CVS commit: pkgsrc/biology/cdhit

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Dec 17 17:57:55 UTC 2021

Modified Files:
        pkgsrc/biology/cdhit: Makefile PLIST distinfo

Log Message:
biology/cdhit: Update to 4.8.1

Add support for gzipped input

Changes: https://github.com/weizhongli/cdhit/releases


To generate a diff of this commit:
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/cdhit/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/cdhit/PLIST
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/cdhit/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/cdhit/Makefile
diff -u pkgsrc/biology/cdhit/Makefile:1.8 pkgsrc/biology/cdhit/Makefile:1.9
--- pkgsrc/biology/cdhit/Makefile:1.8   Mon May 24 19:49:10 2021
+++ pkgsrc/biology/cdhit/Makefile       Fri Dec 17 17:57:55 2021
@@ -1,11 +1,6 @@
-# $NetBSD: Makefile,v 1.8 2021/05/24 19:49:10 wiz Exp $
-#
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
+# $NetBSD: Makefile,v 1.9 2021/12/17 17:57:55 bacon Exp $
 
-DISTNAME=      cdhit-4.6.4
-PKGREVISION=   5
+DISTNAME=      cdhit-4.8.1
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=weizhongli/}
 GITHUB_TAG=    V${PKGVERSION_NOREV}
@@ -26,7 +21,7 @@ SUBST_CLASSES+=               compiler
 SUBST_STAGE.compiler=  pre-configure
 SUBST_MESSAGE.compiler=        Fixing hardcoded compiler name
 SUBST_FILES.compiler=  ${MAKE_FILE}
-SUBST_SED.compiler=    -e 's|g++|${CXX:Q}|g'
+SUBST_SED.compiler=    -e 's|g++|'${CXX:Q}'|g'
 
 SUBST_CLASSES+=                bash
 SUBST_STAGE.bash=      pre-configure
@@ -34,7 +29,13 @@ SUBST_MESSAGE.bash=  Fixing bash path
 SUBST_FILES.bash=      cd-hit-2d-para.pl cd-hit-para.pl
 SUBST_SED.bash=                -e 's|/bin/bash|${PREFIX}/bin/bash|g'
 
-MAKE_FLAGS+=           openmp=yes PREFIX=${DESTDIR}${PREFIX}/bin
+MAKE_FLAGS+=           PREFIX=${DESTDIR}${PREFIX}/bin
+
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == "Darwin"
+MAKE_FLAGS+=           openmp=no
+.endif
 
 DOCDIR=                        ${PREFIX}/share/doc/cdhit
 INSTALLATION_DIRS+=    bin ${DOCDIR}
@@ -42,4 +43,5 @@ INSTALLATION_DIRS+=   bin ${DOCDIR}
 post-install:
        ${INSTALL_DATA} ${WRKSRC}/doc/cdhit-user-guide.pdf ${DESTDIR}${DOCDIR}
 
+.include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/cdhit/PLIST
diff -u pkgsrc/biology/cdhit/PLIST:1.1 pkgsrc/biology/cdhit/PLIST:1.2
--- pkgsrc/biology/cdhit/PLIST:1.1      Mon Oct 12 16:48:08 2015
+++ pkgsrc/biology/cdhit/PLIST  Fri Dec 17 17:57:55 2021
@@ -1,8 +1,10 @@
-@comment $NetBSD: PLIST,v 1.1 2015/10/12 16:48:08 leot Exp $
+@comment $NetBSD: PLIST,v 1.2 2021/12/17 17:57:55 bacon Exp $
+bin/FET.pl
 bin/cd-hit
 bin/cd-hit-2d
 bin/cd-hit-2d-para.pl
 bin/cd-hit-454
+bin/cd-hit-clstr_2_blm8.pl
 bin/cd-hit-div
 bin/cd-hit-div.pl
 bin/cd-hit-est
@@ -12,6 +14,8 @@ bin/clstr2tree.pl
 bin/clstr2txt.pl
 bin/clstr2xml.pl
 bin/clstr_cut.pl
+bin/clstr_list.pl
+bin/clstr_list_sort.pl
 bin/clstr_merge.pl
 bin/clstr_merge_noorder.pl
 bin/clstr_quality_eval.pl

Index: pkgsrc/biology/cdhit/distinfo
diff -u pkgsrc/biology/cdhit/distinfo:1.4 pkgsrc/biology/cdhit/distinfo:1.5
--- pkgsrc/biology/cdhit/distinfo:1.4   Tue Oct 26 10:03:38 2021
+++ pkgsrc/biology/cdhit/distinfo       Fri Dec 17 17:57:55 2021
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.4 2021/10/26 10:03:38 nia Exp $
+$NetBSD: distinfo,v 1.5 2021/12/17 17:57:55 bacon Exp $
 
-BLAKE2s (cdhit-4.6.4.tar.gz) = bb6cdf9becde665d460c96beaa44f23c617c606e133a4094b162335bb57bf35a
-SHA512 (cdhit-4.6.4.tar.gz) = 01e4de21643667d943055a8dd3447610a57d6e0aac2f7a8133543c5d2c50b60e3a164accaf3131770b679553ec3c6863bd20ae2a57870de142282311b46c567d
-Size (cdhit-4.6.4.tar.gz) = 1148426 bytes
+BLAKE2s (cdhit-4.8.1.tar.gz) = 3660fc912a66ed9ce75ea07c913271e3a63b8e4050a2c26e9a99ba4e4ff919be
+SHA512 (cdhit-4.8.1.tar.gz) = 28f350c67079f000b4102126a29d2eed110c636fb32a8a53699b60e6f3447348ea3838fe87a4dd952895d62491298394a314254e91036f6a23b1956b1e237a64
+Size (cdhit-4.8.1.tar.gz) = 945639 bytes