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Gentoo's Bugzilla – Attachment 880905 Details for
Bug 920917
sci-biology/emboss-6.6.0-r2 - ajreg.c: error: assignment to struct real_pcre from incompatible pointer type pcre {aka struct real_pcre8_or_16 } [-Winc
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sci-biology:emboss-6.6.0-r2:20231229-021617.log
sci-biology:emboss-6.6.0-r2:20231229-021617.log (text/plain), 60.04 KB, created by
Toralf Förster
on 2023-12-29 09:21:10 UTC
(
hide
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Description:
sci-biology:emboss-6.6.0-r2:20231229-021617.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2023-12-29 09:21:10 UTC
Size:
60.04 KB
patch
obsolete
> * Package: sci-biology/emboss-6.6.0-r2:0 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: X abi_x86_64 amd64 elibc_glibc kernel_linux pdf png > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox > >>>> Unpacking source... >>>> Unpacking EMBOSS-6.6.0.tar.gz to /var/tmp/portage/sci-biology/emboss-6.6.0-r2/work >>>> Unpacking emboss-6.6.0-patches-r1.tar.xz to /var/tmp/portage/sci-biology/emboss-6.6.0-r2/work >>>> Source unpacked in /var/tmp/portage/sci-biology/emboss-6.6.0-r2/work >>>> Preparing source in /var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0 ... > * Applying emboss-6.6.0-fix-build-system.patch ... > [ ok ] > * Applying emboss-6.6.0-FORTIFY_SOURCE-fix.patch ... > [ ok ] > * Applying emboss-6.6.0-plplot-declarations.patch ... > [ ok ] > * Applying emboss-6.6.0-qa-implicit-declarations.patch ... > [ ok ] > * Applying emboss-6.6.0-C99-bool.patch ... > [ ok ] > * Applying emboss-6.6.0-Wimplicit-function-declaration.patch ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0' ... > * Running 'libtoolize --install --copy --force --automake' ... > [ ok ] > * Running 'aclocal -I m4 --system-acdir=/var/tmp/portage/sci-biology/emboss-6.6.0-r2/temp/aclocal' ... > [ ok ] > * Moving configure.in to configure.ac (bug #426262) > * Running 'autoconf --force' ... > [ ok ] > * Running 'autoheader' ... > [ ok ] > * Running 'automake --add-missing --copy --force-missing' ... > [ ok ] > * Running elibtoolize in: EMBOSS-6.6.0/ > * Applying portage/1.2.0 patch ... > * Applying sed/1.5.6 patch ... > * Applying as-needed/2.4.3 patch ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0 ... > * econf: updating EMBOSS-6.6.0/config.guess with /usr/share/gnuconfig/config.guess > * econf: updating EMBOSS-6.6.0/config.sub with /usr/share/gnuconfig/config.sub >./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --disable-static --docdir=/usr/share/doc/emboss-6.6.0-r2 --htmldir=/usr/share/doc/emboss-6.6.0-r2/html --with-sysroot=/ --libdir=/usr/lib64 --enable-shared --with-x --with-pngdriver=/usr --with-hpdf=/usr --without-mysql --without-postgresql --enable-large --without-java --enable-systemlibs >checking for gawk... gawk >checking for x86_64-pc-linux-gnu-icc... no >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking whether the C compiler works... yes >checking for C compiler default output file name... a.out >checking for suffix of executables... >checking whether we are cross compiling... no >checking for suffix of object files... o >checking whether the compiler supports GNU C... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... none needed >checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes >checking for x86_64-pc-linux-gnu-icpc... no >checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ >checking whether the compiler supports GNU C++... yes >checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes >checking for x86_64-pc-linux-gnu-g++ option to enable C++11 features... none needed >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for a BSD-compatible install... /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c >checking whether ln -s works... yes >checking whether make sets $(MAKE)... yes >checking for a race-free mkdir -p... /bin/mkdir -p >checking whether build environment is sane... yes >checking whether make supports the include directive... yes (GNU style) >checking whether make supports nested variables... yes >checking dependency style of x86_64-pc-linux-gnu-gcc... none >checking dependency style of x86_64-pc-linux-gnu-g++... none >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking how to print strings... printf >checking for a sed that does not truncate output... /bin/sed >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for fgrep... /bin/grep -F >checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B >checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm >checking the maximum length of command line arguments... 1572864 >checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop >checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-file... no >checking for file... file >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-dlltool... x86_64-pc-linux-gnu-dlltool >checking how to associate runtime and link libraries... printf %s\n >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok >checking for sysroot... / >checking for a working dd... /bin/dd >checking how to truncate binary pipes... /bin/dd bs=4096 count=1 >checking for x86_64-pc-linux-gnu-mt... no >checking for mt... no >checking if : is a manifest tool... no >checking for stdio.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for strings.h... yes >checking for sys/stat.h... yes >checking for sys/types.h... yes >checking for unistd.h... yes >checking for vfork.h... no >checking for dlfcn.h... yes >checking for objdir... .libs >checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/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... no >checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E >checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (cached) GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking for X... libraries , headers >checking for gethostbyname... yes >checking for connect... yes >checking for remove... yes >checking for shmat... yes >checking for IceConnectionNumber in -lICE... yes >checking for dirent.h that defines DIR... yes >checking for library containing opendir... none required >checking for egrep... (cached) /bin/grep -E >checking for unistd.h... (cached) yes >checking for TargetConfig.h... no >checking whether byte ordering is bigendian... no >checking for an ANSI C-conforming const... yes >checking for inline... inline >checking for pid_t... yes >checking for size_t... yes >checking whether struct tm is in sys/time.h or time.h... time.h >checking whether getpgrp requires zero arguments... yes >checking for strftime... yes >checking for fork... yes >checking for vfork... yes >checking for vprintf... yes >checking for working fork... yes >checking for working vfork... (cached) yes >checking for memmove... yes >checking for X11/Xlib.h... yes >checking for socket in -lc... yes >checking for main in -lm... yes >checking if docroot is given... no >checking if gcc profiling is selected... no >checking if gcov coverage is selected... no >configure: checking for EMBOSS pre-indexed databases >checking for ./emboss/index/edam.xac... yes >checking for Java JNI... no >checking for Java JNI OS... no >checking for authorisation type... no >checking for threading type... no >checking whether to look for pdf support... yes >checking for HPDF_New in -lhpdf... yes >PDF support found >checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config >checking pkg-config is at least version 0.9.0... yes >checking whether to look for axis2c support... no >checking if png driver is wanted... yes >checking for inflateEnd in -lz... yes >checking for png_destroy_read_struct in -lpng... yes >checking for gdImageCreateFromPng in -lgd... yes >PNG libraries found >checking for large file support... yes >checking for PCRE... yes >checking for EXPAT... yes >checking for ZLIB... yes >checking for PLPLOT... no >checking for PLPLOT... yes >checking for purify... no >checking for cygwin... no >checking for savestats... no >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating ajax/Makefile >config.status: creating ajax/acd/Makefile >config.status: creating ajax/ajaxdb/Makefile >config.status: creating ajax/core/Makefile >config.status: creating ajax/ensembl/Makefile >config.status: creating ajax/expat/Makefile >config.status: creating ajax/graphics/Makefile >config.status: creating ajax/pcre/Makefile >config.status: creating ajax/zlib/Makefile >config.status: creating doc/Makefile >config.status: creating doc/manuals/Makefile >config.status: creating doc/programs/Makefile >config.status: creating doc/programs/html/Makefile >config.status: creating doc/programs/text/Makefile >config.status: creating doc/tutorials/Makefile >config.status: creating emboss/Makefile >config.status: creating emboss/acd/Makefile >config.status: creating emboss/data/AAINDEX/Makefile >config.status: creating emboss/data/CODONS/Makefile >config.status: creating emboss/data/JASPAR_CNE/Makefile >config.status: creating emboss/data/JASPAR_CORE/Makefile >config.status: creating emboss/data/JASPAR_FAM/Makefile >config.status: creating emboss/data/JASPAR_PBM/Makefile >config.status: creating emboss/data/JASPAR_PBM_HLH/Makefile >config.status: creating emboss/data/JASPAR_PBM_HOMEO/Makefile >config.status: creating emboss/data/JASPAR_PHYLOFACTS/Makefile >config.status: creating emboss/data/JASPAR_POLII/Makefile >config.status: creating emboss/data/JASPAR_SPLICE/Makefile >config.status: creating emboss/data/Makefile >config.status: creating emboss/data/OBO/Makefile >config.status: creating emboss/data/PRINTS/Makefile >config.status: creating emboss/data/PROSITE/Makefile >config.status: creating emboss/data/REBASE/Makefile >config.status: creating emboss/data/TAXONOMY/Makefile >config.status: creating emboss/index/Makefile >config.status: creating jemboss/Makefile >config.status: creating jemboss/runJemboss.sh >config.status: creating jemboss/images/Makefile >config.status: creating jemboss/lib/Makefile >config.status: creating jemboss/lib/axis/Makefile >config.status: creating jemboss/resources/Makefile >config.status: creating jemboss/utils/Makefile >config.status: creating nucleus/Makefile >config.status: creating plplot/Makefile >config.status: creating plplot/lib/Makefile >config.status: creating test/Makefile >config.status: creating test/data/Makefile >config.status: creating test/embl/Makefile >config.status: creating test/genbank/Makefile >config.status: creating test/pir/Makefile >config.status: creating test/swiss/Makefile >config.status: creating test/swnew/Makefile >config.status: creating test/testdb/Makefile >config.status: creating ajax/core/config.h >config.status: executing depfiles commands >config.status: executing libtool commands >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0 ... >make -j4 >Making all in ajax >make[1]: Entering directory '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/ajax' >Making all in core >make[2]: Entering directory '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/ajax/core' >make all-am >make[3]: Entering directory '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/ajax/core' >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajalign.lo `test -f 'ajalign.c' || echo './'`ajalign.c >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajarr.lo `test -f 'ajarr.c' || echo './'`ajarr.c >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajassem.lo `test -f 'ajassem.c' || echo './'`ajassem.c >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajassemread.lo `test -f 'ajassemread.c' || echo './'`ajassemread.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajarr.c -fPIC -DPIC -o .libs/libajax_la-ajarr.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajassemread.c -fPIC -DPIC -o .libs/libajax_la-ajassemread.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajassem.c -fPIC -DPIC -o .libs/libajax_la-ajassem.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajalign.c -fPIC -DPIC -o .libs/libajax_la-ajalign.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajassemwrite.lo `test -f 'ajassemwrite.c' || echo './'`ajassemwrite.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajassemwrite.c -fPIC -DPIC -o .libs/libajax_la-ajassemwrite.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajassert.lo `test -f 'ajassert.c' || echo './'`ajassert.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajassert.c -fPIC -DPIC -o .libs/libajax_la-ajassert.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajbamindex.lo `test -f 'ajbamindex.c' || echo './'`ajbamindex.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajbamindex.c -fPIC -DPIC -o .libs/libajax_la-ajbamindex.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajbase.lo `test -f 'ajbase.c' || echo './'`ajbase.c >ajbamindex.c: In function 'bamIndexLoadCore': >ajbamindex.c:720:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] > 720 | fread(magic, 1, 4, fp); > | ^~~~~~~~~~~~~~~~~~~~~~ >ajbamindex.c:731:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] > 731 | fread(&idx->n, 4, 1, fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >ajbamindex.c:747:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] > 747 | fread(&n_bin, 4, 1, fp); > | ^~~~~~~~~~~~~~~~~~~~~~~ >ajbamindex.c:756:13: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] > 756 | fread(&binid, 4, 1, fp); > | ^~~~~~~~~~~~~~~~~~~~~~~ >ajbamindex.c:765:13: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] > 765 | fread(&binlist->n, 4, 1, fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ >ajbamindex.c:773:13: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] > 773 | fread(binlist->list, 16, binlist->n, fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >ajbamindex.c:799:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] > 799 | fread(&index2->n, 4, 1, fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >ajbamindex.c:807:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] > 807 | fread(index2->offset, index2->n, 8, fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajbase.c -fPIC -DPIC -o .libs/libajax_la-ajbase.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajcall.lo `test -f 'ajcall.c' || echo './'`ajcall.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajcall.c -fPIC -DPIC -o .libs/libajax_la-ajcall.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajcigar.lo `test -f 'ajcigar.c' || echo './'`ajcigar.c >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajcod.lo `test -f 'ajcod.c' || echo './'`ajcod.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajcigar.c -fPIC -DPIC -o .libs/libajax_la-ajcigar.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajcod.c -fPIC -DPIC -o .libs/libajax_la-ajcod.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajdan.lo `test -f 'ajdan.c' || echo './'`ajdan.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajdan.c -fPIC -DPIC -o .libs/libajax_la-ajdan.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajdmx.lo `test -f 'ajdmx.c' || echo './'`ajdmx.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajdmx.c -fPIC -DPIC -o .libs/libajax_la-ajdmx.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajdom.lo `test -f 'ajdom.c' || echo './'`ajdom.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajdom.c -fPIC -DPIC -o .libs/libajax_la-ajdom.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajdomain.lo `test -f 'ajdomain.c' || echo './'`ajdomain.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajdomain.c -fPIC -DPIC -o .libs/libajax_la-ajdomain.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajexcept.lo `test -f 'ajexcept.c' || echo './'`ajexcept.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajexcept.c -fPIC -DPIC -o .libs/libajax_la-ajexcept.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajfeat.lo `test -f 'ajfeat.c' || echo './'`ajfeat.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajfeat.c -fPIC -DPIC -o .libs/libajax_la-ajfeat.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajfeatread.lo `test -f 'ajfeatread.c' || echo './'`ajfeatread.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajfeatread.c -fPIC -DPIC -o .libs/libajax_la-ajfeatread.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajfeatwrite.lo `test -f 'ajfeatwrite.c' || echo './'`ajfeatwrite.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajfeatwrite.c -fPIC -DPIC -o .libs/libajax_la-ajfeatwrite.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajfile.lo `test -f 'ajfile.c' || echo './'`ajfile.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajfile.c -fPIC -DPIC -o .libs/libajax_la-ajfile.o >ajfile.c: In function 'ajFileNewListinPathWild': >ajfile.c:1527:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 1527 | !readdir_r(dp,(struct dirent *)buf,&de) > | ^ >In file included from /usr/include/features.h:503, > from /usr/include/sys/types.h:25, > from ajarch.h:33, > from ajdefine.h:48, > from ajlib.h:34, > from ajfile.c:33: >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFileNewListinPathWildExclude': >ajfile.c:1629:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 1629 | !readdir_r(dp,(struct dirent *)buf,&de) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFilebuffNewPathWild': >ajfile.c:3222:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 3222 | !readdir_r(dp,(struct dirent *)buf,&de) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFilebuffNewPathWildExclude': >ajfile.c:3325:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 3325 | !readdir_r(dp,(struct dirent *)buf,&de) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFilewildnameExistsDir': >ajfile.c:7138:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 7138 | !readdir_r(dp,(struct dirent *)buf,&de) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajDirnamePrintRecursiveIgnore': >ajfile.c:7475:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 7475 | !readdir_r(indir,(struct dirent *)buf,&dp) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFilelistAddDirectory': >ajfile.c:7703:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 7703 | !readdir_r(indir,(struct dirent *)buf,&dp) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFilelistAddPath': >ajfile.c:7876:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 7876 | !readdir_r(indir,(struct dirent *)buf,&dp) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFilelistAddPathDir': >ajfile.c:7997:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 7997 | !readdir_r(indir,(struct dirent *)buf,&dp) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFilelistAddPathWild': >ajfile.c:8106:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 8106 | !readdir_r(indir,(struct dirent *)buf,&dp) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFilelistAddPathWildDir': >ajfile.c:8217:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 8217 | !readdir_r(indir,(struct dirent *)buf,&dp) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFilelistAddPathWildRecursiveIgnore': >ajfile.c:8423:9: warning: 'readdir_r' is deprecated [-Wdeprecated-declarations] > 8423 | !readdir_r(indir,(struct dirent *)buf,&dp) > | ^ >/usr/include/dirent.h:191:12: note: declared here > 191 | extern int __REDIRECT (readdir_r, > | ^~~~~~~~~~ >ajfile.c: In function 'ajFileSetEof': >ajfile.c:2408:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] > 2408 | fread(&c, 1, 1, file->fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajfiledata.lo `test -f 'ajfiledata.c' || echo './'`ajfiledata.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajfiledata.c -fPIC -DPIC -o .libs/libajax_la-ajfiledata.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajfileio.lo `test -f 'ajfileio.c' || echo './'`ajfileio.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajfileio.c -fPIC -DPIC -o .libs/libajax_la-ajfileio.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajfmt.lo `test -f 'ajfmt.c' || echo './'`ajfmt.c >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajftp.lo `test -f 'ajftp.c' || echo './'`ajftp.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajfmt.c -fPIC -DPIC -o .libs/libajax_la-ajfmt.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajhttp.lo `test -f 'ajhttp.c' || echo './'`ajhttp.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajftp.c -fPIC -DPIC -o .libs/libajax_la-ajftp.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajhttp.c -fPIC -DPIC -o .libs/libajax_la-ajhttp.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajindex.lo `test -f 'ajindex.c' || echo './'`ajindex.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajindex.c -fPIC -DPIC -o .libs/libajax_la-ajindex.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajjava.lo `test -f 'ajjava.c' || echo './'`ajjava.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajjava.c -fPIC -DPIC -o .libs/libajax_la-ajjava.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajlist.lo `test -f 'ajlist.c' || echo './'`ajlist.c >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajmath.lo `test -f 'ajmath.c' || echo './'`ajmath.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajlist.c -fPIC -DPIC -o .libs/libajax_la-ajlist.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajmath.c -fPIC -DPIC -o .libs/libajax_la-ajmath.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajmatrices.lo `test -f 'ajmatrices.c' || echo './'`ajmatrices.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajmatrices.c -fPIC -DPIC -o .libs/libajax_la-ajmatrices.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajmem.lo `test -f 'ajmem.c' || echo './'`ajmem.c >libtool: 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-DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajmess.c -fPIC -DPIC -o .libs/libajax_la-ajmess.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajnam.lo `test -f 'ajnam.c' || echo './'`ajnam.c >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajnexus.lo `test -f 'ajnexus.c' || echo './'`ajnexus.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajnam.c -fPIC -DPIC -o .libs/libajax_la-ajnam.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajnexus.c -fPIC -DPIC -o .libs/libajax_la-ajnexus.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajobo.lo `test -f 'ajobo.c' || echo './'`ajobo.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajobo.c -fPIC -DPIC -o .libs/libajax_la-ajobo.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajoboread.lo `test -f 'ajoboread.c' || echo './'`ajoboread.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajoboread.c -fPIC -DPIC -o .libs/libajax_la-ajoboread.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajobowrite.lo `test -f 'ajobowrite.c' || echo './'`ajobowrite.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajobowrite.c -fPIC -DPIC -o .libs/libajax_la-ajobowrite.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajpat.lo `test -f 'ajpat.c' || echo './'`ajpat.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajpat.c -fPIC -DPIC -o .libs/libajax_la-ajpat.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajpdb.lo `test -f 'ajpdb.c' || echo './'`ajpdb.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajpdb.c -fPIC -DPIC -o .libs/libajax_la-ajpdb.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajpdbio.lo `test -f 'ajpdbio.c' || echo './'`ajpdbio.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajpdbio.c -fPIC -DPIC -o .libs/libajax_la-ajpdbio.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajphylo.lo `test -f 'ajphylo.c' || echo './'`ajphylo.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajphylo.c -fPIC -DPIC -o .libs/libajax_la-ajphylo.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajquery.lo `test -f 'ajquery.c' || echo './'`ajquery.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajquery.c -fPIC -DPIC -o .libs/libajax_la-ajquery.o >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajrange.lo `test -f 'ajrange.c' || echo './'`ajrange.c >/bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"Linux\"" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c -o libajax_la-ajreg.lo `test -f 'ajreg.c' || echo './'`ajreg.c >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajrange.c -fPIC -DPIC -o .libs/libajax_la-ajrange.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DNO_AUTH -DAJAX_FIXED_ROOT=\"/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ajreg.c -fPIC -DPIC -o .libs/libajax_la-ajreg.o >ajreg.c: In function 'ajRegCompC': >ajreg.c:95:15: error: assignment to 'struct real_pcre *' from incompatible pointer type 'pcre *' {aka 'struct real_pcre8_or_16 *'} [-Wincompatible-pointer-types] > 95 | ret->pcre = pcre_compile(rexp, options, &errptr, &errpos, tableptr); > | ^ >ajreg.c: In function 'ajRegCompCaseC': >ajreg.c:158:15: error: assignment to 'struct real_pcre *' from incompatible pointer type 'pcre *' {aka 'struct real_pcre8_or_16 *'} [-Wincompatible-pointer-types] > 158 | ret->pcre = pcre_compile(rexp, options, &errptr, &errpos, tableptr); > | ^ >ajreg.c: In function 'ajRegExec': >ajreg.c:208:28: error: passing argument 1 of 'pcre_exec' from incompatible pointer type [-Wincompatible-pointer-types] > 208 | status = pcre_exec(prog->pcre, prog->extra, ajStrGetPtr(str), > | ~~~~^~~~~~ > | | > | struct real_pcre * >In file included from ajreg.h:42, > from ajreg.c:34: >/usr/include/pcre.h:573:30: note: expected 'const pcre *' {aka 'const struct real_pcre8_or_16 *'} but argument is of type 'struct real_pcre *' > 573 | PCRE_EXP_DECL int pcre_exec(const pcre *, const pcre_extra *, PCRE_SPTR, > | ^~~~~~~~~~~~ >ajreg.c: In function 'ajRegExecC': >ajreg.c:259:28: error: passing argument 1 of 'pcre_exec' from incompatible pointer type [-Wincompatible-pointer-types] > 259 | status = pcre_exec(prog->pcre, prog->extra, str, strlen(str), > | ~~~~^~~~~~ > | | > | struct real_pcre * >/usr/include/pcre.h:573:30: note: expected 'const pcre *' {aka 'const struct real_pcre8_or_16 *'} but argument is of type 'struct real_pcre *' > 573 | PCRE_EXP_DECL int pcre_exec(const pcre *, const pcre_extra *, PCRE_SPTR, > | ^~~~~~~~~~~~ >ajreg.c: In function 'ajRegExecall': >ajreg.c:313:39: error: passing argument 1 of 'pcre_dfa_exec' from incompatible pointer type [-Wincompatible-pointer-types] > 313 | prog->matches = pcre_dfa_exec(prog->pcre, prog->extra, > | ~~~~^~~~~~ > | | > | struct real_pcre * >/usr/include/pcre.h:567:34: note: expected 'const pcre *' {aka 'const struct real_pcre8_or_16 *'} but argument is of type 'struct real_pcre *' > 567 | PCRE_EXP_DECL int pcre_dfa_exec(const pcre *, const pcre_extra *, > | ^~~~~~~~~~~~ >ajreg.c: In function 'ajRegExecallC': >ajreg.c:371:39: error: passing argument 1 of 'pcre_dfa_exec' from incompatible pointer type [-Wincompatible-pointer-types] > 371 | prog->matches = pcre_dfa_exec(prog->pcre, prog->extra, > | ~~~~^~~~~~ > | | > | struct real_pcre * >/usr/include/pcre.h:567:34: note: expected 'const pcre *' {aka 'const struct real_pcre8_or_16 *'} but argument is of type 'struct real_pcre *' > 567 | PCRE_EXP_DECL int pcre_dfa_exec(const pcre *, const pcre_extra *, > | ^~~~~~~~~~~~ >make[3]: *** [Makefile:1233: libajax_la-ajreg.lo] Error 1 >make[3]: *** Waiting for unfinished jobs.... >make[3]: Leaving directory '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/ajax/core' >make[2]: *** [Makefile:722: all] Error 2 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/ajax/core' >make[1]: *** [Makefile:413: all-recursive] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0/ajax' >make: *** [Makefile:453: all-recursive] Error 1 > * ERROR: sci-biology/emboss-6.6.0-r2::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/emboss-6.6.0-r2::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/emboss-6.6.0-r2::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:emboss-6.6.0-r2:20231229-021617.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0' > * S: '/var/tmp/portage/sci-biology/emboss-6.6.0-r2/work/EMBOSS-6.6.0' >
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