From owner-svn-ports-all@FreeBSD.ORG Wed Dec 3 01:40:56 2014 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 1D632CF; Wed, 3 Dec 2014 01:40:56 +0000 (UTC) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) (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 F27EC30B; Wed, 3 Dec 2014 01:40:55 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.9/8.14.9) with ESMTP id sB31etTt078376; Wed, 3 Dec 2014 01:40:55 GMT (envelope-from danfe@FreeBSD.org) Received: (from danfe@localhost) by svn.freebsd.org (8.14.9/8.14.9/Submit) id sB31et3F078373; Wed, 3 Dec 2014 01:40:55 GMT (envelope-from danfe@FreeBSD.org) Message-Id: <201412030140.sB31et3F078373@svn.freebsd.org> X-Authentication-Warning: svn.freebsd.org: danfe set sender to danfe@FreeBSD.org using -f From: Alexey Dokuchaev Date: Wed, 3 Dec 2014 01:40:55 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r373799 - head/biology/ugene X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.18-1 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 03 Dec 2014 01:40:56 -0000 Author: danfe Date: Wed Dec 3 01:40:54 2014 New Revision: 373799 URL: https://svnweb.freebsd.org/changeset/ports/373799 QAT: https://qat.redports.org/buildarchive/r373799/ Log: Update to version 1.15.0. Modified: head/biology/ugene/Makefile head/biology/ugene/distinfo head/biology/ugene/pkg-plist Modified: head/biology/ugene/Makefile ============================================================================== --- head/biology/ugene/Makefile Wed Dec 3 00:32:18 2014 (r373798) +++ head/biology/ugene/Makefile Wed Dec 3 01:40:54 2014 (r373799) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= ugene -DISTVERSION= 1.14.2 +DISTVERSION= 1.15.0 CATEGORIES= biology science MASTER_SITES= http://ugene.unipro.ru/downloads/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \ @@ -74,10 +74,8 @@ post-patch: .for x in ugenecl ugeneui plugins_checker @${ECHO_CMD} 'LIBS += -lexecinfo' >> ${WRKSRC}/src/${x}/${x}.pro .endfor -# missing linefeeds at EOF irk gcc4.2 - @(cd ${WRKSRC}/src && ${FIND} -E . -type f -regex '.*\.(cpp|h)' | \ - while read f; do if [ "`${TAIL} -c 1 "$$f"`" ]; then \ - ${ECHO_CMD} >&2 "$${f#./} lacks newline at EOF, fixing"; \ - ${ECHO_CMD} >> "$$f"; fi; done) +# remove BOM that gcc4.2 trips upon + @env LANG=C ${REINPLACE_CMD} -e 's,^...,,' \ + ${WRKSRC}/src/include/U2Formats/MysqlUpgradeTask.h .include Modified: head/biology/ugene/distinfo ============================================================================== --- head/biology/ugene/distinfo Wed Dec 3 00:32:18 2014 (r373798) +++ head/biology/ugene/distinfo Wed Dec 3 01:40:54 2014 (r373799) @@ -1,5 +1,5 @@ -SHA256 (ugene/ugene-1.14.2.tar.gz) = deea01b9a5386094fa2d7e48db9d529afd9520ed0d6bc5bb2fb40493ae861a3a -SIZE (ugene/ugene-1.14.2.tar.gz) = 19800763 +SHA256 (ugene/ugene-1.15.0.tar.gz) = 8ab1bd3009a568c2d2d8176bb4b038891b231fe930f31a9568852773f9c10b36 +SIZE (ugene/ugene-1.15.0.tar.gz) = 20197629 SHA256 (ugene/QueryDesigner_UserManual.pdf) = 2add11809ecc3225abfef417ad8d5435fed76a662081f461abb36e3d4b31cfcd SIZE (ugene/QueryDesigner_UserManual.pdf) = 824781 SHA256 (ugene/UniproUGENE_UserManual.pdf) = c4aa20246988978c6b40a06f7753f78d204ee3155cb8876a3d665b9ebf5641db Modified: head/biology/ugene/pkg-plist ============================================================================== --- head/biology/ugene/pkg-plist Wed Dec 3 00:32:18 2014 (r373798) +++ head/biology/ugene/pkg-plist Wed Dec 3 01:40:54 2014 (r373799) @@ -201,6 +201,10 @@ lib/ugene/plugins/liborf_marker.so lib/ugene/plugins/liborf_marker.so.1 lib/ugene/plugins/liborf_marker.so.1.0 lib/ugene/plugins/liborf_marker.so.1.0.0 +lib/ugene/plugins/libpcr.so +lib/ugene/plugins/libpcr.so.1 +lib/ugene/plugins/libpcr.so.1.0 +lib/ugene/plugins/libpcr.so.1.0.0 lib/ugene/plugins/libperf_monitor.so lib/ugene/plugins/libperf_monitor.so.1 lib/ugene/plugins/libperf_monitor.so.1.0 @@ -245,10 +249,6 @@ lib/ugene/plugins/libsmith_waterman.so lib/ugene/plugins/libsmith_waterman.so.1 lib/ugene/plugins/libsmith_waterman.so.1.0 lib/ugene/plugins/libsmith_waterman.so.1.0.0 -lib/ugene/plugins/libsnp_effect.so -lib/ugene/plugins/libsnp_effect.so.1 -lib/ugene/plugins/libsnp_effect.so.1.0 -lib/ugene/plugins/libsnp_effect.so.1.0.0 lib/ugene/plugins/libtest_runner.so lib/ugene/plugins/libtest_runner.so.1 lib/ugene/plugins/libtest_runner.so.1.0 @@ -275,6 +275,8 @@ lib/ugene/plugins/opencl_support.license lib/ugene/plugins/opencl_support.plugin lib/ugene/plugins/orf_marker.license lib/ugene/plugins/orf_marker.plugin +lib/ugene/plugins/pcr.license +lib/ugene/plugins/pcr.plugin lib/ugene/plugins/perf_monitor.license lib/ugene/plugins/perf_monitor.plugin lib/ugene/plugins/phylip.license @@ -297,8 +299,6 @@ lib/ugene/plugins/sitecon.license lib/ugene/plugins/sitecon.plugin lib/ugene/plugins/smith_waterman.license lib/ugene/plugins/smith_waterman.plugin -lib/ugene/plugins/snp_effect.license -lib/ugene/plugins/snp_effect.plugin lib/ugene/plugins/test_runner.license lib/ugene/plugins/test_runner.plugin %%NOX64%%lib/ugene/plugins/umuscle.license @@ -373,7 +373,9 @@ share/pixmaps/ugene.xpm %%DATADIR%%/cmdline/convert-seq.uwl %%DATADIR%%/cmdline/das_annotation.uwl %%DATADIR%%/cmdline/extract-sequence.uwl -%%DATADIR%%/cmdline/extract_consensus.uwl +%%DATADIR%%/cmdline/extract_consensus_sequence.uwl +%%DATADIR%%/cmdline/extract_consensus_string.uwl +%%DATADIR%%/cmdline/extract_coverage.uwl %%DATADIR%%/cmdline/fetch-sequence.uwl %%DATADIR%%/cmdline/find-orfs.uwl %%DATADIR%%/cmdline/find-repeats.uwl @@ -1385,6 +1387,8 @@ share/pixmaps/ugene.xpm %%DATADIR%%/weight_matrix/vtml160.txt %%DATADIR%%/weight_matrix/vtml200.txt %%DATADIR%%/workflow_samples/Alignment/basic_align.uwl +%%DATADIR%%/workflow_samples/Alignment/extract_msa_consensus_as_seq.uwl +%%DATADIR%%/workflow_samples/Alignment/extract_msa_consensus_as_text.uwl %%DATADIR%%/workflow_samples/Conversions/faqual2fastq.uwl %%DATADIR%%/workflow_samples/Conversions/msa2clustal.uwl %%DATADIR%%/workflow_samples/Conversions/query2alignment.uwl @@ -1401,12 +1405,28 @@ share/pixmaps/ugene.xpm %%DATADIR%%/workflow_samples/Data merging/tfbs.uwl %%DATADIR%%/workflow_samples/HMMER/build-test-HMM.uwl %%DATADIR%%/workflow_samples/HMMER/searchHMM.uwl +%%DATADIR%%/workflow_samples/NGS/assembly/spades_paired.uwl +%%DATADIR%%/workflow_samples/NGS/assembly/spades_single.uwl +%%DATADIR%%/workflow_samples/NGS/assembly.uwl %%DATADIR%%/workflow_samples/NGS/call_variants.uwl %%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq.uwl %%DATADIR%%/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl %%DATADIR%%/workflow_samples/NGS/cistrome.uwl %%DATADIR%%/workflow_samples/NGS/consensus.uwl +%%DATADIR%%/workflow_samples/NGS/chipseq_coverage.uwl +%%DATADIR%%/workflow_samples/NGS/extract_coverage.uwl %%DATADIR%%/workflow_samples/NGS/extract_transcript_seq.uwl +%%DATADIR%%/workflow_samples/NGS/raw_chip.uwl +%%DATADIR%%/workflow_samples/NGS/raw_dna.uwl +%%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_paired.uwl +%%DATADIR%%/workflow_samples/NGS/raw_ngs/chipseq/chipseq_single.uwl +%%DATADIR%%/workflow_samples/NGS/raw_ngs/dnaseq/dna_paired.uwl +%%DATADIR%%/workflow_samples/NGS/raw_ngs/dnaseq/dna_single.uwl +%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_paired.uwl +%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_single.uwl +%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_paired.uwl +%%DATADIR%%/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_single.uwl +%%DATADIR%%/workflow_samples/NGS/raw_rna.uwl %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main.uwl %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl @@ -1414,11 +1434,11 @@ share/pixmaps/ugene.xpm %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl %%DATADIR%%/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl %%DATADIR%%/workflow_samples/NGS/tuxedo.uwl -%%DATADIR%%/workflow_samples/Scenarios/extract_consensus.uwl %%DATADIR%%/workflow_samples/Scenarios/filter_matched.uwl %%DATADIR%%/workflow_samples/Scenarios/find_inverted_repeats.uwl %%DATADIR%%/workflow_samples/Scenarios/find_sequences.uwl %%DATADIR%%/workflow_samples/Scenarios/gene_by_gene_report.uwl +%%DATADIR%%/workflow_samples/Scenarios/group_primers_pairs.uwl %%DATADIR%%/workflow_samples/Scenarios/merge_sequence_annotation.uwl %%DATADIR%%/workflow_samples/Scenarios/remote_blasting.uwl %%DATADIR%%/workflow_samples/Scenarios/translate_seq_and_compl.uwl