sci-biology:embassy-mse-3.0.0.660-r1:20240517-200901.log

sci-biology:embassy-mse-3.0.0.660-r1:20240517-200901.log (text/plain), 26.28 KB, created by Toralf Förster on 2024-05-18 07:50:42 UTC

 * Package:    sci-biology/embassy-mse-3.0.0.660-r1:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking embassy-mse-3.0.0.660.tar.gz to /var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work
>>> Preparing source in /var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650 ...
 * Applying embassy-mse-3.0.0.650_fix-build-system.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650' ...
 * Running 'libtoolize --install --copy --force --automake' ...
 [ ok ]
 * Running 'aclocal -I m4 --system-acdir=/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/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: MSE-3.0.0.650/
 *   Applying portage/1.2.0 patch ...
 *   Applying sed/1.5.6 patch ...
 *   Applying as-needed/2.4.3 patch ...
 *   Applying color-record/2.4.7 patch ...
 *   Applying openmp/2.4.7 patch ...
 *   Applying verbose-pic/2.4.7 patch ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650 ...
 * econf: updating MSE-3.0.0.650/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating MSE-3.0.0.650/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/embassy-mse-3.0.0.660-r1 --htmldir=/usr/share/doc/embassy-mse-3.0.0.660-r1/html --with-sysroot=/ --libdir=/usr/lib64 --enable-shared --without-x --without-pngdriver --without-hpdf --without-mysql --without-postgresql --enable-large --without-java --enable-systemlibs --enable-curses
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... /usr/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... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/libexec/gcc/x86_64-pc-linux-gnu/ld
checking if the linker (/usr/libexec/gcc/x86_64-pc-linux-gnu/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/libexec/gcc/x86_64-pc-linux-gnu/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... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for x86_64-pc-linux-gnu-mt... no
checking for mt... mt
checking if mt 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/libexec/gcc/x86_64-pc-linux-gnu/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/libexec/gcc/x86_64-pc-linux-gnu/ld -m elf_x86_64
checking if the linker (/usr/libexec/gcc/x86_64-pc-linux-gnu/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/libexec/gcc/x86_64-pc-linux-gnu/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/libexec/gcc/x86_64-pc-linux-gnu/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... disabled
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for egrep... (cached) /usr/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 strdup... yes
checking for strstr... yes
checking for strchr... yes
checking for erand48... yes
checking for memmove... 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 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... no
checking if png driver is wanted... no
checking for large file support... yes
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 for plplotd... no
checking for plplot... yes
checking for purify... no
checking for cygwin... no
checking for savestats... no
checking for ncurses... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating h/Makefile
config.status: creating ckit/Makefile
config.status: creating src/Makefile
config.status: creating emboss_acd/Makefile
config.status: creating emboss_doc/Makefile
config.status: creating emboss_doc/html/Makefile
config.status: creating emboss_doc/text/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650 ...
make -j4 
Making all in ckit
make[1]: Entering directory '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650/ckit'
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o datafiles.lo datafiles.c
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o next.lo next.c
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o seqentry.lo seqentry.c
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o strings.lo strings.c
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c seqentry.c  -fPIC -DPIC -o .libs/seqentry.o
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c next.c  -fPIC -DPIC -o .libs/next.o
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c datafiles.c  -fPIC -DPIC -o .libs/datafiles.o
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c strings.c  -fPIC -DPIC -o .libs/strings.o
datafiles.c: In function 'ShowGCGEnzymes':
datafiles.c:226:17: warning: 'fgets' writing 511 bytes into a region of size 256 overflows the destination [-Wstringop-overflow=]
  226 |         while ( fgets(line,511,enzFile) != NULL)
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
datafiles.c:214:6: note: destination object 'line' of size 256
  214 | char line[256];
      |      ^~~~
In file included from /usr/include/stdio.h:980,
                 from datafiles.c:6:
/usr/include/bits/stdio2.h:196:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)'
  196 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
      | ^~~~~
datafiles.c:232:17: warning: 'fgets' writing 511 bytes into a region of size 256 overflows the destination [-Wstringop-overflow=]
  232 |         while ( fgets(line,511,enzFile) != NULL ) {
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
datafiles.c:214:6: note: destination object 'line' of size 256
  214 | char line[256];
      |      ^~~~
/usr/include/bits/stdio2.h:196:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)'
  196 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
      | ^~~~~
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o gcg.lo gcg.c
In function 'fgets',
    inlined from 'ShowGCGEnzymes' at datafiles.c:226:10:
/usr/include/bits/stdio2.h:202:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  202 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'fgets',
    inlined from 'ShowGCGEnzymes' at datafiles.c:232:10:
/usr/include/bits/stdio2.h:202:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  202 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o pir.lo pir.c
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o seqspec.lo seqspec.c
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c gcg.c  -fPIC -DPIC -o .libs/gcg.o
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o ttyinterface.lo ttyinterface.c
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c pir.c  -fPIC -DPIC -o .libs/pir.o
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c seqspec.c  -fPIC -DPIC -o .libs/seqspec.o
gcg.c: In function 'NextGCGCode':
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c ttyinterface.c  -fPIC -DPIC -o .libs/ttyinterface.o
gcg.c:175:14: warning: 'fgets' writing 39 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  175 |         if ( fgets(code, 39, namesFile) ) {
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcg.c:168:13: note: destination object 'code' of size 20
  168 | static char code[20];
      |             ^~~~
In file included from /usr/include/stdio.h:980,
                 from gcg.c:10:
/usr/include/bits/stdio2.h:196:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)'
  196 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
      | ^~~~~
In function 'fgets',
    inlined from 'NextGCGCode' at gcg.c:175:7:
/usr/include/bits/stdio2.h:202:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  202 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pir.c: In function 'LookupPIR':
pir.c:258:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
  258 |         fread (kode, sizeof(char), 512, indexFile);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o nextseqentry.lo nextseqentry.c
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o readentry.lo readentry.c
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c nextseqentry.c  -fPIC -DPIC -o .libs/nextseqentry.o
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o sequence.lo sequence.c
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o vdb.lo vdb.c
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c readentry.c  -fPIC -DPIC -o .libs/readentry.o
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c sequence.c  -fPIC -DPIC -o .libs/sequence.o
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c vdb.c  -fPIC -DPIC -o .libs/vdb.o
readentry.c: In function 'FindSeqSpec':
readentry.c:402:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  402 |               fgets(line, 256, userFile);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~
readentry.c:411:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  411 |               fgets(headerLine, 512, seqFile);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readentry.c:413:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  413 |               fgets(title, 512, seqFile);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~
readentry.c: In function 'ReadTxt':
readentry.c:728:11: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  728 |           fgets(oneLine, 512, file);  /* Skip codeword line in .REF file */
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~
readentry.c:729:11: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  729 |           fgets(oneLine, 512, file);  /* Skip title line in .REF file    */
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~
readentry.c: In function 'FindSeqSpec':
readentry.c:413:15: warning: 'fgets' writing 512 bytes into a region of size 256 overflows the destination [-Wstringop-overflow=]
  413 |               fgets(title, 512, seqFile);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~
readentry.c:346:13: note: destination object 'title' of size 256
  346 | static char title[256] = "";
      |             ^~~~~
In file included from /usr/include/stdio.h:980,
                 from readentry.c:18:
/usr/include/bits/stdio2.h:196:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)'
  196 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
      | ^~~~~
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src  -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o vms2.lo vms2.c
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -I../h -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -fno-diagnostics-color -O2 -c vms2.c  -fPIC -DPIC -o .libs/vms2.o
In function 'fgets',
    inlined from 'FindSeqSpec' at readentry.c:413:8,
    inlined from 'ReadEntry' at readentry.c:101:7:
/usr/include/bits/stdio2.h:202:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  202 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/sh ../libtool  --tag=CC   --mode=link x86_64-pc-linux-gnu-gcc  -O2 -pipe -march=native -fno-diagnostics-color  -O2 -version-info 1:0:1 -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0 -o libckit.la -rpath /usr/lib64 datafiles.lo next.lo seqentry.lo strings.lo gcg.lo pir.lo seqspec.lo ttyinterface.lo nextseqentry.lo readentry.lo sequence.lo vdb.lo vms2.lo  -lm 
libtool: link: x86_64-pc-linux-gnu-gcc -shared  -fPIC -DPIC  .libs/datafiles.o .libs/next.o .libs/seqentry.o .libs/strings.o .libs/gcg.o .libs/pir.o .libs/seqspec.o .libs/ttyinterface.o .libs/nextseqentry.o .libs/readentry.o .libs/sequence.o .libs/vdb.o .libs/vms2.o   -Wl,--as-needed -lm  -O2 -march=native -O2 -Wl,-O1 -Wl,-z -Wl,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0   -Wl,-soname -Wl,libckit.so.0 -o .libs/libckit.so.0.1.0
libtool: link: (cd ".libs" && rm -f "libckit.so.0" && ln -s "libckit.so.0.1.0" "libckit.so.0")
libtool: link: (cd ".libs" && rm -f "libckit.so" && ln -s "libckit.so.0.1.0" "libckit.so")
libtool: link: ( cd ".libs" && rm -f "libckit.la" && ln -s "../libckit.la" "libckit.la" )
make[1]: Leaving directory '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650/ckit'
Making all in src
make[1]: Entering directory '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650/src'
make  all-am
make[2]: Entering directory '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650/src'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.  -I../h -I/usr/include  -I/usr/include/plplot -D_DEFAULT_SOURCE -D_XOPEN_SOURCE=600 -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64    -O2 -pipe -march=native -fno-diagnostics-color  -O2 -c -o mse.o mse.c
mse.c: In function ‘Initscr’:
mse.c:156:17: error: invalid use of incomplete typedef ‘WINDOW’ {aka ‘struct _win_st’}
  156 |   __Cols=Display->_maxx;
      |                 ^~
mse.c:157:17: error: invalid use of incomplete typedef ‘WINDOW’ {aka ‘struct _win_st’}
  157 |   __Rows=Display->_maxy;
      |                 ^~
make[2]: *** [Makefile:517: mse.o] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650/src'
make[1]: *** [Makefile:396: all] Error 2
make[1]: Leaving directory '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650/src'
make: *** [Makefile:426: all-recursive] Error 1
 * ERROR: sci-biology/embassy-mse-3.0.0.660-r1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/embassy-mse-3.0.0.660-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/embassy-mse-3.0.0.660-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:embassy-mse-3.0.0.660-r1:20240517-200901.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650'
 * S: '/var/tmp/portage/sci-biology/embassy-mse-3.0.0.660-r1/work/MSE-3.0.0.650'