[REL - 84i386-default][biology/garlic] Failed for garlic-1.6 in stage

Thu Jul 10 03:04:20 UTC 2014

You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     maho at FreeBSD.org
Last committer: adamw at FreeBSD.org
Ident:          $FreeBSD: head/biology/garlic/Makefile 360705 2014-07-05 00:15:40Z adamw $
Log URL:        http://beefy1.isc.freebsd.org/bulk/84i386-default/2014-07-09_16h35m32s/logs/garlic-1.6.log
Build URL:      http://beefy1.isc.freebsd.org/bulk/84i386-default/2014-07-09_16h35m32s
Log:

====>> Building biology/garlic
build started at Thu Jul 10 03:03:41 UTC 2014
port directory: /usr/ports/biology/garlic
building for: FreeBSD 84i386-default-job-23 8.4-RELEASE-p10 FreeBSD 8.4-RELEASE-p10 i386
maintained by: maho at FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/garlic/Makefile 360705 2014-07-05 00:15:40Z adamw $
Poudriere version: 3.1-pre
Host OSVERSION: 1100022
Jail OSVERSION: 804000

---Begin Environment---
UNAME_m=i386
UNAME_p=i386
OSVERSION=804000
UNAME_v=FreeBSD 8.4-RELEASE-p10
UNAME_r=8.4-RELEASE-p10
FTP_PASSIVE_MODE=YES
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/build/84i386-default/ref
PKG_EXT=txz
tpid=74532
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNG=1
PKGNAME=garlic-1.6
PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f
PKG_ADD=/usr/local/sbin/pkg-static add
OLDPWD=/usr/local/poudriere/data/build/84i386-default/ref/poudriere/rdeps
PWD=/usr/local/poudriere/data/build/84i386-default/ref/poudriere/pool
MASTERNAME=84i386-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
PKG_VERSION=/poudriere/pkg-static version
PKG_BIN=/usr/local/sbin/pkg-static
---End Environment---

---Begin OPTIONS List---
===> The following configuration options are available for garlic-1.6:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
     OPTIMIZED_CFLAGS=off: Use extra compiler optimizations
===> Use 'make config' to modify these settings
---End OPTIONS List---

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/garlic/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/garlic/work  HOME=/wrkdirs/usr/ports/biology/garlic/work TMPDIR="/tmp" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/garlic/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/garlic/work  HOME=/wrkdirs/usr/ports/biology/garlic/work TMPDIR="/tmp" MAKE=gmake SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/garlic/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/garlic/work  HOME=/wrkdirs/usr/ports/biology/garlic/work TMPDIR="/tmp" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/garlic/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/garlic/work  HOME=/wrkdirs/usr/ports/biology/garlic/work TMPDIR="/tmp" NO_PIE=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing"  CPP="cpp" CPPFLAGS=""  LDFLAGS="" LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing"  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -o root -g wheel -m 555"  BSD_INSTALL_LIB="install  -s -o root -g wheel -m 444"  BSD_INSTALL_SCRIPT="install  -o root -g wheel -m 555"  BSD_INSTALL_DATA="install  -o root -g wheel -m 444"  BSD_INSTALL_MAN="install  -o root -g wheel -m 444"
--End MAKE_ENV--

--PLIST_SUB--
OSREL=8.4
PREFIX=%D
LOCALBASE=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
PORTDATA=""
LIB32DIR=lib
DOCSDIR="share/doc/garlic"
EXAMPLESDIR="share/examples/garlic"
DATADIR="share/garlic"
WWWDIR="www/garlic"
ETCDIR="etc/garlic"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/garlic
DOCSDIR=/usr/local/share/doc/garlic
EXAMPLESDIR=/usr/local/share/examples/garlic
WWWDIR=/usr/local/www/garlic
ETCDIR=/usr/local/etc/garlic
--End SUB_LIST--

---Begin make.conf---
ARCH=i386
MACHINE=i386
MACHINE_ARCH=i386
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
# clean-restricted via poudriere.conf NO_RESTRICTED
#NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
===>  Cleaning for garlic-1.6
=======================<phase: check-sanity   >============================
===========================================================================
=======================<phase: pkg-depends    >============================
===>   garlic-1.6 depends on file: /usr/local/sbin/pkg - not found
===>    Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg
===>   Installing existing package /packages/All/pkg-1.2.7_4.txz
Installing pkg-1.2.7_4... done
If you are upgrading from the old package format, first run:

  # pkg2ng
===>   Returning to build of garlic-1.6
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===> Fetching all distfiles required by garlic-1.6 for building
===========================================================================
=======================<phase: checksum       >============================
===> Fetching all distfiles required by garlic-1.6 for building
=> SHA256 Checksum OK for garlic-1.6.tar.gz.
=> SHA256 Checksum OK for garlic-1.6-doc.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===> Fetching all distfiles required by garlic-1.6 for building
===>  Extracting for garlic-1.6
=> SHA256 Checksum OK for garlic-1.6.tar.gz.
=> SHA256 Checksum OK for garlic-1.6-doc.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for garlic-1.6
===>  Applying FreeBSD patches for garlic-1.6
===========================================================================
=======================<phase: build-depends  >============================
===>   garlic-1.6 depends on executable: gmake - not found
===>    Verifying install for gmake in /usr/ports/devel/gmake
===>   Installing existing package /packages/All/gmake-3.82_1.txz
Installing gmake-3.82_1...Installing gettext-0.18.3.1_1...Installing indexinfo-0.2... done
Installing libiconv-1.14_3... done
 done
 done
===>   Returning to build of garlic-1.6
===>   garlic-1.6 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found
===>    Verifying install for /usr/local/libdata/pkgconfig/x11.pc in /usr/ports/x11/libX11
===>   Installing existing package /packages/All/libX11-1.6.2_2,1.txz
Installing libX11-1.6.2_2,1...Installing kbproto-1.0.6... done
Installing libXau-1.0.8_2...Installing xproto-7.0.25... done
 done
Installing libXdmcp-1.1.1_2... done
Installing libxcb-1.10_2...Installing libpthread-stubs-0.3_5... done
Installing libxml2-2.9.1_1... done
 done
 done
===>   Returning to build of garlic-1.6
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for garlic-1.6
===========================================================================
=======================<phase: build          >============================
===>  Building for garlic-1.6
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include garlic.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include print_usage.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include print_help.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include print_version.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include register.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include alloc_gui.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include alloc_config.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include alloc_mol_complex.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include free_memory.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include display_init.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include disp_color_cap.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include color_shifts.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include calc_params.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include errmsg.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include warnmsg.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include openfile_r.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include read_config.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include open_config_file.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_int.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include ex2ints.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_double.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include ex2doubles.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_phrase.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_index.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include ex_rot_steps.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include ex_trans_steps.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include ex_slab_steps.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include ex_fading_steps.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_args.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include parse_options.c
<snip>
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include exclude_distant.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include draw_bottom.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include draw_top.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include copy_sequence.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include compare.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include draw_comparison.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include neighborhood.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include draw_balls2.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include comparison_mouse.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include structure.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include parse_sec_structure.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include copy_sec_structure.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include load_sec_structure.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include save_sec_structure.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include alloc_sec_structure.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include sec_structure_from.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include create.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include open_template_file.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include read_template_file.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include ex_template_residues.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include count_template_res.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include create_structure.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include required_atoms.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include copy_template_atoms.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include fix_chain.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include reset_phi.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_hncac.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include phi_from_hncac.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include rotate_atom.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include parallel_part.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include reset_psi.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include build_chain.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_ncac.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include translate_range.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include rotate_range.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include apply_structure.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include generate_phi_psi.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_nca.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_c.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include replace.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_n.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include refresh_backbone.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include edit.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include draw_edit_symbol.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include draw_squid.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include draw_seahorse.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include are_atoms_bound.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include bond_partners.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include edit_phi.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include edit_psi.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_cac.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include small_ramachandran.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include edit_omega.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include small_omega.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_h.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_o.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include psi_from_ncacn.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include is_standard.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_four_atoms.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbcg.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbsg.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbcg1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbog.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbog1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgcd.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgod1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgnd1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcg1cd.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgcd1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgsd.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi3_from_cbcgcdne.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi3_from_cbcgcdoe1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi3_from_cbcgcdce.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi3_from_cbcgsdce.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi4_from_cgcdnecz.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi4_from_cgcdcenz.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include chi5_from_cdnecznh1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include is_part_of_ring.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include edit_bond.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include edit_chi2.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_cacb.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include edit_chi1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_cbxg.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include resize_complex.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include membrane.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include inform_user.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include alpha_membrane.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_ca.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_vector.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include alpha_membrane_center.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include init_membrane.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include alpha_normal.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include project_membranes.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include draw_membranes.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include rotate_membrane.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include translate_membrane.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_triplet.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include set.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include set_phi.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include set_psi.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include set_omega.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include set_chi1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include set_chi2.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include set_chi3.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_cgxd.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include set_chi4.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_cdxe.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include set_chi5.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_necz.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include pick_bond.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include nice_bonds.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include covalent.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include covalent2.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include half_nice_bond.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include probe.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include small_atoms.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include small_atoms2.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include draw_sticks.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include half_stick.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include command_refresh.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include acceptor_dipole.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include donor_dipole.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include sticks.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include balls.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include blur.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include blur_main_window.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include group.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include beta_membrane.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include extract_cg.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_tm.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include parse_pattern.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_pattern.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include hyphob_function1.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include hyphob_function2.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include hyphob_function3.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include hyphob_function4.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include hyphob_function5.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include hyphob_function6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include hyphob_function7.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include color_size.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include command_dump.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include is_aromatic.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_2c3.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_2cz3.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_2nz3.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3c4.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3cz4.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3nz4.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3c5.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3cz5.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3nz5.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3p5.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4c5.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4cz5.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4nz5.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3c6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3cz6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_3nz6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4c6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4cz6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4nz6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4p6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5c6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5cz6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5nz6.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4c7.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4cz7.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4nz7.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5c7.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5cz7.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5nz7.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5p7.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_6p7.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4c9.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4cz9.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_4nz9.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5c9.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5cz9.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include select_5nz9.c
cc -c -O2 -pipe -fno-strict-aliasing -I/usr/local/include color_weighted.c
cc -o garlic -L/usr/local/lib garlic.o print_usage.o print_help.o print_version.o register.o alloc_gui.o alloc_config.o alloc_mol_complex.o free_memory.o display_init.o disp_color_cap.o color_shifts.o calc_params.o errmsg.o warnmsg.o openfile_r.o read_config.o open_config_file.o extract_int.o ex2ints.o extract_double.o ex2doubles.o extract_phrase.o extract_index.o ex_rot_steps.o ex_trans_steps.o ex_slab_steps.o ex_fading_steps.o extract_args.o parse_options.o parse_color.o load_font.o prepare_cursor.o print_config.o create_windows.o make_pixmap.o make_pixmap2.o rgbs_from_xcolor.o pixel_from_rgbs.o size_hints.o wmhints.o select_events.o hide_control.o load_complex.o read_file.o fileformat.o is_pdb.o read_pdb.o init_header.o pdb_atom.o extract_field.o copypur.o realloc_pdb.o headerline.o geomcenter.o init_slab.o init_fading.o flip_vector.o translate_complex.o extent.o stereo_data.o strong_bonds.o pseudo_bonds.o check_dist.o add_bond.o event_loop.o alloc_nearest.o init_nearest.o main_re
 fresh.o key_press.o rotation_angle.o rotate.o translation_shift.o translate.o slab_shift.o move_back_slab.o move_front_slab.o fading_shift.o move_back_fading.o move_front_fading.o key_release.o refresh_pixmap.o slab.o no_slab.o planar_slab.o sphere_slab.o half_sphere_slab.o cylin_slab.o half_cylin_slab.o project_atoms.o fading.o prepare_color.o no_fading.o planar_fading.o sphere_fading.o half_sphere_fading.o cylin_fading.o half_cylin_fading.o reset_pos_flag.o atoms_style1.o atoms_style2.o atoms_style3.o atoms_style4.o atoms_style5.o atoms_style6.o atoms_style7.o bonds_style1.o bond_style1_quad1.o bond_style1_quad2.o bond_style1_quad3.o bond_style1_quad4.o bonds_style2.o bond_style2_quad1.o bond_style2_quad2.o bond_style2_quad3.o bond_style2_quad4.o bonds_style3.o interpolate_color.o bond_style3_quad1.o bond_style3_quad2.o bond_style3_quad3.o bond_style3_quad4.o bonds_style4.o add_two_colors.o bond_style4_quad1.o bond_style4_quad2.o bond_style4_quad3.o bond_style4_quad4.o bonds_style
 5.o add_three_colors.o bond_style5_quad1.o b!
 ond_style5_quad2.o bond_style5_quad3.o bond_style5_quad4.o draw_system.o motion_notify.o assign_hyphob.o control_refresh.o print_cursor_names.o main_resize.o init_runtime.o add_char.o input_refresh.o eat_left_char.o eat_right_char.o execute_command1.o execute_command2.o truncate_comm.o create_log_file.o load.o catch.o discard.o select.o full_select.o include.o chains.o residue_ranges.o extract_token.o extract_serials.o residue_names.o atom_names.o exclude.o skip_keyword.o apply_selection.o show.o hide.o color_schemes.o init_colors.o color.o special_select.o select_hetero.o select_element.o select_atoms.o quick_select.o replace_command.o atoms.o bonds.o execute_script.o comm_rotate.o comm_translate.o comm_slab.o comm_fading.o log.o prepare_backbone.o background.o text_background.o text_foreground.o change_slab.o change_fading.o full_colors.o is_old.o font.o cpk.o zebra.o chain.o color_hyphob.o mix_colors.o comm_backbone.o hide_no_refresh.o show_no_refresh.o backbone.o hybonds.o gener
 ate_hybonds.o hybond_style.o show_backbone.o hide_backbone.o pdb_id.o generate_plane.o stereo.o mono.o position.o copy_doubles.o title.o free_runtime.o draw_titles.o foreground.o prepare_oc.o select_complement.o labels.o draw_labels.o assign_radii.o spacefill.o spacefill_color.o draw_balls.o center.o save.o write_line.o big_spheres.o tag.o draw_tags.o tag_position.o button_press.o control_click.o identify_button.o init_buttons.o write_hints.o extract_sequence.o count_residues.o sequence.o parse_sequence.o sequence_from.o load_sequence.o select_sequence.o compare_sequences.o dihedral_angles.o extract_ncaco.o phi_from_cncac.o psi_from_ncaco.o vector_product.o absolute_value.o scalar_product.o omega_from_cacnca.o select_cis_trans.o ramachandran.o draw_ramachandran.o rama_frame.o rama_mouse.o read_fasta.o save_sequence.o wheel.o wheel_top_view.o wheel_bottom_view.o hydrophobicity.o weight_colors.o angle.o radius.o select_sphere.o disulfide_bonds.o venn.o draw_venn.o spacefill2.o sp2_col
 or.o save_seq_w_numbers.o ssb.o select_alter!
 nate.o se!
 lect_model.o color_model.o window.o plot.o draw_plots.o weighted_hydrophobicity.o average_hydrophobicity.o init_hyphob.o plot_mouse.o project_planes.o draw_planes.o plane_extent.o rotate_plane.o translate_plane.o comm_move.o plane.o select_above.o select_below.o big2.o scale.o pattern.o dock.o align_normal.o align_complexes.o docking_window.o docking_resize.o docking_refresh.o docking_project.o list_exposed_polar.o is_polar.o representative_atoms.o exclude_distant.o draw_bottom.o draw_top.o copy_sequence.o compare.o draw_comparison.o neighborhood.o draw_balls2.o comparison_mouse.o structure.o parse_sec_structure.o copy_sec_structure.o load_sec_structure.o save_sec_structure.o alloc_sec_structure.o sec_structure_from.o create.o open_template_file.o read_template_file.o ex_template_residues.o count_template_res.o create_structure.o required_atoms.o copy_template_atoms.o fix_chain.o reset_phi.o extract_hncac.o phi_from_hncac.o rotate_atom.o parallel_part.o reset_psi.o build_chain.o ext
 ract_ncac.o translate_range.o rotate_range.o apply_structure.o generate_phi_psi.o extract_nca.o extract_c.o replace.o extract_n.o refresh_backbone.o edit.o draw_edit_symbol.o draw_squid.o draw_seahorse.o are_atoms_bound.o bond_partners.o edit_phi.o edit_psi.o extract_cac.o small_ramachandran.o edit_omega.o small_omega.o extract_h.o extract_o.o psi_from_ncacn.o is_standard.o extract_four_atoms.o chi1_from_ncacbcg.o chi1_from_ncacbsg.o chi1_from_ncacbcg1.o chi1_from_ncacbog.o chi1_from_ncacbog1.o chi2_from_cacbcgcd.o chi2_from_cacbcgod1.o chi2_from_cacbcgnd1.o chi2_from_cacbcg1cd.o chi2_from_cacbcgcd1.o chi2_from_cacbcgsd.o chi3_from_cbcgcdne.o chi3_from_cbcgcdoe1.o chi3_from_cbcgcdce.o chi3_from_cbcgsdce.o chi4_from_cgcdnecz.o chi4_from_cgcdcenz.o chi5_from_cdnecznh1.o is_part_of_ring.o edit_bond.o edit_chi2.o extract_cacb.o edit_chi1.o extract_cbxg.o resize_complex.o membrane.o inform_user.o alpha_membrane.o extract_ca.o extract_vector.o alpha_membrane_center.o init_membrane.o alpha
 _normal.o project_membranes.o draw_membranes!
 .o rotate!
 _membrane.o translate_membrane.o select_triplet.o set.o set_phi.o set_psi.o set_omega.o set_chi1.o set_chi2.o set_chi3.o extract_cgxd.o set_chi4.o extract_cdxe.o set_chi5.o extract_necz.o pick_bond.o nice_bonds.o covalent.o covalent2.o half_nice_bond.o probe.o small_atoms.o small_atoms2.o draw_sticks.o half_stick.o command_refresh.o acceptor_dipole.o donor_dipole.o sticks.o balls.o blur.o blur_main_window.o group.o beta_membrane.o extract_cg.o select_tm.o parse_pattern.o select_pattern.o hyphob_function1.o hyphob_function2.o hyphob_function3.o hyphob_function4.o hyphob_function5.o hyphob_function6.o hyphob_function7.o color_size.o command_dump.o is_aromatic.o select_2c3.o select_2cz3.o select_2nz3.o select_3c4.o select_3cz4.o select_3nz4.o select_3c5.o select_3cz5.o select_3nz5.o select_3p5.o select_4c5.o select_4cz5.o select_4nz5.o select_3c6.o select_3cz6.o select_3nz6.o select_4c6.o select_4cz6.o select_4nz6.o select_4p6.o select_5c6.o select_5cz6.o select_5nz6.o select_4c7.o sel
 ect_4cz7.o select_4nz7.o select_5c7.o select_5cz7.o select_5nz7.o select_5p7.o select_6p7.o select_4c9.o select_4cz9.o select_4nz9.o select_5c9.o select_5cz9.o select_5nz9.o color_weighted.o -lX11 -lm
===========================================================================
=======================<phase: run-depends    >============================
===>   garlic-1.6 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found
===========================================================================
=======================<phase: stage          >============================
===>  Staging for garlic-1.6
===>   Generating temporary packing list
/bin/mkdir -p /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/garlic
install  -s -o root -g wheel -m 555 /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/garlic       /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/bin
install  -o root -g wheel -m 444    /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/.garlicrc    /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/garlic
install  -o root -g wheel -m 444    /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/residues.pdb /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/garlic
install  -o root -g wheel -m 444    /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/*.pdb        /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/examples/garlic
install  -o root -g wheel -m 444    /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/*.script     /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/examples/garlic
(cd /wrkdirs/usr/ports/biology/garlic/work/doc ; /usr/bin/tar xfz /portdistfiles/garlic-1.6-doc.tar.gz )
cd: /wrkdirs/usr/ports/biology/garlic/work/doc: No such file or directory
*** Error code 2

Stop in /usr/ports/biology/garlic.
===>  Cleaning for garlic-1.6