=> Bootstrap dependency digest>=20010302: found digest-20160304
===> 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-0.12.13nb25
=> Tool dependency glib2-tools-[0-9]*: found glib2-tools-2.56.2
=> Tool dependency libtool-base>=2.4.2nb9: found libtool-base-2.4.6nb1
=> Tool dependency intltool>=0.40.0: found intltool-0.51.0nb3
=> Tool dependency gmake>=3.81: found gmake-4.2.1nb1
=> Tool dependency perl>=5.0: found perl-5.28.0nb1
=> Tool dependency pkgconf-[0-9]*: found pkgconf-1.4.1nb1
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency gnome-doc-utils>=0.8.0: found gnome-doc-utils-0.20.10nb2
=> Build dependency xorgproto>=2016.1: found xorgproto-2018.4
=> Build dependency xcb-proto>=1.4: found xcb-proto-1.13
=> Build dependency eigen>=2.0beta3: found eigen-2.0.17
=> Build dependency cwrappers>=20150314: found cwrappers-20180325
=> Full dependency GConf>=2.32.4nb5: found GConf-3.2.3nb1
=> Full dependency shared-mime-info>=1.0nb1: found shared-mime-info-1.10
=> Full dependency gnome-mime-data>=2.18.0nb7: found gnome-mime-data-2.18.0nb7
=> Full dependency rarian>=0.6.0: found rarian-0.8.1nb4
=> Full dependency gtkglext>=1.2.0nb35: found gtkglext-1.2.0nb36
=> Full dependency goffice0.8>=0.8.17nb23: found goffice0.8-0.8.17nb23
=> Full dependency desktop-file-utils>=0.10nb1: found desktop-file-utils-0.23nb1
=> Full dependency chemical-mime-data>=0.1.94: found chemical-mime-data-0.1.94
=> Full dependency bodr>=8: found bodr-9nb8
=> Full dependency openbabel>=2.3.0nb4: found openbabel-2.3.2nb6
===> Overriding tools for gnome-chemistry-utils-0.12.13nb25
===> Extracting for gnome-chemistry-utils-0.12.13nb25
===> Patching for gnome-chemistry-utils-0.12.13nb25
=> Applying pkgsrc patches for gnome-chemistry-utils-0.12.13nb25
=> Verifying /data/pkgsrc/biology/gnome-chemistry-utils/patches/patch-libs_gccv_text.cc
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/gnome-chemistry-utils/patches/patch-libs_gcu_loader-error.h
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/gnome-chemistry-utils/patches/patch-libs_gcu_spectrumdoc.cc
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/gnome-chemistry-utils/patches/patch-programs_crystal_document.cc
=> Applying pkgsrc patch /data/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-0.12.13nb25
===> Configuring for gnome-chemistry-utils-0.12.13nb25
=> 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 pbulkXXX -g users
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... plaintar
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... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking dependency style of clang... gcc3
checking for library containing strerror... none required
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking dependency style of clang++... gcc3
checking how to run the C preprocessor... clang -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 clang... /usr/bin/ld
checking if the linker (/usr/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 /usr/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 clang 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 clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fPIC -DPIC
checking if clang PIC flag -fPIC -DPIC works... yes
checking if clang static flag -static works... yes
checking if clang supports -c -o file.o... rm: conftest*: No such file or directory
yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/usr/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... clang++ -E
checking for ld used by clang++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the clang++ linker (/usr/bin/ld) supports shared libraries... yes
checking for clang++ option to produce PIC... -fPIC -DPIC
checking if clang++ PIC flag -fPIC -DPIC works... yes
checking if clang++ static flag -static works... yes
checking if clang++ supports -c -o file.o... rm: conftest*: No such file or directory
yes
checking if clang++ supports -c -o file.o... (cached) yes
checking whether the clang++ linker (/usr/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... /data/scratch/biology/gnome-chemistry-utils/work/.tools/bin/intltool-update
checking for intltool-merge... /data/scratch/biology/gnome-chemistry-utils/work/.tools/bin/intltool-merge
checking for intltool-extract... /data/scratch/biology/gnome-chemistry-utils/work/.tools/bin/intltool-extract
checking for xgettext... /data/scratch/biology/gnome-chemistry-utils/work/.tools/bin/xgettext
checking for msgmerge... /data/scratch/biology/gnome-chemistry-utils/work/.tools/bin/msgmerge
checking for msgfmt... /data/scratch/biology/gnome-chemistry-utils/work/.tools/bin/msgfmt
checking for gmsgfmt... /data/scratch/biology/gnome-chemistry-utils/work/.tools/bin/msgfmt
checking for perl... /usr/pkg/bin/perl
checking for perl >= 5.8.1... 5.28.0
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) /data/scratch/biology/gnome-chemistry-utils/work/.tools/bin/msgfmt
checking for dcgettext... yes
checking if msgfmt accepts -c... yes
checking for gmsgfmt... (cached) /data/scratch/biology/gnome-chemistry-utils/work/.tools/bin/msgfmt
checking for xgettext... (cached) /data/scratch/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... yes
checking for x11... yes
checking for OB22... yes
checking for gconftool-2... /data/scratch/biology/gnome-chemistry-utils/work/.buildlink/bin/gconftool-2
Using config source  for schema installation
Using /usr/pkg/share/gconf/schemas as install directory for schema files
checking pkg-config is at least version 0.16... yes
checking for mozilla-config... no
checking for MOZILLA... no
configure: WARNING: mozilla-config not found. Mozilla/Netscape plugin will not be built
configure: WARNING: Mozilla plugins directory has not been set, the plugin will not be built
checking for gnumeric... no
checking for exp10... no
checking for xmllint... /usr/pkg/bin/xmllint
checking for xmllint >= 2.6.24...... yes
checking for optional xmllint options to use...... 
checking for xsltproc... /usr/pkg/bin/xsltproc
checking for optional xsltproc options to use...... 
checking for man... /usr/bin/man
checking for gdk-pixbuf-csource... gdk-pixbuf-csource
configure: creating ./config.status
config.status: creating Makefile
config.status: creating database/Makefile
config.status: creating docs/Makefile
config.status: creating docs/help/Makefile
config.status: creating docs/help/3d/Makefile
config.status: creating docs/help/calc/Makefile
config.status: creating docs/help/crystal/Makefile
config.status: creating docs/help/paint/Makefile
config.status: creating docs/help/spectra/Makefile
config.status: creating docs/help/table/Makefile
config.status: creating docs/man/gcu_entities.dtd
config.status: creating docs/man/Makefile
config.status: creating docs/reference/Makefile
config.status: creating docs/reference/Doxyfile
config.status: creating dtds/Makefile
config.status: creating libs/Makefile
config.status: creating libs/gccv/Makefile
config.status: creating libs/gcp/Makefile
config.status: creating libs/gcu/Makefile
config.status: creating plugins/Makefile
config.status: creating plugins/loaders/Makefile
config.status: creating plugins/loaders/cdx/Makefile
config.status: creating plugins/loaders/cdxml/Makefile
config.status: creating plugins/loaders/cif/Makefile
config.status: creating plugins/loaders/cml/Makefile
config.status: creating plugins/paint/Makefile
config.status: creating plugins/paint/arrows/Makefile
config.status: creating plugins/paint/arrows/org.gnome.gchemutils.paint.plugins.arrows.gschema.xml.in
config.status: creating plugins/paint/atoms/Makefile
config.status: creating plugins/paint/bonds/Makefile
config.status: creating plugins/paint/cycles/Makefile
config.status: creating plugins/paint/residues/Makefile
config.status: creating plugins/paint/selection/Makefile
config.status: creating plugins/paint/templates/Makefile
config.status: creating plugins/paint/text/Makefile
config.status: creating plugins/paint/wikipedia/Makefile
config.status: creating mozilla-plugin/Makefile
config.status: creating gnumeric/Makefile
config.status: creating gnumeric/plugin.xml.in
config.status: creating goffice/Makefile
config.status: creating pixmaps/Makefile
config.status: creating po/Makefile.in
config.status: creating samples/Makefile
config.status: creating schemas/Makefile
config.status: creating schemas/org.gnome.gchemutils.gschema.xml.in
config.status: creating schemas/org.gnome.gchemutils.crystal.gschema.xml.in
config.status: creating schemas/org.gnome.gchemutils.paint.gschema.xml.in
config.status: creating programs/Makefile
config.status: creating programs/3d/Makefile
config.status: creating programs/3d/gchem3d.desktop.in
config.status: creating programs/calc/Makefile
config.status: creating programs/calc/gchemcalc.desktop.in
config.status: creating programs/crystal/Makefile
config.status: creating programs/crystal/gcrystal.desktop.in
config.status: creating programs/paint/Makefile
config.status: creating programs/paint/gchempaint.desktop.in
config.status: creating programs/spectra/Makefile
config.status: creating programs/spectra/gspectrum.desktop.in
config.status: creating programs/table/Makefile
config.status: creating programs/table/gchemtable.desktop.in
config.status: creating templates/Makefile
config.status: creating templates/paint/Makefile
config.status: creating themes/Makefile
config.status: creating themes/paint/Makefile
config.status: creating tests/Makefile
config.status: creating ui/Makefile
config.status: creating ui/calc/Makefile
config.status: creating ui/crystal/Makefile
config.status: creating ui/libgcu/Makefile
config.status: creating ui/paint/Makefile
config.status: creating ui/table/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
rm: libtoolT: No such file or directory
config.status: executing default-1 commands
config.status: executing po/stamp-it commands
=> Overriding intltool.
=> Modifying libtool scripts to use pkgsrc libtool
=> Modifying libtool scripts to use pkgsrc depcomp