head 1.12; access; symbols pkgsrc-2023Q4:1.12.0.30 pkgsrc-2023Q4-base:1.12 pkgsrc-2023Q3:1.12.0.28 pkgsrc-2023Q3-base:1.12 pkgsrc-2023Q2:1.12.0.26 pkgsrc-2023Q2-base:1.12 pkgsrc-2023Q1:1.12.0.24 pkgsrc-2023Q1-base:1.12 pkgsrc-2022Q4:1.12.0.22 pkgsrc-2022Q4-base:1.12 pkgsrc-2022Q3:1.12.0.20 pkgsrc-2022Q3-base:1.12 pkgsrc-2022Q2:1.12.0.18 pkgsrc-2022Q2-base:1.12 pkgsrc-2022Q1:1.12.0.16 pkgsrc-2022Q1-base:1.12 pkgsrc-2021Q4:1.12.0.14 pkgsrc-2021Q4-base:1.12 pkgsrc-2021Q3:1.12.0.12 pkgsrc-2021Q3-base:1.12 pkgsrc-2021Q2:1.12.0.10 pkgsrc-2021Q2-base:1.12 pkgsrc-2021Q1:1.12.0.8 pkgsrc-2021Q1-base:1.12 pkgsrc-2020Q4:1.12.0.6 pkgsrc-2020Q4-base:1.12 pkgsrc-2020Q3:1.12.0.4 pkgsrc-2020Q3-base:1.12 pkgsrc-2020Q2:1.12.0.2 pkgsrc-2020Q2-base:1.12 pkgsrc-2020Q1:1.11.0.2 pkgsrc-2020Q1-base:1.11 pkgsrc-2019Q4:1.9.0.46 pkgsrc-2019Q4-base:1.9 pkgsrc-2019Q3:1.9.0.42 pkgsrc-2019Q3-base:1.9 pkgsrc-2019Q2:1.9.0.40 pkgsrc-2019Q2-base:1.9 pkgsrc-2019Q1:1.9.0.38 pkgsrc-2019Q1-base:1.9 pkgsrc-2018Q4:1.9.0.36 pkgsrc-2018Q4-base:1.9 pkgsrc-2018Q3:1.9.0.34 pkgsrc-2018Q3-base:1.9 pkgsrc-2018Q2:1.9.0.32 pkgsrc-2018Q2-base:1.9 pkgsrc-2018Q1:1.9.0.30 pkgsrc-2018Q1-base:1.9 pkgsrc-2017Q4:1.9.0.28 pkgsrc-2017Q4-base:1.9 pkgsrc-2017Q3:1.9.0.26 pkgsrc-2017Q3-base:1.9 pkgsrc-2017Q2:1.9.0.22 pkgsrc-2017Q2-base:1.9 pkgsrc-2017Q1:1.9.0.20 pkgsrc-2017Q1-base:1.9 pkgsrc-2016Q4:1.9.0.18 pkgsrc-2016Q4-base:1.9 pkgsrc-2016Q3:1.9.0.16 pkgsrc-2016Q3-base:1.9 pkgsrc-2016Q2:1.9.0.14 pkgsrc-2016Q2-base:1.9 pkgsrc-2016Q1:1.9.0.12 pkgsrc-2016Q1-base:1.9 pkgsrc-2015Q4:1.9.0.10 pkgsrc-2015Q4-base:1.9 pkgsrc-2015Q3:1.9.0.8 pkgsrc-2015Q3-base:1.9 pkgsrc-2015Q2:1.9.0.6 pkgsrc-2015Q2-base:1.9 pkgsrc-2015Q1:1.9.0.4 pkgsrc-2015Q1-base:1.9 pkgsrc-2014Q4:1.9.0.2 pkgsrc-2014Q4-base:1.9 pkgsrc-2014Q3:1.8.0.18 pkgsrc-2014Q3-base:1.8 pkgsrc-2014Q2:1.8.0.16 pkgsrc-2014Q2-base:1.8 pkgsrc-2014Q1:1.8.0.14 pkgsrc-2014Q1-base:1.8 pkgsrc-2013Q4:1.8.0.12 pkgsrc-2013Q4-base:1.8 pkgsrc-2013Q3:1.8.0.10 pkgsrc-2013Q3-base:1.8 pkgsrc-2013Q2:1.8.0.8 pkgsrc-2013Q2-base:1.8 pkgsrc-2013Q1:1.8.0.6 pkgsrc-2013Q1-base:1.8 pkgsrc-2012Q4:1.8.0.4 pkgsrc-2012Q4-base:1.8 pkgsrc-2012Q3:1.8.0.2 pkgsrc-2012Q3-base:1.8 pkgsrc-2012Q2:1.7.0.16 pkgsrc-2012Q2-base:1.7 pkgsrc-2012Q1:1.7.0.14 pkgsrc-2012Q1-base:1.7 pkgsrc-2011Q4:1.7.0.12 pkgsrc-2011Q4-base:1.7 pkgsrc-2011Q3:1.7.0.10 pkgsrc-2011Q3-base:1.7 pkgsrc-2011Q2:1.7.0.8 pkgsrc-2011Q2-base:1.7 pkgsrc-2011Q1:1.7.0.6 pkgsrc-2011Q1-base:1.7 pkgsrc-2010Q4:1.7.0.4 pkgsrc-2010Q4-base:1.7 pkgsrc-2010Q3:1.7.0.2 pkgsrc-2010Q3-base:1.7 pkgsrc-2010Q2:1.6.0.10 pkgsrc-2010Q2-base:1.6 pkgsrc-2010Q1:1.6.0.8 pkgsrc-2010Q1-base:1.6 pkgsrc-2009Q4:1.6.0.6 pkgsrc-2009Q4-base:1.6 pkgsrc-2009Q3:1.6.0.4 pkgsrc-2009Q3-base:1.6 pkgsrc-2009Q2:1.6.0.2 pkgsrc-2009Q2-base:1.6 pkgsrc-2009Q1:1.4.0.14 pkgsrc-2009Q1-base:1.4 pkgsrc-2008Q4:1.4.0.12 pkgsrc-2008Q4-base:1.4 pkgsrc-2008Q3:1.4.0.10 pkgsrc-2008Q3-base:1.4 cube-native-xorg:1.4.0.8 cube-native-xorg-base:1.4 pkgsrc-2008Q2:1.4.0.6 pkgsrc-2008Q2-base:1.4 cwrapper:1.4.0.4 pkgsrc-2008Q1:1.4.0.2 pkgsrc-2008Q1-base:1.4 pkgsrc-2007Q4:1.3.0.8 pkgsrc-2007Q4-base:1.3 pkgsrc-2007Q3:1.3.0.6 pkgsrc-2007Q3-base:1.3 pkgsrc-2007Q2:1.3.0.4 pkgsrc-2007Q2-base:1.3 pkgsrc-2007Q1:1.3.0.2 pkgsrc-2007Q1-base:1.3 pkgsrc-2006Q4:1.2.0.2 pkgsrc-2006Q4-base:1.2 pkgsrc-2006Q3:1.1.1.1.0.12 pkgsrc-2006Q3-base:1.1.1.1 pkgsrc-2006Q2:1.1.1.1.0.10 pkgsrc-2006Q2-base:1.1.1.1 pkgsrc-2006Q1:1.1.1.1.0.8 pkgsrc-2006Q1-base:1.1.1.1 pkgsrc-2005Q4:1.1.1.1.0.6 pkgsrc-2005Q4-base:1.1.1.1 pkgsrc-2005Q3:1.1.1.1.0.4 pkgsrc-2005Q3-base:1.1.1.1 pkgsrc-2005Q2:1.1.1.1.0.2 pkgsrc-2005Q2-base:1.1.1.1 pkgsrc-base:1.1.1.1 TNF:1.1.1; locks; strict; comment @# @; 1.12 date 2020.05.20.06.09.06; author rillig; state Exp; branches; next 1.11; commitid YzMn9nHhuSomwW8C; 1.11 date 2020.01.26.05.26.15; author rillig; state Exp; branches; next 1.10; commitid uxXvYG0sFCxwZ9UB; 1.10 date 2020.01.18.23.30.09; author rillig; state Exp; branches; next 1.9; commitid shGUwZfkr7sleeTB; 1.9 date 2014.10.09.14.06.01; author wiz; state Exp; branches; next 1.8; commitid fBDATFVmQ3454xTx; 1.8 date 2012.09.11.20.32.13; author asau; state Exp; branches; next 1.7; 1.7 date 2010.09.19.07.13.37; author obache; state Exp; branches; next 1.6; 1.6 date 2009.06.12.19.07.29; author rillig; state Exp; branches; next 1.5; 1.5 date 2009.05.16.23.40.13; author zafer; state Exp; branches; next 1.4; 1.4 date 2008.03.03.01.10.06; author jlam; state Exp; branches; next 1.3; 1.3 date 2007.01.07.09.13.48; author rillig; state Exp; branches; next 1.2; 1.2 date 2006.10.04.20.47.03; author wiz; state Exp; branches; next 1.1; 1.1 date 2005.03.26.17.05.01; author minskim; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 2005.03.26.17.05.01; author minskim; state Exp; branches; next ; desc @@ 1.12 log @mark packages that fail with -Werror=char-subscripts These packages are susceptible to bugs when confronted with non-ASCII characters. See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=94182. It takes some time to analyze and fix these individually, therefore they are only marked as "needs work". @ text @# $NetBSD: Makefile,v 1.11 2020/01/26 05:26:15 rillig Exp $ # DISTNAME= ${PKGNAME:S/-//} PKGNAME= lucy-1.20 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=lucy/} MAINTAINER= dprice@@cs.nmsu.edu HOMEPAGE= http://lucy.sourceforge.net/ COMMENT= Sequence Cleanup Program #LICENSE= LICENSE file say "artistic", but bit differ. WRKSRC= ${WRKDIR}/${PKGNAME_NOREV}p AUTO_MKDIRS= yes PTHREAD_AUTO_VARS= yes # abi.c: In function 'abi_align': # abi.c:195:16: error: array subscript has type 'char' [-Werror=char-subscripts] # if (badness[a[i]][b[j]]) { # ^ # Maybe fix this later. BUILDLINK_TRANSFORM+= rm:-Werror=char-subscripts do-install: ${INSTALL_PROGRAM} ${WRKSRC}/lucy ${DESTDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/lucy.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1 cd ${WRKSRC} && ${INSTALL_DATA} PUC19 PUC19splice PUC19splice.for \ PUC19splice.rev atie.seq atie.qul atie.2nd pSPORT1splice \ pSPORT1vector ARMTM40TR.seq ARMTM40TR.qul lucy.ps lucy.debug \ ${DESTDIR}${PREFIX}/share/examples/lucy .include "../../mk/pthread.buildlink3.mk" .include "../../mk/bsd.pkg.mk" @ 1.11 log @all: migrate some SourceForge homepage URLs back from https to http https://mail-index.netbsd.org/pkgsrc-changes/2020/01/18/msg205146.html In the above commit, the homepage URLs were migrated from http to https, assuming that SourceForge would use the same host names for both http and https connections. This assumption was wrong. Their documentation at https://sourceforge.net/p/forge/documentation/Custom%20VHOSTs/ states that the https URLs use the domain sourceforge.io instead. To make the homepages from the above commit reachable again, pkglint has been extended to check for reachable homepages. This check is only enabled when the --network command line option is given. Each of the homepages that referred to https://$project.sourceforge.net before was migrated to https://$project.sourceforge.io (27), and if that was not reachable, to the fallback URL http://$project.sourceforge.net (163). @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.10 2020/01/18 23:30:09 rillig Exp $ d19 7 @ 1.10 log @all: migrate several HOMEPAGEs to https pkglint --only "https instead of http" -r -F With manual adjustments afterwards since pkglint 19.4.4 fixed a few indentations in unrelated lines. This mainly affects projects hosted at SourceForce, as well as freedesktop.org, CTAN and GNU. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.9 2014/10/09 14:06:01 wiz Exp $ d10 1 a10 1 HOMEPAGE= https://lucy.sourceforge.net/ @ 1.9 log @Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.8 2012/09/11 20:32:13 asau Exp $ d10 1 a10 1 HOMEPAGE= http://lucy.sourceforge.net/ @ 1.8 log @"user-destdir" is default these days @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.7 2010/09/19 07:13:37 obache Exp $ a13 2 PKG_INSTALLATION_TYPES= overwrite pkgviews @ 1.7 log @Update lucy to 1.20. Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.6 2009/06/12 19:07:29 rillig Exp $ a14 1 PKG_DESTDIR_SUPPORT= user-destdir @ 1.6 log @Made the Makefile simpler. Removed unnecessary .gz suffix from man pages. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.5 2009/05/16 23:40:13 zafer Exp $ d4 2 a5 1 DISTNAME= lucy-1.18p d7 1 a7 1 MASTER_SITES= # ftp://ftp.tigr.org/pub/software/Lucy/ d12 1 d17 2 d20 1 d24 1 a24 1 ${INSTALL_DATA} ${WRKSRC}/lucy.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1 @ 1.5 log @update homepage, update master site. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.4 2008/03/03 01:10:06 jlam Exp $ d15 1 a15 1 INSTALLATION_DIRS= bin ${PKGMANDIR}/man1 d20 3 a22 5 ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/examples/lucy .for EXAMPLE in PUC19 PUC19splice PUC19splice.for PUC19splice.rev \ atie.seq atie.qul atie.2nd pSPORT1splice pSPORT1vector ARMTM40TR.seq \ ARMTM40TR.qul lucy.ps lucy.debug ${INSTALL_DATA} ${WRKSRC}/${EXAMPLE} \ a23 1 .endfor @ 1.4 log @Mechanical changes to add full DESTDIR support to packages that install their files via a custom do-install target. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.3 2007/01/07 09:13:48 rillig Exp $ d6 1 a6 1 MASTER_SITES= ftp://ftp.tigr.org/pub/software/Lucy/ d9 1 a9 1 HOMEPAGE= http://www.tigr.org/software/ @ 1.3 log @Mechanically replaced man/* with ${PKGMANDIR}/* in the definition of INSTALLATION_DIRS, as well as all occurrences of ${PREFIX}/man with ${PREFIX}/${PKGMANDIR}. Fixes PR 35265, although I did not use the patch provided therein. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.2 2006/10/04 20:47:03 wiz Exp $ d13 1 d18 3 a20 3 ${INSTALL_PROGRAM} ${WRKSRC}/lucy ${PREFIX}/bin ${INSTALL_DATA} ${WRKSRC}/lucy.1 ${PREFIX}/${PKGMANDIR}/man1 ${INSTALL_DATA_DIR} ${PREFIX}/share/examples/lucy d24 2 a25 1 ${INSTALL_DATA} ${WRKSRC}/${EXAMPLE} ${PREFIX}/share/examples/lucy @ 1.2 log @Update MASTER_SITES and/or HOMEPAGE, from Sergey Svishchev. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.1.1.1 2005/03/26 17:05:01 minskim Exp $ d14 1 a14 1 INSTALLATION_DIRS= bin man/man1 d18 1 a18 1 ${INSTALL_DATA} ${WRKSRC}/lucy.1 ${PREFIX}/man/man1 @ 1.1 log @Initial revision @ text @d1 1 a1 1 # $NetBSD$ d9 1 a9 1 HOMEPAGE= http://www.tigr.org/software @ 1.1.1.1 log @Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program. @ text @@