CVS commit: pkgsrc/biology/kallisto

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/kallisto
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Sat, 4 Nov 2023 14:35:07 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Nov  4 14:35:07 UTC 2023

Modified Files:
        pkgsrc/biology/kallisto: Makefile PLIST distinfo
        pkgsrc/biology/kallisto/patches: patch-CMakeLists.txt
            patch-src_CMakeLists.txt patch-src_kseq.h
Added Files:
        pkgsrc/biology/kallisto/patches: 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_main.cpp

Log Message:
biology/kallisto: Update to 0.50.1

Update kallisto index version to 13
A few other new features
Changes: https://github.com/pachterlab/kallisto/releases


To generate a diff of this commit:
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/kallisto/Makefile \
    pkgsrc/biology/kallisto/distinfo
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/kallisto/PLIST
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt \
    pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt
cvs rdiff -u -r0 -r1.1 \
    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 -r1.1 -r1.2 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:1.5 pkgsrc/biology/kallisto/Makefile:1.6
--- pkgsrc/biology/kallisto/Makefile:1.5        Wed Dec 28 15:27:17 2022
+++ pkgsrc/biology/kallisto/Makefile    Sat Nov  4 14:35:07 2023
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.5 2022/12/28 15:27:17 bacon Exp $
+# $NetBSD: Makefile,v 1.6 2023/11/04 14:35:07 bacon Exp $
 
-DISTNAME=      kallisto-0.48.0
+DISTNAME=      kallisto-0.50.1
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=pachterlab/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}
@@ -19,7 +19,9 @@ SUBST_STAGE.test=     pre-configure
 SUBST_FILES.test=      kallisto-test
 SUBST_SED.test=                -e 's|/usr/local/share/kallisto|${DATADIR}|g'
 
-CMAKE_ARGS+=           -DUSE_HDF5:BOOL=ON
+CMAKE_ARGS+=           -DUSE_HDF5:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
+# Build fails on 8-core Mac M1
+MAKE_JOBS_SAFE=                no
 INSTALLATION_DIRS+=    ${DATADIR}
 
 DATADIR=               ${PREFIX}/share/kallisto
Index: pkgsrc/biology/kallisto/distinfo
diff -u pkgsrc/biology/kallisto/distinfo:1.5 pkgsrc/biology/kallisto/distinfo:1.6
--- pkgsrc/biology/kallisto/distinfo:1.5        Sun Feb 27 01:57:27 2022
+++ pkgsrc/biology/kallisto/distinfo    Sat Nov  4 14:35:07 2023
@@ -1,8 +1,15 @@
-$NetBSD: distinfo,v 1.5 2022/02/27 01:57:27 bacon Exp $
+$NetBSD: distinfo,v 1.6 2023/11/04 14:35:07 bacon Exp $
 
-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-0.50.1.tar.gz) = 2fcdb884dd3f8c381b16648862551c1632780b5f942c4c1296b7581a48092054
+SHA512 (kallisto-0.50.1.tar.gz) = 767319f1b96d29c10dba9a66410764978eb8dcf36186d247821458e977a76adab7c871675e10e56d7e85ac312cd0c75c7651008f612db998699a95e0c63cb8e9
+Size (kallisto-0.50.1.tar.gz) = 5947303 bytes
+SHA1 (patch-CMakeLists.txt) = 2672475d3fd0f3b837cafc9faa62cdc094f6fd4b
+SHA1 (patch-ext_bifrost_CMakeLists.txt) = ff5cebb2f38c4fa90bd651690ef58e588396c2ac
+SHA1 (patch-ext_bifrost_src_BitContainer.cpp) = 88a3b8b0d53bc4e96ec02f38f3f6e6bbd1e80dd7
+SHA1 (patch-ext_bifrost_src_ColorSet.cpp) = 55bb84a31ca97d21e6eefd44e2d3d6391f1e9304
+SHA1 (patch-ext_bifrost_src_libpopcnt.h) = 3f31a47f40f341b1f6f72552b06990a81946e425
+SHA1 (patch-ext_bifrost_src_strict__fstream.hpp) = a4eab7784c3502fcc79ba0c87d31ac7275e5043c
+SHA1 (patch-src_Bootstrap.h) = 29a07a6fbaedf4387b70afb3b2caeb1a9b17f8e8
+SHA1 (patch-src_CMakeLists.txt) = 33d0e3cf985d2e400315788d3ee1c74987a6ebee
+SHA1 (patch-src_kseq.h) = 034e65bdcf5d3851b4e3d65afd06843bdff0d8a9
+SHA1 (patch-src_main.cpp) = 65c9af813f558cebd6086a95b56a499aab02e566

Index: pkgsrc/biology/kallisto/PLIST
diff -u pkgsrc/biology/kallisto/PLIST:1.3 pkgsrc/biology/kallisto/PLIST:1.4
--- pkgsrc/biology/kallisto/PLIST:1.3   Sun Feb 27 01:57:27 2022
+++ pkgsrc/biology/kallisto/PLIST       Sat Nov  4 14:35:07 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.3 2022/02/27 01:57:27 bacon Exp $
+@comment $NetBSD: PLIST,v 1.4 2023/11/04 14:35:07 bacon Exp $
 bin/kallisto
 bin/kallisto-test
 share/kallisto/test/README.md

Index: pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt
diff -u pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt:1.3 pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt:1.4
--- pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt:1.3    Sun Feb 27 01:57:27 2022
+++ pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt        Sat Nov  4 14:35:07 2023
@@ -1,22 +1,50 @@
-$NetBSD: patch-CMakeLists.txt,v 1.3 2022/02/27 01:57:27 bacon Exp $
+$NetBSD: patch-CMakeLists.txt,v 1.4 2023/11/04 14:35:07 bacon Exp $
 
-# Unbundle htslib
+# Unbundle htslib and zlib, use gmake
 
---- CMakeLists.txt.orig        2022-02-26 16:36:13.527572702 +0000
+--- CMakeLists.txt.orig        2023-06-27 10:45:00.000000000 +0000
 +++ 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)
Index: pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt
diff -u pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt:1.3 pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt:1.4
--- pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt:1.3        Sun Feb 27 01:57:27 2022
+++ pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt    Sat Nov  4 14:35:07 2023
@@ -1,30 +1,26 @@
-$NetBSD: patch-src_CMakeLists.txt,v 1.3 2022/02/27 01:57:27 bacon Exp $
+$NetBSD: patch-src_CMakeLists.txt,v 1.4 2023/11/04 14:35:07 bacon Exp $
 
 # 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)

Index: pkgsrc/biology/kallisto/patches/patch-src_kseq.h
diff -u pkgsrc/biology/kallisto/patches/patch-src_kseq.h:1.1 pkgsrc/biology/kallisto/patches/patch-src_kseq.h:1.2
--- pkgsrc/biology/kallisto/patches/patch-src_kseq.h:1.1        Sun Feb 27 01:57:27 2022
+++ pkgsrc/biology/kallisto/patches/patch-src_kseq.h    Sat Nov  4 14:35:07 2023
@@ -1,15 +1,16 @@
-$NetBSD: patch-src_kseq.h,v 1.1 2022/02/27 01:57:27 bacon Exp $
+$NetBSD: patch-src_kseq.h,v 1.2 2023/11/04 14:35:07 bacon Exp $
 
-# Unbundle htslib
+# Portability
 
---- 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)

Added files:

Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
diff -u /dev/null pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.1
--- /dev/null   Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt    Sat Nov  4 14:35:07 2023
@@ -0,0 +1,44 @@
+$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.1 2023/11/04 14:35:07 bacon Exp $
+
+# Portability
+
+--- ext/bifrost/CMakeLists.txt.orig    2023-06-27 10:45:00.000000000 +0000
++++ ext/bifrost/CMakeLists.txt
+@@ -7,18 +7,12 @@ find_package(Threads REQUIRED)
+ # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1.
+ SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE")
+ SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE")
+-# Enable architecture optimizations
+-SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH")
+-# Enable AVX2 instructions
+-SET(ENABLE_AVX2 "ON" CACHE STRING "ENABLE_AVX2")
++SET(CMAKE_VERBOSE_MAKEFILE "ON")
+ 
+ # Set some default compile flags
+ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11")
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+ 
+-set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops")
+-
+-
+ #check if we are on arm64 and apple, if so, disable AVX2
+ if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
+       message("Disabling AVX2 instructions on arm64")
+@@ -30,8 +24,6 @@ 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=${COMPILATION_ARCH}")
+ endif(COMPILATION_ARCH MATCHES "OFF")
+ 
+ if(ENABLE_AVX2 MATCHES "OFF")
+@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
+               set(CMAKE_EXE_LINKER_FLAGS "-pg")
+       else(CMAKE_BUILD_TYPE MATCHES Profile)
+               message("Build type: Release")
+-              add_compile_options(-O3)
++              add_compile_options(-O2)
+       endif(CMAKE_BUILD_TYPE MATCHES Profile) 
+ endif(CMAKE_BUILD_TYPE MATCHES Debug)
+ 
Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp
diff -u /dev/null pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp:1.1
--- /dev/null   Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp      Sat Nov  4 14:35:07 2023
@@ -0,0 +1,11 @@
+$NetBSD: patch-ext_bifrost_src_BitContainer.cpp,v 1.1 2023/11/04 14:35:07 bacon Exp $
+
+# vfscanf() not found on NetBSD 9
+
+--- ext/bifrost/src/BitContainer.cpp.orig      2023-11-01 12:46:19.000000000 +0000
++++ ext/bifrost/src/BitContainer.cpp
+@@ -1,3 +1,4 @@
++#include <cstdio>
+ #include "BitContainer.hpp"
+ 
+ BitContainer::BitContainer() : setBits(localBitVector) {}
Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp
diff -u /dev/null pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp:1.1
--- /dev/null   Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp  Sat Nov  4 14:35:07 2023
@@ -0,0 +1,11 @@
+$NetBSD: patch-ext_bifrost_src_ColorSet.cpp,v 1.1 2023/11/04 14:35:07 bacon Exp $
+
+# vfscanf() not found on NetBSD 9
+
+--- ext/bifrost/src/ColorSet.cpp.orig  2023-11-03 12:48:11.435933052 +0000
++++ ext/bifrost/src/ColorSet.cpp
+@@ -1,3 +1,4 @@
++#include <cstdio>
+ #include "ColorSet.hpp"
+ 
+ UnitigColors::UnitigColors() : setBits(localBitVector) {}
Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h
diff -u /dev/null pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h:1.1
--- /dev/null   Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h   Sat Nov  4 14:35:07 2023
@@ -0,0 +1,22 @@
+$NetBSD: patch-ext_bifrost_src_libpopcnt.h,v 1.1 2023/11/04 14:35:07 bacon Exp $
+
+# Use native popcnt
+
+--- ext/bifrost/src/libpopcnt.h.orig   2023-07-24 12:34:08.037669065 +0000
++++ ext/bifrost/src/libpopcnt.h
+@@ -32,6 +32,8 @@
+ #ifndef LIBPOPCNT_H
+ #define LIBPOPCNT_H
+ 
++#ifndef __NetBSD__
++
+ #include <stdint.h>
+ 
+ #ifndef __has_builtin
+@@ -584,4 +586,6 @@ static inline uint64_t popcnt(const void
+ 
+ #endif
+ 
++#endif /* NetBSD */
++
+ #endif /* LIBPOPCNT_H */
Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp
diff -u /dev/null pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp:1.1
--- /dev/null   Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp   Sat Nov  4 14:35:07 2023
@@ -0,0 +1,15 @@
+$NetBSD: patch-ext_bifrost_src_strict__fstream.hpp,v 1.1 2023/11/04 14:35:07 bacon Exp $
+
+# 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) {
Index: pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h
diff -u /dev/null pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h:1.1
--- /dev/null   Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h       Sat Nov  4 14:35:07 2023
@@ -0,0 +1,14 @@
+$NetBSD: patch-src_Bootstrap.h,v 1.1 2023/11/04 14:35:07 bacon Exp $
+
+# Portability
+
+--- 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>
+ 
Index: pkgsrc/biology/kallisto/patches/patch-src_main.cpp
diff -u /dev/null pkgsrc/biology/kallisto/patches/patch-src_main.cpp:1.1
--- /dev/null   Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-src_main.cpp  Sat Nov  4 14:35:07 2023
@@ -0,0 +1,14 @@
+$NetBSD: patch-src_main.cpp,v 1.1 2023/11/04 14:35:07 bacon Exp $
+
+# Portability
+
+--- src/main.cpp.orig  2023-11-01 12:46:19.000000000 +0000
++++ src/main.cpp
+@@ -11,6 +11,7 @@
+ #include <limits>
+ 
+ #include <cstdio>
++#include <unistd.h>   // rmdir()
+ 
+ #include "common.h"
+ #include "ProcessReads.h"

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