=> Bootstrap dependency digest>=20010302: found digest-20121220 => Checksum SHA1 OK for gromacs-4.5.5.tar.gz => Checksum RMD160 OK for gromacs-4.5.5.tar.gz ===> Installing dependencies for gromacs-4.5.5nb3 ========================================================================== The supported build options for gromacs are: mpi x11 The currently selected options are: mpi x11 You can select which build options to use by setting PKG_DEFAULT_OPTIONS or the following variable. Its current value is shown: PKG_OPTIONS.gromacs (not defined) ========================================================================== => Tool dependency libtool-base>=2.2.6bnb3: found libtool-base-2.4.2nb3 => Tool dependency pkg-config>=0.25: found pkg-config-0.28 => Tool dependency checkperms>=1.1: found checkperms-1.11 => Build dependency x11-links>=0.78: found x11-links-0.79 => Full dependency perl>=5.0: found perl-5.18.0nb1 => Full dependency mpich>=3: found mpich-3.0.4nb1 => Full dependency fftw>=3.1nb1: found fftw-3.3.3nb1 => Full dependency gsl>=1.5nb1: found gsl-1.15 => Full dependency libxml2>=2.8.0nb2: found libxml2-2.9.1 ===> Overriding tools for gromacs-4.5.5nb3 ===> Extracting for gromacs-4.5.5nb3 ===> Patching for gromacs-4.5.5nb3 => Applying pkgsrc patches for gromacs-4.5.5nb3 => Verifying /usr/pkgsrc/biology/gromacs/patches/patch-aa => Applying pkgsrc patch /usr/pkgsrc/biology/gromacs/patches/patch-aa Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-aa,v 1.3 2013/04/01 08:00:16 sbd Exp $ | |Allow flags to contain commas. | |--- share/template/Makefile.in.orig 2011-09-21 12:38:30.000000000 +0000 |+++ share/template/Makefile.in -------------------------- Patching file share/template/Makefile.in using Plan A... Hunk #1 succeeded at 250. Hunk #2 succeeded at 569. done => Verifying /usr/pkgsrc/biology/gromacs/patches/patch-ad => Applying pkgsrc patch /usr/pkgsrc/biology/gromacs/patches/patch-ad Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ad,v 1.1 2010/05/16 12:04:03 asau Exp $ | |Libtool wants tag nowadays. | |--- src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile.in.orig 2010-05-15 00:44:35.000000000 +0400 |+++ src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile.in 2010-05-15 00:49:20.000000000 +0400 -------------------------- Patching file src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile.in using Plan A... Hunk #1 succeeded at 91 (offset 5 lines). done => Verifying /usr/pkgsrc/biology/gromacs/patches/patch-ae => Applying pkgsrc patch /usr/pkgsrc/biology/gromacs/patches/patch-ae Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ae,v 1.1 2010/06/17 09:26:16 asau Exp $ | |Modern libtool requires tag. | |--- src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile.in.orig 2009-12-06 21:18:53.000000000 +0000 |+++ src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile.in 2010-06-17 07:55:04.000000000 +0000 -------------------------- Patching file src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile.in using Plan A... Hunk #1 succeeded at 91 (offset 5 lines). done => Verifying /usr/pkgsrc/biology/gromacs/patches/patch-ag => Applying pkgsrc patch /usr/pkgsrc/biology/gromacs/patches/patch-ag Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ag,v 1.2 2010/09/03 20:52:39 asau Exp $ | |Modern libtool requires tag. | |--- src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in.orig 2010-07-30 22:55:04.000000000 +0400 |+++ src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in 2010-07-31 11:57:35.000000000 +0400 -------------------------- Patching file src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in using Plan A... Hunk #1 succeeded at 71. done => Verifying /usr/pkgsrc/biology/gromacs/patches/patch-ah => Applying pkgsrc patch /usr/pkgsrc/biology/gromacs/patches/patch-ah Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ah,v 1.2 2010/09/03 20:52:39 asau Exp $ | |Modern libtool requires tag. | |--- src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in.orig 2010-07-30 22:55:04.000000000 +0400 |+++ src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in 2010-07-31 11:58:30.000000000 +0400 -------------------------- Patching file src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in using Plan A... Hunk #1 succeeded at 71. done => Verifying /usr/pkgsrc/biology/gromacs/patches/patch-ai => Applying pkgsrc patch /usr/pkgsrc/biology/gromacs/patches/patch-ai Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ai,v 1.1 2010/06/17 09:26:16 asau Exp $ | |Modern libtool requires tag. | |--- src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile.in.orig 2009-12-06 21:18:54.000000000 +0000 |+++ src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile.in 2010-06-17 07:58:21.000000000 +0000 -------------------------- Patching file src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile.in using Plan A... Hunk #1 succeeded at 92 (offset 6 lines). done => Verifying /usr/pkgsrc/biology/gromacs/patches/patch-aj => Applying pkgsrc patch /usr/pkgsrc/biology/gromacs/patches/patch-aj Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-aj,v 1.1 2010/06/17 09:26:16 asau Exp $ | |Modern libtool requires tag. | |--- src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile.in.orig 2009-12-06 21:18:54.000000000 +0000 |+++ src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile.in 2010-06-17 07:59:09.000000000 +0000 -------------------------- Patching file src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile.in using Plan A... Hunk #1 succeeded at 91 (offset 5 lines). done ===> Creating toolchain wrappers for gromacs-4.5.5nb3 ===> Configuring for gromacs-4.5.5nb3 => 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 => Replacing Perl interpreter in scripts/demux.pl scripts/xplor2gmx.pl. => Fixing locale directory references. => Checking for portability problems in extracted files checking build system type... i386--netbsdelf checking host system type... i386--netbsdelf checking for a BSD-compatible install... /usr/bin/install -c -o kristerw -g wheel checking whether build environment is sane... yes checking for a thread-safe mkdir -p... config/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 for i386--netbsdelf-cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc *** Error code 1 Stop. make: stopped in /usr/pkgsrc/biology/gromacs *** Error code 1 Stop. make: stopped in /usr/pkgsrc/biology/gromacs