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Maintainer: mauri...@arareko.net Last committer: eha...@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/91amd64-default/2014-06-04_21h01m33s/logs/p5-bioperl-run-1.6.1_4.log Build URL: http://beefy2.isc.freebsd.org/bulk/91amd64-default/2014-06-04_21h01m33s Log: ====>> Building biology/p5-bioperl-run build started at Thu Jun 5 09:35:30 UTC 2014 port directory: /usr/ports/biology/p5-bioperl-run building for: FreeBSD 91amd64-default-job-04 9.1-RELEASE-p13 FreeBSD 9.1-RELEASE-p13 amd64 maintained by: mauri...@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: 1100013 Jail OSVERSION: 901000 ---Begin Environment--- 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/91amd64-default/ref PKG_EXT=txz tpid=30800 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/91amd64-default/ref/poudriere/rdeps PWD=/usr/local/poudriere/data/build/91amd64-default/ref/poudriere/pool MASTERNAME=91amd64-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" 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--- 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 =======================<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_10... 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_2...Installing freeglut-2.8.1_2...Installing libGLU-9.0.0...Installing libGL-7.6.1_4...Installing dri2proto-2.8... done Installing libX11-1.6.2_2,1...Installing kbproto-1.0.6... done <snip> done Installing libXaw-1.0.12_2,2...Installing libXp-1.0.2_2,1...Installing printproto-1.0.5... done done Installing libXpm-3.5.11_2... done done Installing libltdl-2.4.2_3... done Installing pango-1.34.1_4...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 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. Since FreeBSD has new USB stack, freeglut normally doesn't build on FreeBSD 8 (yet). To workaround this a small patch adds one include file and comments out content of one function (only leaves return NULL). This might cause side effects. Joysticks do not work, and there might be ports that do not compile or applications that crash because of this. Do not hesitate to contact x...@freebsd.org if there are any issues and side effects because of this. ==== 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 file: /usr/local/lib/perl5/site_perl/5.16/Module/Build.pm - not found ===> Verifying install for /usr/local/lib/perl5/site_perl/5.16/Module/Build.pm 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 _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
