kallisto: Begin work on 0.50.0 update

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: kallisto: Begin work on 0.50.0 update
From: Jason W. Bacon <bacon%NetBSD.org@localhost>
Date: Mon, 24 Jul 2023 02:40:27 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Jul 23 21:40:27 2023 -0500
Changeset:	244b7ea5e2cfaa580a3822fca68c90492b417fe2

Modified Files:
	kallisto/Makefile
	kallisto/distinfo
	kallisto/patches/patch-CMakeLists.txt
	kallisto/patches/patch-src_CMakeLists.txt
	kallisto/patches/patch-src_kseq.h
Added Files:
	kallisto/patches/patch-ext_bifrost_CMakeLists.txt
	kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp
	kallisto/patches/patch-src_Bootstrap.h

Log Message:
kallisto: Begin work on 0.50.0 update

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=244b7ea5e2cfaa580a3822fca68c90492b417fe2

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

diffstat:
 kallisto/Makefile                                  |  2 +-
 kallisto/distinfo                                  | 15 ++++----
 kallisto/patches/patch-CMakeLists.txt              | 40 +++++++++++++++++-----
 kallisto/patches/patch-ext_bifrost_CMakeLists.txt  | 11 ++++++
 .../patch-ext_bifrost_src_strict__fstream.hpp      | 15 ++++++++
 kallisto/patches/patch-src_Bootstrap.h             | 10 ++++++
 kallisto/patches/patch-src_CMakeLists.txt          | 36 ++++++++-----------
 kallisto/patches/patch-src_kseq.h                  | 13 +++----
 8 files changed, 97 insertions(+), 45 deletions(-)

diffs:
diff --git a/kallisto/Makefile b/kallisto/Makefile
index 809c49ea56..a509dafb0e 100644
--- a/kallisto/Makefile
+++ b/kallisto/Makefile
@@ -1,6 +1,6 @@
 # $NetBSD: Makefile,v 1.1 2018/12/21 19:00:56 bacon Exp $
 
-DISTNAME=	kallisto-0.48.0
+DISTNAME=	kallisto-0.50.0
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=pachterlab/}
 GITHUB_TAG=	v${PKGVERSION_NOREV}
diff --git a/kallisto/distinfo b/kallisto/distinfo
index cd04220b91..346c872404 100644
--- a/kallisto/distinfo
+++ b/kallisto/distinfo
@@ -1,8 +1,11 @@
 $NetBSD$
 
-BLAKE2s (kallisto-0.48.0.tar.gz) = c31cdd71591d4784e5b48560dd2c8ed19f8baa77317f0c05441a75f7deb39d64
-SHA512 (kallisto-0.48.0.tar.gz) = 6325660c18c98b591bfa0f293f55f13fa45b58acf86dead3b0c9cd88942c9d3dfa548cf0b8f05fb89697845b7047627b8fcdfba4237a5876463311a6f7127feb
-Size (kallisto-0.48.0.tar.gz) = 2706838 bytes
-SHA1 (patch-CMakeLists.txt) = 9c96f53ec2e280b7f778ae04b002783559730df7
-SHA1 (patch-src_CMakeLists.txt) = dde489a9299207d189d3f94b875bb1929c958897
-SHA1 (patch-src_kseq.h) = c35bca57fb85367e8646a4b771449da7dbfbb439
+BLAKE2s (kallisto-0.50.0.tar.gz) = aac5851f8f3c92f655ad7d248d30faa6d74c3d0c81d23607050d38417ca886f3
+SHA512 (kallisto-0.50.0.tar.gz) = be43f4070102a5a8ed259460044b02e243ad80ce79e8dc66bc5b8062feeaa792837b1df9c0bc6c2e9f3dc4bb807f77ff3eae6d25e30f5049dfef8514f1a07457
+Size (kallisto-0.50.0.tar.gz) = 5939018 bytes
+SHA1 (patch-CMakeLists.txt) = afb94f2cce3006fbaee452373445f5c82904fe75
+SHA1 (patch-ext_bifrost_CMakeLists.txt) = b102318a748809a42f4ad5cff361af06874bcf36
+SHA1 (patch-ext_bifrost_src_strict__fstream.hpp) = a4eab7784c3502fcc79ba0c87d31ac7275e5043c
+SHA1 (patch-src_Bootstrap.h) = 02aa0f3d928cd49ba23bf9bb08831e445c54a589
+SHA1 (patch-src_CMakeLists.txt) = 7c41c43b1659c2d58f189d3bfe57ea8826c015e5
+SHA1 (patch-src_kseq.h) = 4b6617f46b43fd7cdcd410295338804768d34bc2
diff --git a/kallisto/patches/patch-CMakeLists.txt b/kallisto/patches/patch-CMakeLists.txt
index 7aecab8deb..7c6d4c95b5 100644
--- a/kallisto/patches/patch-CMakeLists.txt
+++ b/kallisto/patches/patch-CMakeLists.txt
@@ -1,22 +1,46 @@
-$NetBSD$
-
-# Unbundle htslib
-
---- CMakeLists.txt.orig	2022-02-26 16:36:13.527572702 +0000
+--- CMakeLists.txt.orig	2023-06-27 10:45:00 UTC
 +++ CMakeLists.txt
-@@ -43,15 +43,6 @@ ENDIF(LINK MATCHES static)
+@@ -56,42 +56,16 @@ ENDIF(LINK MATCHES static)
  
  
  include(ExternalProject)
+-if (USE_BAM)
 -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 
+-    CONFIGURE_COMMAND autoreconf -i && autoheader &&  autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure
 -        --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
 -    BUILD_COMMAND make lib-static
 -    INSTALL_COMMAND ""
 -)
+-endif(USE_BAM)
  
- include_directories(${htslib_PREFIX}/src/htslib)
+ ExternalProject_Add(bifrost
+     PREFIX ${PROJECT_SOURCE_DIR}/ext/bifrost
+     SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/bifrost
+     BUILD_IN_SOURCE 1
+     CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS}
+-    BUILD_COMMAND cd build && make
++    BUILD_COMMAND cd build && gmake
+     INSTALL_COMMAND ""
+ )
  
+-if (ZLIBNG)
+-    message("zlib-ng enabled.")
+-    ExternalProject_Add(zlib-ng
+-    PREFIX ${PROJECT_SOURCE_DIR}/ext/zlib-ng
+-    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng
+-    BUILD_IN_SOURCE 1
+-    CONFIGURE_COMMAND mkdir -p zlib-ng && cd zlib-ng && cmake .. -DZLIB_COMPAT=ON -DZLIB_ENABLE_TESTS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX}
+-    BUILD_COMMAND cd zlib-ng && make
+-    INSTALL_COMMAND ""
+-    )
+-endif(ZLIBNG)
+-
+-if (USE_BAM)
+-include_directories(${htslib_PREFIX}/src/htslib)
+-endif(USE_BAM)
+ include_directories(${EXT_PROJECTS_DIR}/bifrost/build/src)
+ 
+ ExternalProject_Get_Property(bifrost install_dir)
diff --git a/kallisto/patches/patch-ext_bifrost_CMakeLists.txt b/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
new file mode 100644
index 0000000000..c4c22a5e06
--- /dev/null
+++ b/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
@@ -0,0 +1,11 @@
+--- ext/bifrost/CMakeLists.txt.orig	2023-07-14 14:27:24 UTC
++++ ext/bifrost/CMakeLists.txt
+@@ -30,8 +30,6 @@ if(COMPILATION_ARCH MATCHES "OFF")
+ 	message("Disabling native architecture compilation (including AVX2)")
+ else(COMPILATION_ARCH MATCHES "OFF")
+ 	message("Compilation architecture: ${COMPILATION_ARCH}")
+-	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=${COMPILATION_ARCH}")
+-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${COMPILATION_ARCH}")
+ endif(COMPILATION_ARCH MATCHES "OFF")
+ 
+ if(ENABLE_AVX2 MATCHES "OFF")
diff --git a/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp b/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp
new file mode 100644
index 0000000000..b5814a56fc
--- /dev/null
+++ b/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- ext/bifrost/src/strict_fstream.hpp.orig	2023-06-27 10:45:00.000000000 +0000
++++ ext/bifrost/src/strict_fstream.hpp
+@@ -64,7 +64,7 @@ static std::string strerror()
+     } else {
+         return "Unknown error (" + std::to_string(err_num) + ")";
+     }
+-#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__)
++#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) || defined(__FreeBSD__) || defined(__NetBSD__)
+ // XSI-compliant strerror_r()
+     const int err_num = errno; // See above
+     if (strerror_r(err_num, buff.data(), buff.size()) == 0) {
diff --git a/kallisto/patches/patch-src_Bootstrap.h b/kallisto/patches/patch-src_Bootstrap.h
new file mode 100644
index 0000000000..6fc3bd4528
--- /dev/null
+++ b/kallisto/patches/patch-src_Bootstrap.h
@@ -0,0 +1,10 @@
+--- src/Bootstrap.h.orig	2020-04-01 16:56:42 UTC
++++ src/Bootstrap.h
+@@ -1,6 +1,7 @@
+ #ifndef KALLISTO_BOOTSTRAP_H
+ #define KALLISTO_BOOTSTRAP_H
+ 
++#include <sys/types.h>
+ #include <mutex>
+ #include <thread>
+ 
diff --git a/kallisto/patches/patch-src_CMakeLists.txt b/kallisto/patches/patch-src_CMakeLists.txt
index a655d54f4a..c7927b9e14 100644
--- a/kallisto/patches/patch-src_CMakeLists.txt
+++ b/kallisto/patches/patch-src_CMakeLists.txt
@@ -1,30 +1,22 @@
-$NetBSD$
-
-# Unbundle htslib
-
---- src/CMakeLists.txt.orig	2022-02-26 16:35:26.912550601 +0000
+--- src/CMakeLists.txt.orig	2023-07-06 14:07:38 UTC
 +++ src/CMakeLists.txt
-@@ -3,15 +3,13 @@ file(GLOB headers *.h *.hpp)
+@@ -3,10 +3,6 @@ file(GLOB headers *.h *.hpp)
  
  list(REMOVE_ITEM sources main.cpp)
  
+-if (USE_BAM)
 -include_directories(../ext/htslib)
+-endif(USE_BAM)
 -
- add_library(kallisto_core ${sources} ${headers})
- target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
- 
- add_executable(kallisto main.cpp)
+ add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
  
+ add_library(kallisto_core ${sources} ${headers})
+@@ -17,7 +13,7 @@ add_executable(kallisto main.cpp)
  find_package( Threads REQUIRED )
--target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
-+target_link_libraries(kallisto kallisto_core pthread hts)
- 
- if(LINK MATCHES static)
-     set(BUILD_SHARED_LIBS OFF)
-@@ -62,4 +60,4 @@ else()
- endif(LINK MATCHES static)
- 
- 
--install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
-\ No newline at end of file
-+install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
+ ExternalProject_Get_Property(bifrost install_dir)
+ if (USE_BAM)
+-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a)
++target_link_libraries(kallisto kallisto_core pthread hts ${install_dir}/build/src/libbifrost.a)
+ else()
+ target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a)
+ endif(USE_BAM)
diff --git a/kallisto/patches/patch-src_kseq.h b/kallisto/patches/patch-src_kseq.h
index 7b748edbf1..f7712a023f 100644
--- a/kallisto/patches/patch-src_kseq.h
+++ b/kallisto/patches/patch-src_kseq.h
@@ -1,15 +1,12 @@
-$NetBSD$
-
-# Unbundle htslib
-
---- src/kseq.h.orig	2022-02-26 16:37:08.929391121 +0000
+--- src/kseq.h.orig	2019-11-04 16:28:52 UTC
 +++ src/kseq.h
-@@ -27,6 +27,8 @@ SOFTWARE.
- #include <ctype.h>
+@@ -32,6 +32,9 @@
  #include <string.h>
  #include <stdlib.h>
+ 
 +// Prevent redefinition of kstring_t below
 +#include <htslib/kstring.h>
- 
++
  #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
  #define KS_SEP_TAB   1 // isspace() && !' '
+ #define KS_SEP_LINE  2 // line separator: "\n" (Unix) or "\r\n" (Windows)
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