CVS commit: pkgsrc/biology/kallisto

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu Jul 23 19:22:00 UTC 2020

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

Log Message:
biology/kallisto: Upgrade to 0.46.1

Minor enhancements since 0.45
0.46.2 is available, but has serious regressions.
Reverted to bundled htslib 1.4.1, since kallisto source contains modified
htslib files that are incompatible with the current 1.10.2 package.


To generate a diff of this commit:
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/kallisto/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/kallisto/PLIST \
    pkgsrc/biology/kallisto/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/kallisto/Makefile
diff -u pkgsrc/biology/kallisto/Makefile:1.2 pkgsrc/biology/kallisto/Makefile:1.3
--- pkgsrc/biology/kallisto/Makefile:1.2        Wed May  1 12:38:54 2019
+++ pkgsrc/biology/kallisto/Makefile    Thu Jul 23 19:22:00 2020
@@ -1,29 +1,29 @@
-# $NetBSD: Makefile,v 1.2 2019/05/01 12:38:54 bacon Exp $
+# $NetBSD: Makefile,v 1.3 2020/07/23 19:22:00 bacon Exp $
 
-DISTNAME=      kallisto-${PV}
-PKGREVISION=   1
+DISTNAME=      kallisto-0.46.1
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=pachterlab/}
-GITHUB_TAG=    v${PV}
+GITHUB_TAG=    v${PKGVERSION_NOREV}
 
 MAINTAINER=    bacon%NetBSD.org@localhost
 HOMEPAGE=      https://pachterlab.github.io/kallisto/
 COMMENT=       Quantify abundances of transcripts from RNA-Seq data
 LICENSE=       2-clause-bsd
 
+USE_TOOLS+=    autoconf gmake pax
 USE_LANGUAGES= c c++
-USE_TOOLS+=    pax
 USE_CMAKE=     yes
 
 SUBST_CLASSES+=                test
-SUBST_STAGE.test=      post-build
+SUBST_STAGE.test=      pre-configure
 SUBST_FILES.test=      kallisto-test
 SUBST_SED.test=                -e 's|/usr/local/share/kallisto|${DATADIR}|g'
 
-PV=            0.45.0
-DATADIR=       ${PREFIX}/share/kallisto
+CMAKE_ARGS+=           -DUSE_HDF5:BOOL=ON
+MAKE_JOBS_SAFE=                no      # Doesn't finished bundled htslib first
+INSTALLATION_DIRS+=    ${DATADIR}
 
-INSTALLATION_DIRS=     bin ${DATADIR}
+DATADIR=               ${PREFIX}/share/kallisto
 
 post-extract:
        ${CP} ${FILESDIR}/kallisto-test ${WRKSRC}
@@ -32,7 +32,6 @@ post-install:
        ${INSTALL_SCRIPT} ${WRKSRC}/kallisto-test ${DESTDIR}${PREFIX}/bin
        cd ${WRKSRC} && pax -rw test ${DESTDIR}${DATADIR}
 
-.include "../../biology/htslib/buildlink3.mk"
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../archivers/libaec/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"

Index: pkgsrc/biology/kallisto/PLIST
diff -u pkgsrc/biology/kallisto/PLIST:1.1 pkgsrc/biology/kallisto/PLIST:1.2
--- pkgsrc/biology/kallisto/PLIST:1.1   Fri Dec 21 19:00:56 2018
+++ pkgsrc/biology/kallisto/PLIST       Thu Jul 23 19:22:00 2020
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2018/12/21 19:00:56 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2020/07/23 19:22:00 bacon Exp $
 bin/kallisto
 bin/kallisto-test
 share/kallisto/test/README.md
Index: pkgsrc/biology/kallisto/distinfo
diff -u pkgsrc/biology/kallisto/distinfo:1.1 pkgsrc/biology/kallisto/distinfo:1.2
--- pkgsrc/biology/kallisto/distinfo:1.1        Fri Dec 21 19:00:56 2018
+++ pkgsrc/biology/kallisto/distinfo    Thu Jul 23 19:22:00 2020
@@ -1,8 +1,6 @@
-$NetBSD: distinfo,v 1.1 2018/12/21 19:00:56 bacon Exp $
+$NetBSD: distinfo,v 1.2 2020/07/23 19:22:00 bacon Exp $
 
-SHA1 (kallisto-0.45.0.tar.gz) = ab0890c5d675d678dbcf415a86512b4694b3a4a6
-RMD160 (kallisto-0.45.0.tar.gz) = f482f7525dde0bfc2425cf803812c1c7748c882e
-SHA512 (kallisto-0.45.0.tar.gz) = b120c36ccb4725b19307c3e90c7f9b73b87efc53f08d3f2c12fc2e4b7afc3c03c52ba07dff623c9c8ad5a7e89c1eeb907389ccf3e4440236e81a0611500639e2
-Size (kallisto-0.45.0.tar.gz) = 2250430 bytes
-SHA1 (patch-CMakeLists.txt) = 2817091347e35898fec0bab77e8d9cc5ca5fff3f
-SHA1 (patch-src_CMakeLists.txt) = 2ef72024591c5216fbf44fb7cdfa4a8330b0c81a
+SHA1 (kallisto-0.46.1.tar.gz) = e39adb9801049836dcd7ac52e775f64af4d0a51b
+RMD160 (kallisto-0.46.1.tar.gz) = 8e42c5c52f19ec2e37f8591f7472a969b479bfd4
+SHA512 (kallisto-0.46.1.tar.gz) = 53a4db8fd5e0585693d8cd683651b4bdcc84c724a19e80a6162f1844fd491eb2d4e3180be2d9aabea7d49c9cbe0a05250f41da7d1de89d5d6cb6a8806f1afb7d
+Size (kallisto-0.46.1.tar.gz) = 2254560 bytes