From owner-freebsd-pkg-fallout@FreeBSD.ORG Fri Jun 13 08:18:17 2014 Return-Path: Delivered-To: pkg-fallout@FreeBSD.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 7C31E13B for ; Fri, 13 Jun 2014 08:18:17 +0000 (UTC) Received: from beefy2.isc.freebsd.org (beefy2.isc.freebsd.org [IPv6:2001:4f8:3:ffe0:4072:0:16:39]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 5AAE02EB8; Fri, 13 Jun 2014 08:18:17 +0000 (UTC) Received: from beefy2.isc.freebsd.org (localhost [127.0.0.1]) by beefy2.isc.freebsd.org (8.14.9/8.14.9) with ESMTP id s5D8IHcg064464; Fri, 13 Jun 2014 08:18:17 GMT (envelope-from pkg-fallout-builder@FreeBSD.org) Received: (from root@localhost) by beefy2.isc.freebsd.org (8.14.9/8.14.9/Submit) id s5D8IGiE064137; Fri, 13 Jun 2014 08:18:16 GMT (envelope-from pkg-fallout-builder@FreeBSD.org) Date: Fri, 13 Jun 2014 08:18:16 GMT From: pkg-fallout-builder@FreeBSD.org Message-Id: <201406130818.s5D8IGiE064137@beefy2.isc.freebsd.org> To: mauricio@arareko.net Subject: [REL - 10amd64-default][biology/p5-bioperl-run] Failed for p5-bioperl-run-1.6.1_4 in configure Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 13 Jun 2014 08:18:17 -0000 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@arareko.net Last committer: ehaupt@FreeBSD.org Ident: $FreeBSD: head/biology/p5-bioperl-run/Makefile 345397 2014-02-21 13:35:26Z ehaupt $ Log URL: http://beefy2.isc.freebsd.org/bulk/10amd64-default/2014-06-12_19h04m15s/logs/p5-bioperl-run-1.6.1_4.log Build URL: http://beefy2.isc.freebsd.org/bulk/10amd64-default/2014-06-12_19h04m15s Log: ====>> Building biology/p5-bioperl-run build started at Fri Jun 13 08:17:44 UTC 2014 port directory: /usr/ports/biology/p5-bioperl-run building for: FreeBSD 10amd64-default-job-10 10.0-RELEASE-p3 FreeBSD 10.0-RELEASE-p3 amd64 maintained by: mauricio@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: 1000510 ---Begin Environment--- OSVERSION=1000510 UNAME_v=FreeBSD 10.0-RELEASE-p3 UNAME_r=10.0-RELEASE-p3 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/build/10amd64-default/ref PKG_EXT=txz tpid=53467 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/10amd64-default/ref/poudriere/rdeps PWD=/usr/local/poudriere/data/build/10amd64-default/ref/poudriere/pool MASTERNAME=10amd64-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=10.0 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--- 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 ran via poudriere.conf NO_RESTRICTED #NO_RESTRICTED=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ===> Cleaning for p5-bioperl-run-1.6.1_4 =================================================== =========================================================================== =================================================== ===> 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 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by p5-bioperl-run-1.6.1_4 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for p5-bioperl-run-1.6.1_4 =========================================================================== =================================================== ===> 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 done Installing jpeg-8_5... done Installing png-1.5.18... done Installing tiff-4.0.3_3...Installing jbigkit-1.6... done 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 =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. *** Error code 25 Stop. make: stopped in /usr/ports/biology/p5-bioperl-run ===> Cleaning for p5-bioperl-run-1.6.1_4