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Date:      Mon, 3 Aug 2020 15:45:22 +0000 (UTC)
From:      "Jason W. Bacon" <jwb@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r544077 - in head/biology/kallisto: . files
Message-ID:  <202008031545.073FjMcW064533@repo.freebsd.org>

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Author: jwb
Date: Mon Aug  3 15:45:21 2020
New Revision: 544077
URL: https://svnweb.freebsd.org/changeset/ports/544077

Log:
  biology/kallisto: Revert to 0.46.1
  
  0.46.2 has long-standing regressions that are not being addressed, including
  a seg fault when using --genomebam.
  Also revert to bundled htslib in preparation for biology/htslib upgrade
  to 1.10.  Kallisto source contains modified bits of htslib 1.4.1 that are
  incompatible with htslib > 1.9.

Added:
  head/biology/kallisto/files/patch-ext_htslib_configure.ac   (contents, props changed)
Deleted:
  head/biology/kallisto/files/patch-src_CMakeLists.txt
Modified:
  head/biology/kallisto/Makefile
  head/biology/kallisto/distinfo
  head/biology/kallisto/files/patch-CMakeLists.txt

Modified: head/biology/kallisto/Makefile
==============================================================================
--- head/biology/kallisto/Makefile	Mon Aug  3 15:30:38 2020	(r544076)
+++ head/biology/kallisto/Makefile	Mon Aug  3 15:45:21 2020	(r544077)
@@ -2,8 +2,8 @@
 
 PORTNAME=		kallisto
 DISTVERSIONPREFIX=	v
-DISTVERSION=		0.46.2
-PORTREVISION=		1
+DISTVERSION=		0.46.1
+PORTEPOCH=		1
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -12,11 +12,11 @@ COMMENT=	Quantify abundances of transcripts from RNA-S
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
+BUILD_DEPENDS=	autoconf>=0:devel/autoconf
 LIB_DEPENDS=	libhdf5.so:science/hdf5 \
-		libsz.so:science/szip \
-		libhts.so:biology/htslib
+		libsz.so:science/szip
 
-USES=		cmake:noninja compiler:c++11-lang localbase:ldflags
+USES=		cmake:noninja compiler:c++11-lang gmake localbase:ldflags
 USE_GITHUB=	yes
 GH_ACCOUNT=	pachterlab
 
@@ -26,10 +26,11 @@ PORTEXAMPLES=		*
 PLIST_FILES=		bin/kallisto
 EXAMPLES_PLIST_FILES=	bin/kallisto-test
 
-# hdf5 is being phased out and is no longer build in by default, but is still
-# required for Sleuth and other downstream tools.  Remove this after Sleuth
-# et all catch up.
-CMAKE_ARGS+=	-DUSE_HDF5:BOOL=ON
+# hdf5 is being phased out and is no longer built in by default, but is still
+# required for Sleuth (requires kallisto bootstrap estimates) and other
+# downstream tools.  Remove this after Sleuth et all catch up.
+CMAKE_ARGS+=		-DUSE_HDF5:BOOL=ON
+MAKE_JOBS_UNSAFE=	yes
 
 OPTIONS_DEFINE=	EXAMPLES
 

Modified: head/biology/kallisto/distinfo
==============================================================================
--- head/biology/kallisto/distinfo	Mon Aug  3 15:30:38 2020	(r544076)
+++ head/biology/kallisto/distinfo	Mon Aug  3 15:45:21 2020	(r544077)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1581611719
-SHA256 (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 10bab0c2929d8c345750e02735b305bbbfa89e8a48f42c4b9af44f3d44ff4c82
-SIZE (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 2693857
+TIMESTAMP = 1595454023
+SHA256 (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231
+SIZE (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 2254560

Modified: head/biology/kallisto/files/patch-CMakeLists.txt
==============================================================================
--- head/biology/kallisto/files/patch-CMakeLists.txt	Mon Aug  3 15:30:38 2020	(r544076)
+++ head/biology/kallisto/files/patch-CMakeLists.txt	Mon Aug  3 15:45:21 2020	(r544077)
@@ -1,25 +1,11 @@
---- CMakeLists.txt.orig	2018-12-20 14:20:05 UTC
+--- CMakeLists.txt.orig	2020-07-22 22:36:50 UTC
 +++ CMakeLists.txt
-@@ -34,22 +34,6 @@ ELSE(LINK MATCHES shared)
-     message("shared build")
- ENDIF(LINK MATCHES static)
- 
--
--include(ExternalProject)
--ExternalProject_Add(htslib
--    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
--    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
--    BUILD_IN_SOURCE 1
--    CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure 
--        --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
+@@ -42,7 +42,7 @@ ExternalProject_Add(htslib
+     BUILD_IN_SOURCE 1
+     CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure 
+         --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
 -    BUILD_COMMAND make lib-static
--    INSTALL_COMMAND ""
--)
--
--include_directories(${htslib_PREFIX}/src/htslib)
--
--
--
- # add_compile_options(-Wdeprecated-register)
++    BUILD_COMMAND gmake lib-static
+     INSTALL_COMMAND ""
+ )
  
- add_subdirectory(src)

Added: head/biology/kallisto/files/patch-ext_htslib_configure.ac
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/kallisto/files/patch-ext_htslib_configure.ac	Mon Aug  3 15:45:21 2020	(r544077)
@@ -0,0 +1,11 @@
+--- ext/htslib/configure.ac.orig	2019-11-04 16:28:52 UTC
++++ ext/htslib/configure.ac
+@@ -23,7 +23,7 @@
+ # DEALINGS IN THE SOFTWARE.
+ 
+ dnl Process this file with autoconf to produce a configure script
+-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
++AC_INIT([HTSlib], [1.4.1],
+         [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
+ AC_PREREQ(2.63)  dnl This version introduced 4-argument AC_CHECK_HEADER
+ AC_CONFIG_SRCDIR(hts.c)



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