* Package: sci-chemistry/chemtool-1.6.14 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc gnome kernel_linux nls userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking chemtool-1.6.14.tar.gz to /var/tmp/portage/sci-chemistry/chemtool-1.6.14/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/chemtool-1.6.14/work >>> Preparing source in /var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14 ... * Applying 1.6.13-no-underlinking.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14' ... * Running autopoint --force ... [ ok ] * Running aclocal -I m4 ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --foreign --force-missing ... [ ok ] * Running elibtoolize in: chemtool-1.6.14/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14" * econf: updating chemtool-1.6.14/config.sub with /usr/share/gnuconfig/config.sub * econf: updating chemtool-1.6.14/config.guess with /usr/share/gnuconfig/config.guess /var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14/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 --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/chemtool-1.6.14 --without-kdedir --with-gnomedir=/usr --disable-emf --enable-undo --enable-menu checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether NLS is requested... yes checking for msgfmt... /usr/bin/msgfmt checking for gmsgfmt... /usr/bin/gmsgfmt checking for xgettext... /usr/bin/xgettext checking for msgmerge... /usr/bin/msgmerge checking whether make supports the include directive... yes (GNU style) 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 we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for ld used by 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 shared library run path origin... done checking whether NLS is requested... yes checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... (cached) yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... (cached) yes checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none checking whether make sets $(MAKE)... (cached) yes checking whether ln -s works... yes checking for cp... /bin/cp checking for rm... /bin/rm checking for main in -libs... no checking for acos in -lm... yes checking for pkg-config... /usr/bin/pkg-config checking for GTK version and compile options ... checking for x86_64-pc-linux-gnu-pkg-config... (cached) /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GTK... yes checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E 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 grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for XOpenDisplay in -lX11... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking libintl.h usability... yes checking libintl.h presence... yes checking for libintl.h... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for working POSIX fnmatch... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for getcwd... yes checking for getwd... yes checking for mkdir... yes checking for strtod... yes checking for strtol... yes checking for KDE ... no checking for GNOME ... apparently in /usr no checking whether to enable libundo... yes checking whether to use pull-down menus... yes checking whether to enable emf output... no checking whether standard GTK dialogs should be used instead of our own... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src-cht/Makefile config.status: creating m4/Makefile config.status: creating po/Makefile.in config.status: WARNING: 'po/Makefile.in.in' seems to ignore the --datarootdir setting config.status: creating po/Makefile config.status: creating config.h config.status: executing default-1 commands config.status: creating po/POTFILES config.status: creating po/Makefile config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14" make -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14' Making all in m4 make[2]: Entering directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14/m4' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14/m4' Making all in po make[2]: Entering directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14/po' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14/po' Making all in src-cht make[2]: Entering directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14/src-cht' x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common cht.c -o cht make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14/src-cht' make[2]: Entering directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14' x86_64-pc-linux-gnu-gcc -DLOCALEDIR=\"/usr/share/locale\" -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/libffi/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/uuid -I/usr/include/libdrm -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/atk-1.0 -pthread -DGTK2 -O2 -pipe -march=native -fno-common -c -o main.o main.c In file included from /usr/include/string.h:494, from /usr/include/glib-2.0/glib/gtestutils.h:30, from /usr/include/glib-2.0/glib.h:85, from /usr/include/glib-2.0/gobject/gbinding.h:28, from /usr/include/glib-2.0/glib-object.h:23, from /usr/include/glib-2.0/gio/gioenums.h:28, from /usr/include/glib-2.0/gio/giotypes.h:28, from /usr/include/glib-2.0/gio/gio.h:26, from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30, from /usr/include/gtk-2.0/gdk/gdk.h:32, from /usr/include/gtk-2.0/gdk/gdkprivate.h:30, from /usr/include/gtk-2.0/gdk/gdkx.h:30, from main.c:18: In function ‘strncpy’, inlined from ‘file_ok_sel’ at main.c:3027:7: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c: In function ‘file_ok_sel’: main.c:3027:35: note: length computed here 3027 | strncpy (datadir, filename, strlen (filename) - strlen (tempstr) + 1); | ^~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DLOCALEDIR=\"/usr/share/locale\" -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/libffi/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/uuid -I/usr/include/libdrm -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/atk-1.0 -pthread -DGTK2 -O2 -pipe -march=native -fno-common -c -o draw.o draw.c x86_64-pc-linux-gnu-gcc -DLOCALEDIR=\"/usr/share/locale\" -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/libffi/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/uuid -I/usr/include/libdrm -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/atk-1.0 -pthread -DGTK2 -O2 -pipe -march=native -fno-common -c -o graph.o graph.c x86_64-pc-linux-gnu-gcc -DLOCALEDIR=\"/usr/share/locale\" -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/libffi/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/uuid -I/usr/include/libdrm -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/atk-1.0 -pthread -DGTK2 -O2 -pipe -march=native -fno-common -c -o chemproc.o chemproc.c x86_64-pc-linux-gnu-gcc -DLOCALEDIR=\"/usr/share/locale\" -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/libffi/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/uuid -I/usr/include/libdrm -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/atk-1.0 -pthread -DGTK2 -O2 -pipe -march=native -fno-common -c -o undo.o undo.c x86_64-pc-linux-gnu-gcc -DLOCALEDIR=\"/usr/share/locale\" -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/libffi/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/uuid -I/usr/include/libdrm -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/atk-1.0 -pthread -DGTK2 -O2 -pipe -march=native -fno-common -c -o inout.o inout.c inout.c: In function ‘import_pdb’: inout.c:732:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 732 | (void)fgets (line, (int)sizeof (line), fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ inout.c: In function ‘check_babel’: inout.c:6054:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 6054 | (void)fgets (data, 80, xfile); | ^~~~~~~~~~~~~~~~~~~~~~~ inout.c: In function ‘check_fig2sxd’: inout.c:6133:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 6133 | fscanf (xfile, "%s", myname); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DGTK2 -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o chemtool main.o draw.o graph.o chemproc.o undo.o inout.o -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lX11 -lX11 -lm /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: graph.o:(.bss+0x1b8): multiple definition of `babelout'; draw.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: graph.o:(.bss+0x1c0): multiple definition of `outmode'; draw.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: graph.o:(.bss+0x1c8): multiple definition of `outtype'; draw.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: graph.o:(.bss+0x1d0): multiple definition of `babelin'; draw.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: graph.o:(.bss+0x1d8): multiple definition of `inmode'; draw.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: graph.o:(.bss+0x1e0): multiple definition of `intype'; draw.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: chemproc.o:(.bss+0x0): multiple definition of `babelout'; draw.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: chemproc.o:(.bss+0x8): multiple definition of `outmode'; draw.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: chemproc.o:(.bss+0x10): multiple definition of `outtype'; draw.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: chemproc.o:(.bss+0x18): multiple definition of `babelin'; draw.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: chemproc.o:(.bss+0x20): multiple definition of `inmode'; draw.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: chemproc.o:(.bss+0x28): multiple definition of `intype'; draw.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inout.o:(.bss+0x118): multiple definition of `babelin'; draw.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inout.o:(.bss+0x100): multiple definition of `babelout'; draw.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inout.o:(.bss+0x120): multiple definition of `inmode'; draw.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inout.o:(.bss+0x128): multiple definition of `intype'; draw.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inout.o:(.bss+0x108): multiple definition of `outmode'; draw.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inout.o:(.bss+0x110): multiple definition of `outtype'; draw.o:(.bss+0x10): first defined here collect2: error: ld returned 1 exit status make[2]: *** [Makefile:533: chemtool] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14' make[1]: *** [Makefile:610: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14' make: *** [Makefile:434: all] Error 2 * ERROR: sci-chemistry/chemtool-1.6.14::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-chemistry/chemtool-1.6.14::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/chemtool-1.6.14::gentoo'`. * The complete build log is located at '/var/log/portage/sci-chemistry:chemtool-1.6.14:20200204-104608.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14' * S: '/var/tmp/portage/sci-chemistry/chemtool-1.6.14/work/chemtool-1.6.14'