whether ln -s works... yes
checking for library containing pthread_create... -lpthread
checking for cos in -lm... yes
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checking alloca.h usability... yes
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checking fcntl.h usability... yes
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checking limits.h usability... yes
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checking stddef.h usability... yes
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checking for inline... inline
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checking for _LARGEFILE_SOURCE value needed for large files... no
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checking for GNU libc compatible realloc... yes
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checking for gethostbyaddr... yes
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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[1]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/missing autoconf
/bin/bash ./config.status --recheck
running CONFIG_SHELL=/bin/bash /bin/bash ./configure --disable-dependency-tracking --prefix=/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/Rhtslib CC=gcc CFLAGS=-g -O2 -Wall -fpic LDFLAGS=-L/usr/local/lib CPPFLAGS=-I/usr/local/include CPP=gcc -E --no-create --no-recursion
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
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... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking 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-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
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... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
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) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (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... yes
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... yes
checking for pid_t... yes
checking for mode_t... yes
checking whether fdatasync is declared... yes
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... yes
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... yes
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... yes
checking whether memrchr is declared without a macro... yes
checking whether rawmemchr is declared without a macro... yes
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... yes
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... yes
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... needs runtime check
checking whether fcntl is declared without a macro... yes
checking whether openat is declared without a macro... yes
checking for library containing fdatasync... none required
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... almost
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... yes
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... yes
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... yes
checking whether mkdtemp is declared without a macro... yes
checking whether mkostemp is declared without a macro... yes
checking whether mkostemps is declared without a macro... yes
checking whether mkstemp is declared without a macro... yes
checking whether mkstemps is declared without a macro... yes
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... yes
checking whether random is declared without a macro... yes
checking whether random_r is declared without a macro... yes
checking whether realpath is declared without a macro... yes
checking whether rpmatch is declared without a macro... yes
checking whether secure_getenv is declared without a macro... yes
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... yes
checking whether srandom is declared without a macro... yes
checking whether srandom_r is declared without a macro... yes
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... yes
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... yes
checking whether mknod is declared without a macro... yes
checking whether mknodat is declared without a macro... yes
checking whether stat is declared without a macro... yes
checking whether utimensat is declared without a macro... yes
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... yes
checking whether environ is declared without a macro... yes
checking whether euidaccess is declared without a macro... yes
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... yes
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... yes
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... yes
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... -lpthread
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... yes
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... 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
 /bin/bash ./config.status
config.status: creating Makefile
config.status: creating test/Makefile
config.status: creating lib/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/missing autoheader)
rm -f stamp-h1
touch config.h.in
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make  all-recursive
make[2]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
Making all in lib
make[3]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/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
/bin/mkdir -p 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''@|1|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''@|1|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''@|1|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 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
/bin/mkdir -p 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
/bin/mkdir -p 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
/bin/mkdir -p 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
/bin/mkdir -p 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
/bin/mkdir -p 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
/bin/mkdir -p 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''@|1|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
make[4]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
make[5]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -I/usr/local/include  -g -O2 -Wall -fpic -c -o fd-hook.lo fd-hook.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c fd-hook.c  -fPIC -DPIC -o .libs/fd-hook.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c fd-hook.c -o fd-hook.o >/dev/null 2>&1
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -I/usr/local/include  -g -O2 -Wall -fpic -c -o sys_socket.lo sys_socket.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c sys_socket.c  -fPIC -DPIC -o .libs/sys_socket.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c sys_socket.c -o sys_socket.o >/dev/null 2>&1
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -I/usr/local/include  -g -O2 -Wall -fpic -c -o unistd.lo unistd.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c unistd.c  -fPIC -DPIC -o .libs/unistd.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c unistd.c -o unistd.o >/dev/null 2>&1
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -I/usr/local/include  -g -O2 -Wall -fpic -c -o fcntl.lo fcntl.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c fcntl.c  -fPIC -DPIC -o .libs/fcntl.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c fcntl.c -o fcntl.o >/dev/null 2>&1
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -g -O2 -Wall -fpic  -no-undefined   -L/usr/local/lib -o libgnu.la  fd-hook.lo sys_socket.lo unistd.lo fcntl.lo  -lz -lm -lpthread 
libtool: link: ar cru .libs/libgnu.a .libs/fd-hook.o .libs/sys_socket.o .libs/unistd.o .libs/fcntl.o 
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libgnu.a
libtool: link: ( cd ".libs" && rm -f "libgnu.la" && ln -s "../libgnu.la" "libgnu.la" )
make[5]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
make[4]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
make[3]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
Making all in test
make[3]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/test'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/test'
make[3]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-kfunc.lo `test -f 'kfunc.c' || echo './'`kfunc.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c kfunc.c  -fPIC -DPIC -o .libs/libhts_la-kfunc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c kfunc.c -o libhts_la-kfunc.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-knetfile.lo `test -f 'knetfile.c' || echo './'`knetfile.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c knetfile.c  -fPIC -DPIC -o .libs/libhts_la-knetfile.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c knetfile.c -o libhts_la-knetfile.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-kstring.lo `test -f 'kstring.c' || echo './'`kstring.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c kstring.c  -fPIC -DPIC -o .libs/libhts_la-kstring.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c kstring.c -o libhts_la-kstring.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-bgzf.lo `test -f 'bgzf.c' || echo './'`bgzf.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c bgzf.c  -fPIC -DPIC -o .libs/libhts_la-bgzf.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c bgzf.c -o libhts_la-bgzf.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-faidx.lo `test -f 'faidx.c' || echo './'`faidx.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c faidx.c  -fPIC -DPIC -o .libs/libhts_la-faidx.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c faidx.c -o libhts_la-faidx.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-hfile.lo `test -f 'hfile.c' || echo './'`hfile.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c hfile.c  -fPIC -DPIC -o .libs/libhts_la-hfile.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c hfile.c -o libhts_la-hfile.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-hfile_net.lo `test -f 'hfile_net.c' || echo './'`hfile_net.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c hfile_net.c  -fPIC -DPIC -o .libs/libhts_la-hfile_net.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c hfile_net.c -o libhts_la-hfile_net.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-hts.lo `test -f 'hts.c' || echo './'`hts.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c hts.c  -fPIC -DPIC -o .libs/libhts_la-hts.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c hts.c -o libhts_la-hts.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-regidx.lo `test -f 'regidx.c' || echo './'`regidx.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c regidx.c  -fPIC -DPIC -o .libs/libhts_la-regidx.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c regidx.c -o libhts_la-regidx.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-sam.lo `test -f 'sam.c' || echo './'`sam.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c sam.c  -fPIC -DPIC -o .libs/libhts_la-sam.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c sam.c -o libhts_la-sam.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-synced_bcf_reader.lo `test -f 'synced_bcf_reader.c' || echo './'`synced_bcf_reader.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c synced_bcf_reader.c  -fPIC -DPIC -o .libs/libhts_la-synced_bcf_reader.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c synced_bcf_reader.c -o libhts_la-synced_bcf_reader.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-vcf_sweep.lo `test -f 'vcf_sweep.c' || echo './'`vcf_sweep.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c vcf_sweep.c  -fPIC -DPIC -o .libs/libhts_la-vcf_sweep.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c vcf_sweep.c -o libhts_la-vcf_sweep.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-tbx.lo `test -f 'tbx.c' || echo './'`tbx.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c tbx.c  -fPIC -DPIC -o .libs/libhts_la-tbx.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c tbx.c -o libhts_la-tbx.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-vcf.lo `test -f 'vcf.c' || echo './'`vcf.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c vcf.c  -fPIC -DPIC -o .libs/libhts_la-vcf.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c vcf.c -o libhts_la-vcf.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o libhts_la-vcfutils.lo `test -f 'vcfutils.c' || echo './'`vcfutils.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c vcfutils.c  -fPIC -DPIC -o .libs/libhts_la-vcfutils.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c vcfutils.c -o libhts_la-vcfutils.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-cram_codecs.lo `test -f 'cram/cram_codecs.c' || echo './'`cram/cram_codecs.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_codecs.c  -fPIC -DPIC -o cram/.libs/libhts_la-cram_codecs.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_codecs.c -o cram/libhts_la-cram_codecs.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-cram_decode.lo `test -f 'cram/cram_decode.c' || echo './'`cram/cram_decode.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_decode.c  -fPIC -DPIC -o cram/.libs/libhts_la-cram_decode.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_decode.c -o cram/libhts_la-cram_decode.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-cram_encode.lo `test -f 'cram/cram_encode.c' || echo './'`cram/cram_encode.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_encode.c  -fPIC -DPIC -o cram/.libs/libhts_la-cram_encode.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_encode.c -o cram/libhts_la-cram_encode.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-cram_index.lo `test -f 'cram/cram_index.c' || echo './'`cram/cram_index.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_index.c  -fPIC -DPIC -o cram/.libs/libhts_la-cram_index.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_index.c -o cram/libhts_la-cram_index.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-cram_io.lo `test -f 'cram/cram_io.c' || echo './'`cram/cram_io.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_io.c  -fPIC -DPIC -o cram/.libs/libhts_la-cram_io.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_io.c -o cram/libhts_la-cram_io.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-cram_samtools.lo `test -f 'cram/cram_samtools.c' || echo './'`cram/cram_samtools.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_samtools.c  -fPIC -DPIC -o cram/.libs/libhts_la-cram_samtools.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_samtools.c -o cram/libhts_la-cram_samtools.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-cram_stats.lo `test -f 'cram/cram_stats.c' || echo './'`cram/cram_stats.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_stats.c  -fPIC -DPIC -o cram/.libs/libhts_la-cram_stats.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/cram_stats.c -o cram/libhts_la-cram_stats.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-files.lo `test -f 'cram/files.c' || echo './'`cram/files.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/files.c  -fPIC -DPIC -o cram/.libs/libhts_la-files.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/files.c -o cram/libhts_la-files.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-mFILE.lo `test -f 'cram/mFILE.c' || echo './'`cram/mFILE.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/mFILE.c  -fPIC -DPIC -o cram/.libs/libhts_la-mFILE.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/mFILE.c -o cram/libhts_la-mFILE.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-md5.lo `test -f 'cram/md5.c' || echo './'`cram/md5.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/md5.c  -fPIC -DPIC -o cram/.libs/libhts_la-md5.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/md5.c -o cram/libhts_la-md5.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -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:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/open_trace_file.c  -fPIC -DPIC -o cram/.libs/libhts_la-open_trace_file.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/open_trace_file.c -o cram/libhts_la-open_trace_file.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-pooled_alloc.lo `test -f 'cram/pooled_alloc.c' || echo './'`cram/pooled_alloc.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/pooled_alloc.c  -fPIC -DPIC -o cram/.libs/libhts_la-pooled_alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/pooled_alloc.c -o cram/libhts_la-pooled_alloc.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-rANS_static.lo `test -f 'cram/rANS_static.c' || echo './'`cram/rANS_static.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/rANS_static.c  -fPIC -DPIC -o cram/.libs/libhts_la-rANS_static.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/rANS_static.c -o cram/libhts_la-rANS_static.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-sam_header.lo `test -f 'cram/sam_header.c' || echo './'`cram/sam_header.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/sam_header.c  -fPIC -DPIC -o cram/.libs/libhts_la-sam_header.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/sam_header.c -o cram/libhts_la-sam_header.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-string_alloc.lo `test -f 'cram/string_alloc.c' || echo './'`cram/string_alloc.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/string_alloc.c  -fPIC -DPIC -o cram/.libs/libhts_la-string_alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/string_alloc.c -o cram/libhts_la-string_alloc.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-thread_pool.lo `test -f 'cram/thread_pool.c' || echo './'`cram/thread_pool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/thread_pool.c  -fPIC -DPIC -o cram/.libs/libhts_la-thread_pool.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/thread_pool.c -o cram/libhts_la-thread_pool.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-vlen.lo `test -f 'cram/vlen.c' || echo './'`cram/vlen.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/vlen.c  -fPIC -DPIC -o cram/.libs/libhts_la-vlen.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/vlen.c -o cram/libhts_la-vlen.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.  -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o cram/libhts_la-zfio.lo `test -f 'cram/zfio.c' || echo './'`cram/zfio.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/zfio.c  -fPIC -DPIC -o cram/.libs/libhts_la-zfio.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -Ihtslib -Icram -I./lib -I./htslib -I/usr/local/include -g -O2 -Wall -fpic -c cram/zfio.c -o cram/libhts_la-zfio.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=link gcc  -g -O2 -Wall -fpic   -no-undefined -L/usr/local/lib -o libhts.la -rpath /home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/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 -lpthread 
libtool: link: gcc -shared  -fPIC -DPIC  .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,--whole-archive lib/.libs/libgnu.a -Wl,--no-whole-archive  -L/usr/local/lib -lz -lm -lpthread  -O2   -Wl,-soname -Wl,libhts.so.0 -o .libs/libhts.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libhts.so.0" && ln -s "libhts.so.0.0.0" "libhts.so.0")
libtool: link: (cd ".libs" && rm -f "libhts.so" && ln -s "libhts.so.0.0.0" "libhts.so")
libtool: link: (cd .libs/libhts.lax/libgnu.a && ar x "/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/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/fcntl.o .libs/libhts.lax/libgnu.a/fd-hook.o .libs/libhts.lax/libgnu.a/sys_socket.o .libs/libhts.lax/libgnu.a/unistd.o 
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libhts.a
libtool: link: rm -fr .libs/libhts.lax
libtool: link: ( cd ".libs" && rm -f "libhts.la" && ln -s "../libhts.la" "libhts.la" )
gcc -DHAVE_CONFIG_H -I.  -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o bgzip.o bgzip.c
/bin/bash ./libtool  --tag=CC   --mode=link gcc  -g -O2 -Wall -fpic  -L/usr/local/lib -o bgzip bgzip.o ./libhts.la ./lib/libgnu.la   -lz -lm -lpthread 
libtool: link: gcc -g -O2 -Wall -fpic -o .libs/bgzip bgzip.o  -L/usr/local/lib ./.libs/libhts.so ./lib/.libs/libgnu.a -lz -lm -lpthread -Wl,-rpath -Wl,/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/Rhtslib/lib
gcc -DHAVE_CONFIG_H -I.  -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o htsfile.o htsfile.c
/bin/bash ./libtool  --tag=CC   --mode=link gcc  -g -O2 -Wall -fpic  -L/usr/local/lib -o htsfile htsfile.o ./libhts.la ./lib/libgnu.la   -lz -lm -lpthread 
libtool: link: gcc -g -O2 -Wall -fpic -o .libs/htsfile htsfile.o  -L/usr/local/lib ./.libs/libhts.so ./lib/.libs/libgnu.a -lz -lm -lpthread -Wl,-rpath -Wl,/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/Rhtslib/lib
gcc -DHAVE_CONFIG_H -I.  -I./lib -I./htslib -I/usr/local/include  -g -O2 -Wall -fpic -c -o tabix.o tabix.c
/bin/bash ./libtool  --tag=CC   --mode=link gcc  -g -O2 -Wall -fpic  -L/usr/local/lib -o tabix tabix.o ./libhts.la ./lib/libgnu.la   -lz -lm -lpthread 
libtool: link: gcc -g -O2 -Wall -fpic -o .libs/tabix tabix.o  -L/usr/local/lib ./.libs/libhts.so ./lib/.libs/libgnu.a -lz -lm -lpthread -Wl,-rpath -Wl,/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/Rhtslib/lib
make[3]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
make[2]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
make[1]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
installing libraries and headers...
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Rhtslib.c -o Rhtslib.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o Rhtslib.so Rhtslib.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing libraries and headers...
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Rhtslib.c -o Rhtslib.o
installing to /home/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/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)

name	user	system	elapsed
Rhtslib-package	0.012	0.000	0.013
pkgconfig	0.016	0.000	0.016