=> Bootstrap dependency digest>=20010302: found digest-20190127 ===> Skipping vulnerability checks. WARNING: No /var/db/pkg/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /var/db/pkg fetch-pkg-vulnerabilities'. => Checksum SHA1 OK for gnome-chemistry-utils-0.12.13.tar.bz2 => Checksum RMD160 OK for gnome-chemistry-utils-0.12.13.tar.bz2 => Checksum SHA512 OK for gnome-chemistry-utils-0.12.13.tar.bz2 ===> Installing dependencies for gnome-chemistry-utils-0.12.13nb30 => Tool dependency glib2-tools-[0-9]*: found glib2-tools-2.62.4 => Tool dependency libtool-base>=2.4.2nb9: found libtool-base-2.4.6nb2 => Tool dependency intltool>=0.40.0: found intltool-0.51.0nb4 => Tool dependency gmake>=3.81: found gmake-4.2.1nb1 => Tool dependency perl>=5.0: found perl-5.30.1 => Tool dependency pkgconf-[0-9]*: found pkgconf-1.6.0 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency x11-links>=1.31: found x11-links-1.31 => Build dependency gnome-doc-utils>=0.8.0: found gnome-doc-utils-0.20.10nb3 => Build dependency eigen>=2.0beta3: found eigen-2.0.17nb1 => Build dependency cwrappers>=20150314: found cwrappers-20180325 => Full dependency GConf>=2.32.4nb5: found GConf-3.2.3nb3 => Full dependency shared-mime-info>=1.0nb1: found shared-mime-info-1.10 => Full dependency gnome-mime-data>=2.18.0nb8: found gnome-mime-data-2.18.0nb8 => Full dependency rarian>=0.6.0: found rarian-0.8.1nb4 => Full dependency gtkglext>=1.2.0nb39: found gtkglext-1.2.0nb40 => Full dependency goffice0.8>=0.8.17nb26: found goffice0.8-0.8.17nb26 => Full dependency desktop-file-utils>=0.10nb1: found desktop-file-utils-0.24 => Full dependency chemical-mime-data>=0.1.94: found chemical-mime-data-0.1.94 => Full dependency bodr>=8: found bodr-9nb9 => Full dependency openbabel>=3.0.0nb1: found openbabel-3.0.0nb1 ===> Overriding tools for gnome-chemistry-utils-0.12.13nb30 ===> Extracting for gnome-chemistry-utils-0.12.13nb30 ===> Patching for gnome-chemistry-utils-0.12.13nb30 => Applying pkgsrc patches for gnome-chemistry-utils-0.12.13nb30 => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils/patches/patch-libs_gccv_text.cc => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils/patches/patch-libs_gccv_text.cc Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-libs_gccv_text.cc,v 1.1 2014/09/23 14:33:40 jperkin Exp $ | |Avoid "call of overloaded 'abs(unsigned int)' is ambiguous". | |--- libs/gccv/text.cc.orig 2012-08-11 12:41:27.000000000 +0000 |+++ libs/gccv/text.cc -------------------------- Patching file libs/gccv/text.cc using Plan A... Hunk #1 succeeded at 1208. Hunk #2 succeeded at 1228. done => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils/patches/patch-libs_gcu_loader-error.h => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils/patches/patch-libs_gcu_loader-error.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-libs_gcu_loader-error.h,v 1.1 2013/05/09 13:45:45 joerg Exp $ | |--- libs/gcu/loader-error.h.orig 2013-05-07 20:05:57.000000000 +0000 |+++ libs/gcu/loader-error.h -------------------------- Patching file libs/gcu/loader-error.h using Plan A... Hunk #1 succeeded at 28. done => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils/patches/patch-libs_gcu_spectrumdoc.cc => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils/patches/patch-libs_gcu_spectrumdoc.cc Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-libs_gcu_spectrumdoc.cc,v 1.1 2013/05/09 13:45:45 joerg Exp $ | |--- libs/gcu/spectrumdoc.cc.orig 2013-05-07 20:06:58.000000000 +0000 |+++ libs/gcu/spectrumdoc.cc -------------------------- Patching file libs/gcu/spectrumdoc.cc using Plan A... Hunk #1 succeeded at 1618. done => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils/patches/patch-programs_crystal_document.cc => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils/patches/patch-programs_crystal_document.cc Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-programs_crystal_document.cc,v 1.1 2013/05/09 13:45:45 joerg Exp $ | |--- programs/crystal/document.cc.orig 2013-05-07 20:13:58.000000000 +0000 |+++ programs/crystal/document.cc -------------------------- Patching file programs/crystal/document.cc using Plan A... Hunk #1 succeeded at 607. done ===> Creating toolchain wrappers for gnome-chemistry-utils-0.12.13nb30 ===> Configuring for gnome-chemistry-utils-0.12.13nb30 => Generating pkg-config file for builtin expat package. => Generating pkg-config files for builtin xz package. => Modifying GNU configure scripts to avoid --recheck => Replacing config-guess with pkgsrc versions => Replacing config-sub with pkgsrc versions => Replacing install-sh with pkgsrc version => Checking for portability problems in extracted files WARNING: [check-portability.awk] => Found $RANDOM: WARNING: [check-portability.awk] configure: INTLTOOL_XML_NOMERGE_RULE='%.xml: %.xml.in $(INTLTOOL_MERGE) ; $(INTLTOOL_V_MERGE)_it_tmp_dir=tmp.intltool.$$RANDOM && mkdir $$_it_tmp_dir && LC_ALL=C $(INTLTOOL_MERGE) $(INTLTOOL_V_MERGE_OPTIONS) -x -u $$_it_tmp_dir $< $@ && rmdir $$_it_tmp_dir' Explanation: =========================================================================== The variable $RANDOM is not required for a POSIX-conforming shell, and many implementations of /bin/sh do not support it. It should therefore not be used in shell programs that are meant to be portable across a large number of POSIX-like systems. =========================================================================== checking for a BSD-compatible install... /usr/bin/install -c -o pbulk -g wheel checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... /usr/bin/awk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64--netbsd checking host system type... x86_64--netbsd checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for x86_64--netbsd-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking for library containing strerror... none required checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... yes checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /tmp/biology/gnome-chemistry-utils/work/.cwrapper/bin/ld checking if the linker (/tmp/biology/gnome-chemistry-utils/work/.cwrapper/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking how to convert x86_64--netbsd file names to x86_64--netbsd format... func_convert_file_noop checking how to convert x86_64--netbsd file names to toolchain format... func_convert_file_noop checking for /tmp/biology/gnome-chemistry-utils/work/.cwrapper/bin/ld option to reload object files... -r checking for x86_64--netbsd-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... match_pattern /lib[^/]+(\.so|_pic\.a)$ checking for x86_64--netbsd-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64--netbsd-ar... no checking for ar... ar checking for archiver @FILE support... @ checking for x86_64--netbsd-strip... no checking for strip... strip checking for x86_64--netbsd-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for x86_64--netbsd-mt... no checking for mt... mt checking if mt is a manifest tool... no 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 dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... rm: conftest*: No such file or directory yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/tmp/biology/gnome-chemistry-utils/work/.cwrapper/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... rm: conftest*: No such file or directory no checking dynamic linker characteristics... NetBSD ld.elf_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... c++ -E checking for ld used by c++... /tmp/biology/gnome-chemistry-utils/work/.cwrapper/bin/ld checking if the linker (/tmp/biology/gnome-chemistry-utils/work/.cwrapper/bin/ld) is GNU ld... yes checking whether the c++ linker (/tmp/biology/gnome-chemistry-utils/work/.cwrapper/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... rm: conftest*: No such file or directory yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/tmp/biology/gnome-chemistry-utils/work/.cwrapper/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... NetBSD ld.elf_so checking how to hardcode library paths into programs... immediate checking whether ln -s works... yes checking for bash... /usr/pkg/bin/bash checking if dolt supports this host... no, falling back to libtool checking whether NLS is requested... yes checking for intltool >= 0.40.6... 0.51.0 found checking for intltool-update... /tmp/biology/gnome-chemistry-utils/work/.tools/bin/intltool-update checking for intltool-merge... /tmp/biology/gnome-chemistry-utils/work/.tools/bin/intltool-merge checking for intltool-extract... /tmp/biology/gnome-chemistry-utils/work/.tools/bin/intltool-extract checking for xgettext... /tmp/biology/gnome-chemistry-utils/work/.tools/bin/xgettext checking for msgmerge... /tmp/biology/gnome-chemistry-utils/work/.tools/bin/msgmerge checking for msgfmt... /tmp/biology/gnome-chemistry-utils/work/.tools/bin/msgfmt checking for gmsgfmt... /tmp/biology/gnome-chemistry-utils/work/.tools/bin/msgfmt checking for perl... /usr/pkg/bin/perl checking for perl >= 5.8.1... 5.30.1 checking for XML::Parser... ok checking pkg-config is at least version 0.9.0... yes checking gnome-doc-utils >= 0.3.2... yes checking whether gcc understands -Wno-sign-compare... yes checking what warning flags to pass to the C compiler... -Wall -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wno-sign-compare checking what language compliance flags to pass to the C compiler... checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused -Wshadow -Woverloaded-virtual checking what language compliance flags to pass to the C++ compiler... checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking for LC_MESSAGES... yes checking libintl.h usability... yes checking libintl.h presence... yes checking for libintl.h... yes checking for ngettext in libc... no checking for bindtextdomain in -lintl... yes checking for ngettext in -lintl... yes checking for dgettext in -lintl... yes checking for bind_textdomain_codeset... yes checking for msgfmt... (cached) /tmp/biology/gnome-chemistry-utils/work/.tools/bin/msgfmt checking for dcgettext... yes checking if msgfmt accepts -c... yes checking for gmsgfmt... (cached) /tmp/biology/gnome-chemistry-utils/work/.tools/bin/msgfmt checking for xgettext... (cached) /tmp/biology/gnome-chemistry-utils/work/.tools/bin/xgettext checking for kde-config... no checking for KDE MIME files (.desktop) installation location... ${datarootdir}/mimelnk checking for doxygen... no checking for shared_mime_info... yes checking for cairo... yes checking for gio... yes checking for gtk... yes checking for gtkglext... yes checking for xml... yes checking for gsf... yes checking for goffice... yes checking for chemical_mime_data... yes checking for bodr... yes checking for openbabel... no configure: error: Package requirements (openbabel-2.0 >= 2.1.0) were not met: Package 'openbabel-2.0', required by 'virtual:world', not found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. Alternatively, you may set the environment variables openbabel_CFLAGS and openbabel_LIBS to avoid the need to call pkg-config. See the pkg-config man page for more details. *** Error code 1 Stop. make[1]: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils *** Error code 1 Stop. make: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/gnome-chemistry-utils