Rhtslib 1.2.0
Nathaniel Hayden
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rhtslib | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rhtslib_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Rhtslib.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ... [62s/63s] OK
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
lib 5.7Mb
* 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 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 ... [0s/0s] 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-3.2-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-3.2-bioc/meat/Rhtslib.Rcheck/Rhtslib" \
CC="`"/home/biocbuild/bbs-3.2-bioc/R/bin/R" CMD config CC`" CFLAGS="`"/home/biocbuild/bbs-3.2-bioc/R/bin/R" CMD config CFLAGS` `"/home/biocbuild/bbs-3.2-bioc/R/bin/R" CMD config CPICFLAGS`" \
LDFLAGS="`"/home/biocbuild/bbs-3.2-bioc/R/bin/R" CMD config LDFLAGS`" CPPFLAGS="`"/home/biocbuild/bbs-3.2-bioc/R/bin/R" CMD config CPPFLAGS`" CPP="`"/home/biocbuild/bbs-3.2-bioc/R/bin/R" CMD config CPP`"
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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-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
make all-recursive
make[2]: Entering directory `/home/biocbuild/bbs-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
Making all in lib
make[3]: Entering directory `/home/biocbuild/bbs-3.2-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 stddef.h-t stddef.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_STDDEF_H''@|<stddef.h>|g' \
-e 's|@''HAVE_MAX_ALIGN_T''@|0|g' \
-e 's|@''HAVE_WCHAR_T''@|1|g' \
-e 's|@''REPLACE_NULL''@|0|g' \
< ./stddef.in.h; \
} > stddef.h-t && \
mv stddef.h-t stddef.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-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
make[5]: Entering directory `/home/biocbuild/bbs-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
/bin/bash ../libtool --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c -o fd-hook.lo fd-hook.c
libtool: compile: gcc -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c -o sys_socket.lo sys_socket.c
libtool: compile: gcc -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c -o unistd.lo unistd.c
libtool: compile: gcc -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -g -O2 -Wall -fpic -c -o fcntl.lo fcntl.c
libtool: compile: gcc -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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
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-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
make[4]: Leaving directory `/home/biocbuild/bbs-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
make[3]: Leaving directory `/home/biocbuild/bbs-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/lib'
Making all in test
make[3]: Entering directory `/home/biocbuild/bbs-3.2-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-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib/test'
make[3]: Entering directory `/home/biocbuild/bbs-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
/bin/bash ./libtool --tag=CC --mode=compile gcc -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -g -O2 -Wall -fpic -no-undefined -L/usr/local/lib -o libhts.la -rpath /home/biocbuild/bbs-3.2-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 -std=gnu99 -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-3.2-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
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 -std=gnu99 -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 -std=gnu99 -g -O2 -Wall -fpic -L/usr/local/lib -o bgzip bgzip.o ./libhts.la ./lib/libgnu.la -lz -lm -lpthread
libtool: link: gcc -std=gnu99 -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-3.2-bioc/meat/Rhtslib.Rcheck/Rhtslib/lib
gcc -std=gnu99 -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 -std=gnu99 -g -O2 -Wall -fpic -L/usr/local/lib -o htsfile htsfile.o ./libhts.la ./lib/libgnu.la -lz -lm -lpthread
libtool: link: gcc -std=gnu99 -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-3.2-bioc/meat/Rhtslib.Rcheck/Rhtslib/lib
gcc -std=gnu99 -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 -std=gnu99 -g -O2 -Wall -fpic -L/usr/local/lib -o tabix tabix.o ./libhts.la ./lib/libgnu.la -lz -lm -lpthread
libtool: link: gcc -std=gnu99 -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-3.2-bioc/meat/Rhtslib.Rcheck/Rhtslib/lib
make[3]: Leaving directory `/home/biocbuild/bbs-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
make[2]: Leaving directory `/home/biocbuild/bbs-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
make[1]: Leaving directory `/home/biocbuild/bbs-3.2-bioc/meat/Rhtslib.Rcheck/00_pkg_src/Rhtslib/src/htslib'
installing libraries and headers...
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c Rhtslib.c -o Rhtslib.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o Rhtslib.so Rhtslib.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing libraries and headers...
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c Rhtslib.c -o Rhtslib.o
installing to /home/biocbuild/bbs-3.2-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)