CVS commit: pkgsrc/biology/kallisto

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Sep 20 00:03:15 UTC 2024

Modified Files:
        pkgsrc/biology/kallisto: Makefile PLIST distinfo
        pkgsrc/biology/kallisto/patches: patch-CMakeLists.txt
            patch-ext_bifrost_CMakeLists.txt
            patch-ext_bifrost_src_BitContainer.cpp
            patch-ext_bifrost_src_ColorSet.cpp
            patch-ext_bifrost_src_libpopcnt.h
            patch-ext_bifrost_src_strict__fstream.hpp patch-src_Bootstrap.h
            patch-src_CMakeLists.txt patch-src_kseq.h patch-src_main.cpp

Log Message:
biology/kallisto: Update to 0.51.1

Enhancements to ir-kallisto and pseudoalignments

Changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout


To generate a diff of this commit:
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/kallisto/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/kallisto/PLIST
cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/kallisto/distinfo
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt \
    pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt
cvs rdiff -u -r1.2 -r1.3 \
    pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt \
    pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp \
    pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp \
    pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h \
    pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp \
    pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h \
    pkgsrc/biology/kallisto/patches/patch-src_main.cpp
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/kallisto/patches/patch-src_kseq.h

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:1.8 pkgsrc/biology/kallisto/Makefile:1.9
--- pkgsrc/biology/kallisto/Makefile:1.8        Sun Aug 25 06:18:26 2024
+++ pkgsrc/biology/kallisto/Makefile    Fri Sep 20 00:03:15 2024
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.8 2024/08/25 06:18:26 wiz Exp $
+# $NetBSD: Makefile,v 1.9 2024/09/20 00:03:15 bacon Exp $
 
-DISTNAME=      kallisto-0.51.0
+DISTNAME=      kallisto-0.51.1
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=pachterlab/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}

Index: pkgsrc/biology/kallisto/PLIST
diff -u pkgsrc/biology/kallisto/PLIST:1.5 pkgsrc/biology/kallisto/PLIST:1.6
--- pkgsrc/biology/kallisto/PLIST:1.5   Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/PLIST       Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.5 2024/07/27 12:22:54 bacon Exp $
+@comment $NetBSD: PLIST,v 1.6 2024/09/20 00:03:15 bacon Exp $
 bin/kallisto
 bin/kallisto-test
 share/kallisto/test/README.md

Index: pkgsrc/biology/kallisto/distinfo
diff -u pkgsrc/biology/kallisto/distinfo:1.7 pkgsrc/biology/kallisto/distinfo:1.8
--- pkgsrc/biology/kallisto/distinfo:1.7        Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/distinfo    Fri Sep 20 00:03:15 2024
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.7 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: distinfo,v 1.8 2024/09/20 00:03:15 bacon Exp $
 
-BLAKE2s (kallisto-0.51.0.tar.gz) = 759bef4d378b5ca762196ec7c74f80030d5109175a31806112b59e23c92fa747
-SHA512 (kallisto-0.51.0.tar.gz) = 3616d3030e0bc989d3d43786500dddf1bb8243bb51473695b11ace6eb57b15b6c692b0bdc5463a9075573a267fee8b8dea48165d6af8029f603b19ad56aef661
-Size (kallisto-0.51.0.tar.gz) = 5952096 bytes
+BLAKE2s (kallisto-0.51.1.tar.gz) = 30d30d14d54da30beb3f6b954546acec465a4029be99fb8b0faa353057dea994
+SHA512 (kallisto-0.51.1.tar.gz) = e5e7291e75c9d528bbb26691264a24480e1958e20eb56ce2f84192fe020b0b4c8485c9c143e19aedb0a988e6314acb312ea100cdb6c87c7cd895ef2908f7a149
+Size (kallisto-0.51.1.tar.gz) = 5954250 bytes
 SHA1 (patch-CMakeLists.txt) = 76746ef3999fca26d7cfe597172303ce7b023708
 SHA1 (patch-ext_bifrost_CMakeLists.txt) = 7b28282604691dc985c135f7048cc48fec1ae826
 SHA1 (patch-ext_bifrost_src_BitContainer.cpp) = 88a3b8b0d53bc4e96ec02f38f3f6e6bbd1e80dd7

Index: pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt
diff -u pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt:1.5 pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt:1.6
--- pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt:1.5    Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt        Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-CMakeLists.txt,v 1.5 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-CMakeLists.txt,v 1.6 2024/09/20 00:03:15 bacon Exp $
 
 # Use external htslib
 
Index: pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt
diff -u pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt:1.5 pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt:1.6
--- pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt:1.5        Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt    Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_CMakeLists.txt,v 1.5 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-src_CMakeLists.txt,v 1.6 2024/09/20 00:03:15 bacon Exp $
 
 # Use external htslib
 

Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
diff -u pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.2 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.3
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.2        Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt    Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.2 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.3 2024/09/20 00:03:15 bacon Exp $
 
 # Respect pkgsrc build flags
 
Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp
diff -u pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp:1.2 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp:1.3
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp:1.2  Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp      Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-ext_bifrost_src_BitContainer.cpp,v 1.2 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-ext_bifrost_src_BitContainer.cpp,v 1.3 2024/09/20 00:03:15 bacon Exp $
 
 # vfscanf() not found on NetBSD 9
 
Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp
diff -u pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp:1.2 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp:1.3
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp:1.2      Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp  Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-ext_bifrost_src_ColorSet.cpp,v 1.2 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-ext_bifrost_src_ColorSet.cpp,v 1.3 2024/09/20 00:03:15 bacon Exp $
 
 # vfscanf() not found on NetBSD 9
 
Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h
diff -u pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h:1.2 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h:1.3
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h:1.2       Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h   Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-ext_bifrost_src_libpopcnt.h,v 1.2 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-ext_bifrost_src_libpopcnt.h,v 1.3 2024/09/20 00:03:15 bacon Exp $
 
 # Use native popcnt
 
Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp
diff -u pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp:1.2 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp:1.3
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp:1.2       Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp   Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-ext_bifrost_src_strict__fstream.hpp,v 1.2 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-ext_bifrost_src_strict__fstream.hpp,v 1.3 2024/09/20 00:03:15 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h
diff -u pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h:1.2 pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h:1.3
--- pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h:1.2   Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h       Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_Bootstrap.h,v 1.2 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-src_Bootstrap.h,v 1.3 2024/09/20 00:03:15 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/kallisto/patches/patch-src_main.cpp
diff -u pkgsrc/biology/kallisto/patches/patch-src_main.cpp:1.2 pkgsrc/biology/kallisto/patches/patch-src_main.cpp:1.3
--- pkgsrc/biology/kallisto/patches/patch-src_main.cpp:1.2      Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-src_main.cpp  Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_main.cpp,v 1.2 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-src_main.cpp,v 1.3 2024/09/20 00:03:15 bacon Exp $
 
 # Portability
 

Index: pkgsrc/biology/kallisto/patches/patch-src_kseq.h
diff -u pkgsrc/biology/kallisto/patches/patch-src_kseq.h:1.3 pkgsrc/biology/kallisto/patches/patch-src_kseq.h:1.4
--- pkgsrc/biology/kallisto/patches/patch-src_kseq.h:1.3        Sat Jul 27 12:22:54 2024
+++ pkgsrc/biology/kallisto/patches/patch-src_kseq.h    Fri Sep 20 00:03:15 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_kseq.h,v 1.3 2024/07/27 12:22:54 bacon Exp $
+$NetBSD: patch-src_kseq.h,v 1.4 2024/09/20 00:03:15 bacon Exp $
 
 # Portability