[REL - 91i386-default][biology/p5-bioperl-run] Failed for p5-bioperl-run-1.6.1_4 in configure
pkg-fallout-builder at FreeBSD.org
pkg-fallout-builder at FreeBSD.org
Thu Jun 12 18:07:56 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: mauricio at arareko.net
Last committer: ehaupt at FreeBSD.org
Ident: $FreeBSD: head/biology/p5-bioperl-run/Makefile 345397 2014-02-21 13:35:26Z ehaupt $
Log URL: http://beefy1.isc.freebsd.org/bulk/91i386-default/2014-06-12_04h07m16s/logs/p5-bioperl-run-1.6.1_4.log
Build URL: http://beefy1.isc.freebsd.org/bulk/91i386-default/2014-06-12_04h07m16s
Log:
====>> Building biology/p5-bioperl-run
build started at Thu Jun 12 18:07:19 UTC 2014
port directory: /usr/ports/biology/p5-bioperl-run
building for: FreeBSD 91i386-default-job-19 9.1-RELEASE-p13 FreeBSD 9.1-RELEASE-p13 i386
maintained by: mauricio at arareko.net
Makefile ident: $FreeBSD: head/biology/p5-bioperl-run/Makefile 345397 2014-02-21 13:35:26Z ehaupt $
Poudriere version: 3.1-pre
Host OSVERSION: 1100022
Jail OSVERSION: 901000
---Begin Environment---
UNAME_m=i386
UNAME_p=i386
OSVERSION=901000
UNAME_v=FreeBSD 9.1-RELEASE-p13
UNAME_r=9.1-RELEASE-p13
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/build/91i386-default/ref
PKG_EXT=txz
tpid=74404
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNG=1
PKGNAME=p5-bioperl-run-1.6.1_4
PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f
PKG_ADD=/usr/local/sbin/pkg-static add
OLDPWD=/usr/local/poudriere/data/build/91i386-default/ref/poudriere/rdeps
PWD=/usr/local/poudriere/data/build/91i386-default/ref/poudriere/pool
MASTERNAME=91i386-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 p5-bioperl-run-1.6.1_4:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--CONFIGURE_ARGS--
--install_path lib="/usr/local/lib/perl5/site_perl/5.16" --install_path arch="/usr/local/lib/perl5/site_perl/5.16/mach" --install_path script="/usr/local/bin" --install_path bin="/usr/local/bin" --install_path libdoc="/usr/local/lib/perl5/5.16/man/man3" --install_path bindoc="/usr/local/man/man1" --destdir --create_packlist 0 CC="cc" CCFLAGS="-O2 -pipe -fno-strict-aliasing" PREFIX="/usr/local" INSTALLPRIVLIB="/usr/local/lib" INSTALLARCHLIB="/usr/local/lib"
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
TMPDIR="/tmp" TMPDIR="/tmp" ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl SHELL=/bin/sh CONFIG_SHELL=/bin/sh PERL_EXTUTILS_AUTOINSTALL="--skipdeps" PERL_MM_USE_DEFAULT="YES"
--End CONFIGURE_ENV--
--MAKE_ENV--
TMPDIR="/tmp" 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="" 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=9.1
PREFIX=%D
LOCALBASE=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
PORTDATA=""
LIB32DIR=lib
PERL_VERSION=5.16.3
PERL_VER=5.16
PERL_ARCH=mach
PERL5_MAN3=lib/perl5/5.16/man/man3
SITE_PERL=lib/perl5/site_perl/5.16
DOCSDIR="share/doc/bioperl-run"
EXAMPLESDIR="share/examples/bioperl-run"
DATADIR="share/bioperl-run"
WWWDIR="www/bioperl-run"
ETCDIR="etc/bioperl-run"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/bioperl-run
DOCSDIR=/usr/local/share/doc/bioperl-run
EXAMPLESDIR=/usr/local/share/examples/bioperl-run
WWWDIR=/usr/local/www/bioperl-run
ETCDIR=/usr/local/etc/bioperl-run
--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 p5-bioperl-run-1.6.1_4
=======================<phase: check-sanity >============================
===========================================================================
=======================<phase: pkg-depends >============================
===> p5-bioperl-run-1.6.1_4 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_2.txz
Installing pkg-1.2.7_2... done
If you are upgrading from the old package format, first run:
# pkg2ng
===> Returning to build of p5-bioperl-run-1.6.1_4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> Fetching all distfiles required by p5-bioperl-run-1.6.1_4 for building
===========================================================================
=======================<phase: checksum >============================
===> Fetching all distfiles required by p5-bioperl-run-1.6.1_4 for building
=> SHA256 Checksum OK for BioPerl-run-1.6.1.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> Fetching all distfiles required by p5-bioperl-run-1.6.1_4 for building
===> Extracting for p5-bioperl-run-1.6.1_4
=> SHA256 Checksum OK for BioPerl-run-1.6.1.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for p5-bioperl-run-1.6.1_4
===========================================================================
=======================<phase: build-depends >============================
===> p5-bioperl-run-1.6.1_4 depends on package: p5-bioperl>=1.6.0 - not found
===> Verifying install for p5-bioperl>=1.6.0 in /usr/ports/biology/p5-bioperl
===> Installing existing package /packages/All/p5-bioperl-1.6.923.txz
Installing p5-bioperl-1.6.923...Installing p5-Algorithm-Munkres-0.08...Installing perl5-5.16.3_11... done
done
Installing p5-Array-Compare-2.02...Installing p5-Moose-2.1204,1...Installing p5-Class-Load-XS-0.08...Installing p5-Class-Load-0.21...Installing p5-Data-OptList-0.109...Installing p5-Params-Util-1.07... done
Installing p5-Sub-Install-0.927... done
done
Installing p5-Module-Implementation-0.07...Installing p5-Module-Runtime-0.014... done
Installing p5-Try-Tiny-0.18... done
done
Installing p5-Package-Stash-0.36...Installing p5-Dist-CheckConflicts-0.11... done
Installing p5-Package-Stash-XS-0.28... done
done
done
done
Installing p5-Devel-GlobalDestruction-0.12...Installing p5-Sub-Exporter-Progressive-0.001.011...Installing p5-Sub-Exporter-0.987... done
done
done
Installing p5-Devel-StackTrace-1.32... done
Installing p5-Eval-Closure-0.11... done
Installing p5-List-MoreUtils-0.33... done
Installing p5-MRO-Compat-0.12...Installing p5-Class-C3-0.26...Installing p5-Algorithm-C3-0.09... done
done
done
Installing p5-Package-DeprecationManager-0.13... done
Installing p5-Sub-Name-0.05... done
Installing p5-Task-Weaken-1.04... done
done
done
Installing p5-Bio-ASN1-EntrezGene-1.091... done
Installing p5-Class-AutoClass-1.56...Installing p5-Hash-AutoHash-Args-1.18...Installing p5-Hash-AutoHash-1.17...Installing p5-Tie-ToObject-0.03_1... done
done
done
done
Installing p5-Clone-0.35... done
Installing p5-Convert-Binary-C-0.76... done
Installing p5-DBD-mysql-4.027...Installing mysql55-client-5.5.38... done
Installing p5-DBI-1.631... done
done
Installing p5-Data-Stag-0.14_1...Installing p5-IO-String-1.08... done
done
Installing p5-Error-0.17022... done
Installing p5-GD-SVG-0.33_5...Installing p5-GD-2.53...Installing libgd-2.1.0_3,1...Installing fontconfig-2.11.0_3,1...Installing expat-2.1.0... done
Installing freetype2-2.5.3_2... done
Running fc-cache to build fontconfig cache...
/usr/local/share/fonts: skipping, no such directory
/usr/local/lib/X11/fonts: caching, new cache contents: 0 fonts, 1 dirs
/usr/local/lib/X11/fonts/local: caching, new cache contents: 0 fonts, 0 dirs
/root/.local/share/fonts: skipping, no such directory
/root/.fonts: skipping, no such directory
/usr/local/share/fonts: skipping, no such directory
/usr/local/lib/X11/fonts: caching, new cache contents: 0 fonts, 1 dirs
/root/.local/share/fonts: skipping, no such directory
/root/.fonts: skipping, no such directory
/var/db/fontconfig: cleaning cache directory
/root/.cache/fontconfig: not cleaning non-existent cache directory
/root/.fontconfig: not cleaning non-existent cache directory
fc-cache: succeeded
<snip>
Installing libxml2-2.9.1_1... done
done
done
Installing libXaw-1.0.12_2,2...Installing libXext-1.3.2_2,1...Installing xextproto-7.3.0... done
done
Installing libXmu-1.1.2_2,1...Installing libXt-1.1.4_2,1... done
done
Installing libXp-1.0.2_2,1...Installing printproto-1.0.5... done
done
Installing libXpm-3.5.11_2... done
done
Installing libXrender-0.9.8_2...Installing renderproto-0.11.1... done
done
Installing libltdl-2.4.2_3... done
Installing pango-1.34.1_5...Installing cairo-1.10.2_10,2...Installing pixman-0.32.4_2... done
Installing xcb-util-renderutil-0.3.8_2...Installing xcb-util-0.3.9_3,1... done
done
done
Installing encodings-1.0.4_1,1...Installing font-util-1.3.0_1... done
done
Installing gnomehier-3.0... done
Installing harfbuzz-0.9.28...Installing graphite2-1.2.4... done
Installing icu-52.1... done
done
Installing libXft-2.3.1_2... done
Installing xorg-fonts-truetype-7.7_1...Installing dejavu-2.34_3... done
Installing font-bh-ttf-1.0.3_1...Installing mkfontdir-1.0.7...Installing mkfontscale-1.1.1_1...Installing libfontenc-1.1.2_2... done
done
done
done
Installing font-misc-ethiopic-1.0.3_1... done
Installing font-misc-meltho-1.0.3_1... done
done
done
done
Installing p5-IPC-Run-0.92...Installing p5-IO-Tty-1.11... done
done
Installing p5-Parse-RecDescent-1.967.009_1... done
Installing p5-XML-Twig-3.47...Installing p5-HTML-Tree-5.03...Installing p5-HTML-Parser-3.71...Installing p5-HTML-Tagset-3.20... done
done
done
Installing p5-Text-Iconv-1.7_1... done
Installing p5-Tie-IxHash-1.23... done
Installing p5-XML-Parser-2.41_1... done
Installing p5-XML-XPath-1.13... done
Installing p5-libwww-6.06...Installing p5-Authen-NTLM-1.09...Installing p5-Digest-HMAC-1.03... done
done
Installing p5-Data-Dump-1.22... done
Installing p5-Encode-Locale-1.03... done
Installing p5-File-Listing-6.04...Installing p5-HTTP-Date-6.02... done
done
Installing p5-HTTP-Cookies-6.01...Installing p5-HTTP-Message-6.06_2...Installing p5-IO-HTML-1.00... done
Installing p5-LWP-MediaTypes-6.02... done
Installing p5-URI-1.60... done
done
done
Installing p5-HTTP-Daemon-6.01... done
Installing p5-HTTP-Negotiate-6.01... done
Installing p5-Net-HTTP-6.06...Installing p5-IO-Socket-SSL-1.992...Installing p5-IO-Socket-IP-0.29...Installing p5-Socket-2.014... done
done
Installing p5-Net-SSLeay-1.63... done
done
done
Installing p5-WWW-RobotRules-6.02... done
done
done
done
Installing p5-HTML-TableExtract-2.11...Installing p5-HTML-Element-Extended-1.18... done
done
Installing p5-IO-stringy-2.110... done
Installing p5-Math-Random-0.71... done
Installing p5-PostScript-0.06... done
Installing p5-SOAP-Lite-0.716...Installing p5-Class-Inspector-1.28... done
Installing p5-Crypt-SSLeay-0.64...Installing p5-LWP-Protocol-https-6.04...Installing p5-Mozilla-CA-20130114... done
done
done
Installing p5-MIME-Lite-3.03.0...Installing p5-Email-Date-Format-1.004... done
Installing p5-MIME-Types-2.04... done
Installing p5-Mail-Tools-2.13...Installing p5-TimeDate-2.30_1,1... done
done
done
Installing p5-MIME-Tools-5.505,2...Installing p5-Convert-BinHex-1.123... done
done
done
Installing p5-SVG-Graph-0.04...Installing p5-Math-Spline-0.02...Installing p5-Math-Derivative-0.01... done
done
Installing p5-Statistics-Descriptive-3.0605... done
Installing p5-Tree-DAG_Node-1.22...Installing p5-File-Slurp-Tiny-0.003... done
Installing p5-File-Temp-0.23.01... done
Installing p5-PathTools-3.4000... done
done
done
Installing p5-Set-Scalar-1.26... done
Installing p5-Sort-Naturally-1.03... done
Installing p5-Spreadsheet-ParseExcel-0.59,1...Installing p5-Crypt-RC4-2.02... done
Installing p5-Digest-Perl-MD5-1.9... done
Installing p5-OLE-Storage_Lite-0.19... done
done
Installing p5-Test-Most-0.33...Installing p5-Exception-Class-1.38...Installing p5-Class-Data-Inheritable-0.08... done
done
Installing p5-Test-Deep-0.112...Installing p5-Test-NoWarnings-1.04_1... done
Installing p5-Test-Tester-0.10.9... done
done
Installing p5-Test-Differences-0.610,1...Installing p5-Text-Diff-1.41...Installing p5-Algorithm-Diff-1.1902... done
done
done
Installing p5-Test-Exception-0.32...Installing p5-Sub-Uplevel-0.2400... done
done
Installing p5-Test-Warn-0.30...Installing p5-Carp-1.33.01... done
done
done
Installing p5-Text-Shellwords-1.08... done
Installing p5-Text-Tabs+Wrap-2013.0523... done
Installing p5-XML-DOM-XPath-0.14...Installing p5-XML-DOM-1.44...Installing p5-XML-RegExp-0.04... done
Installing p5-libxml-0.08... done
done
Installing p5-XML-XPathEngine-0.14... done
done
Installing p5-XML-SAX-Writer-0.54...Installing p5-XML-Filter-BufferText-1.01...Installing p5-XML-SAX-0.99_1...Installing p5-XML-NamespaceSupport-1.11... done
Installing p5-XML-SAX-Base-1.08... done
done
done
done
Installing p5-XML-Simple-2.20...Installing p5-XML-SAX-Expat-0.50... done
done
Installing p5-XML-Writer-0.624... done
Installing p5-YAML-0.87... done
done
Note that this release of p5-Moose is incompatible with
older versions of the following modules:
Catalyst <= 5.80017
Devel::REPL <= 1.003008
Fey::ORM <= 0.23
File::ChangeNotify <= 0.15
KiokuDB <= 0.41
MooseX::Aliases <= 0.07
MooseX::AttributeHelpers <= 0.22
MooseX::AttributeInflate <= 0.02
MooseX::Attribute::Prototype <= 0.10
MooseX::ClassAttribute <= 0.13
MooseX::FollowPBP <= 0.02
MooseX::HasDefaults <= 0.02
MooseX::InstanceTracking <= 0.04
MooseX::LazyRequire <= 0.05
MooseX::MethodAttributes <= 0.22
MooseX::NonMoose <= 0.13
MooseX::Params::Validate <= 0.05
MooseX::Role::Cmd <= 0.06
MooseX::Role::WithOverloading <= 0.07
MooseX::SemiAffordanceAccessor <= 0.05
MooseX::Singleton <= 0.22
MooseX::StrictConstructor <= 0.08
MooseX::Types <= 0.19
MooseX::UndefTolerant <= 0.04
namespace::autoclean <= 0.08
Pod::Elemental <= 0.093280
They will need to be updated.
====
Note that some of the standard modules are provided as separate
ports since they require extra dependencies:
bsddb databases/py-bsddb
gdbm databases/py-gdbm
sqlite3 databases/py-sqlite3
tkinter x11-toolkits/py-tkinter
Install them as needed.
====
Make sure that the freetype module is loaded. If it is not, add the following
line to the "Modules" section of your X Windows configuration file:
Load "freetype"
Add the following line to the "Files" section of X Windows configuration file:
FontPath "/usr/local/lib/X11/fonts/dejavu/"
Note: your X Windows configuration file is typically /etc/X11/XF86Config
if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org.
===> Returning to build of p5-bioperl-run-1.6.1_4
===> p5-bioperl-run-1.6.1_4 depends on package: p5-IPC-Run>=0 - found
===> p5-bioperl-run-1.6.1_4 depends on package: p5-Algorithm-Diff>=0 - found
===> p5-bioperl-run-1.6.1_4 depends on package: p5-Module-Build>=0.4205 - not found
===> Verifying install for p5-Module-Build>=0.4205 in /usr/ports/devel/p5-Module-Build
===> Installing existing package /packages/All/p5-Module-Build-0.4205.txz
Installing p5-Module-Build-0.4205... done
===> Returning to build of p5-bioperl-run-1.6.1_4
===> p5-bioperl-run-1.6.1_4 depends on file: /usr/local/bin/perl5.16.3 - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for p5-bioperl-run-1.6.1_4
Invalid prerequisite condition '0/processing XML data/Bio::Tools::Run::EMBOSSacd' for XML::Twig at /usr/local/lib/perl5/site_perl/5.16/Module/Build/Base.pm line 1702.
*** [do-configure] Error code 25
Stop in /usr/ports/biology/p5-bioperl-run.
===> Cleaning for p5-bioperl-run-1.6.1_4
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