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, 27 Jul 2024 12:22:54 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Jul 27 12:22:54 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 0.51.0,1

Add support for long reads to kallisto bus and kallisto quant-tcc

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


To generate a diff of this commit:
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/kallisto/Makefile \
    pkgsrc/biology/kallisto/distinfo
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/kallisto/PLIST
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt \
    pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt
cvs rdiff -u -r1.1 -r1.2 \
    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 -r1.2 -r1.3 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:1.6 pkgsrc/biology/kallisto/Makefile:1.7
--- pkgsrc/biology/kallisto/Makefile:1.6        Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/Makefile    Sat Jul 27 12:22:54 2024
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.6 2023/11/04 14:35:07 bacon Exp $
+# $NetBSD: Makefile,v 1.7 2024/07/27 12:22:54 bacon Exp $
 
-DISTNAME=      kallisto-0.50.1
+DISTNAME=      kallisto-0.51.0
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=pachterlab/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}
Index: pkgsrc/biology/kallisto/distinfo
diff -u pkgsrc/biology/kallisto/distinfo:1.6 pkgsrc/biology/kallisto/distinfo:1.7
--- pkgsrc/biology/kallisto/distinfo:1.6        Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/distinfo    Sat Jul 27 12:22:54 2024
@@ -1,15 +1,15 @@
-$NetBSD: distinfo,v 1.6 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: distinfo,v 1.7 2024/07/27 12:22:54 bacon Exp $
 
-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
+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
+SHA1 (patch-CMakeLists.txt) = 76746ef3999fca26d7cfe597172303ce7b023708
+SHA1 (patch-ext_bifrost_CMakeLists.txt) = 7b28282604691dc985c135f7048cc48fec1ae826
 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_CMakeLists.txt) = 8a66bdca6a15948d60a16016b4b62f79d03deef3
 SHA1 (patch-src_kseq.h) = 034e65bdcf5d3851b4e3d65afd06843bdff0d8a9
 SHA1 (patch-src_main.cpp) = 65c9af813f558cebd6086a95b56a499aab02e566

Index: pkgsrc/biology/kallisto/PLIST
diff -u pkgsrc/biology/kallisto/PLIST:1.4 pkgsrc/biology/kallisto/PLIST:1.5
--- pkgsrc/biology/kallisto/PLIST:1.4   Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/PLIST       Sat Jul 27 12:22:54 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.4 2023/11/04 14:35:07 bacon Exp $
+@comment $NetBSD: PLIST,v 1.5 2024/07/27 12:22:54 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:1.4 pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt:1.5
--- pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt:1.4    Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt        Sat Jul 27 12:22:54 2024
@@ -1,10 +1,28 @@
-$NetBSD: patch-CMakeLists.txt,v 1.4 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-CMakeLists.txt,v 1.5 2024/07/27 12:22:54 bacon Exp $
 
-# Unbundle htslib and zlib, use gmake
+# Use external htslib
 
---- CMakeLists.txt.orig        2023-06-27 10:45:00.000000000 +0000
+--- CMakeLists.txt.orig        2024-07-20 19:07:27.000000000 +0000
 +++ CMakeLists.txt
-@@ -56,42 +56,16 @@ ENDIF(LINK MATCHES static)
+@@ -23,16 +23,12 @@ add_compile_definitions("MAX_KMER_SIZE=$
+ 
+ 
+ option(USE_HDF5 "Compile with HDF5 support" OFF) #OFF by default
+-option(USE_BAM "Compile with HTSLIB support" OFF) # OFF by default
++option(USE_BAM "Compile with HTSLIB support" ON)
+ 
+ if(USE_HDF5)
+     add_compile_definitions("USE_HDF5=ON")
+ endif(USE_HDF5)
+ 
+-if(NOT USE_BAM)
+-    add_compile_definitions("NO_HTSLIB=ON")
+-endif()
+-
+ set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext)
+ set(CMAKE_CXX_FLAGS_PROFILE "-g")
+ 
+@@ -73,42 +69,16 @@ ENDIF(LINK MATCHES static)
  
  
  include(ExternalProject)
@@ -24,7 +42,7 @@ $NetBSD: patch-CMakeLists.txt,v 1.4 2023
      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=${PROJECT_BIFROST_CMAKE_CXX_FLAGS}
+     CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=${MAX_KMER_SIZE} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS} ${DO_ENABLE_AVX2} 
${DO_ENABLE_COMPILATION_ARCH}
 -    BUILD_COMMAND cd build && make
 +    BUILD_COMMAND cd build && gmake
      INSTALL_COMMAND ""
Index: pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt
diff -u pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt:1.4 pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt:1.5
--- pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt:1.4        Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt    Sat Jul 27 12:22:54 2024
@@ -1,8 +1,8 @@
-$NetBSD: patch-src_CMakeLists.txt,v 1.4 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-src_CMakeLists.txt,v 1.5 2024/07/27 12:22:54 bacon Exp $
 
-# Unbundle htslib
+# Use external htslib
 
---- src/CMakeLists.txt.orig    2023-07-06 14:07:38 UTC
+--- src/CMakeLists.txt.orig    2024-07-23 11:52:01.089699466 +0000
 +++ src/CMakeLists.txt
 @@ -3,10 +3,6 @@ file(GLOB headers *.h *.hpp)
  
@@ -12,15 +12,15 @@ $NetBSD: patch-src_CMakeLists.txt,v 1.4 
 -include_directories(../ext/htslib)
 -endif(USE_BAM)
 -
- add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
- 
- add_library(kallisto_core ${sources} ${headers})
-@@ -17,7 +13,7 @@ add_executable(kallisto main.cpp)
+ if(NOT MAX_KMER_SIZE)
+ set(MAX_KMER_SIZE "32")
+ endif()
+@@ -21,7 +17,7 @@ add_executable(kallisto main.cpp)
  find_package( Threads REQUIRED )
  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)
+-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a  -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
++target_link_libraries(kallisto kallisto_core pthread hts ${install_dir}/build/src/libbifrost.a  -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
  else()
- target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a)
+ target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
  endif(USE_BAM)

Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
diff -u pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.1 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.2
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.1        Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt    Sat Jul 27 12:22:54 2024
@@ -1,12 +1,12 @@
-$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.1 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.2 2024/07/27 12:22:54 bacon Exp $
 
-# Portability
+# Respect pkgsrc build flags
 
---- ext/bifrost/CMakeLists.txt.orig    2023-06-27 10:45:00.000000000 +0000
+--- ext/bifrost/CMakeLists.txt.orig    2024-07-23 11:56:13.172038229 +0000
 +++ ext/bifrost/CMakeLists.txt
-@@ -7,18 +7,12 @@ find_package(Threads REQUIRED)
+@@ -6,18 +6,12 @@ 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")
@@ -24,21 +24,24 @@ $NetBSD: patch-ext_bifrost_CMakeLists.tx
  #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}")
+@@ -25,20 +19,6 @@ if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATC
+       set(COMPILATION_ARCH "OFF")
+ endif(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
+ 
+-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=${COMPILATION_ARCH}")
- endif(COMPILATION_ARCH MATCHES "OFF")
- 
- if(ENABLE_AVX2 MATCHES "OFF")
-@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
-               set(CMAKE_EXE_LINKER_FLAGS "-pg")
-       else(CMAKE_BUILD_TYPE MATCHES Profile)
-               message("Build type: Release")
--              add_compile_options(-O3)
-+              add_compile_options(-O2)
-       endif(CMAKE_BUILD_TYPE MATCHES Profile) 
- endif(CMAKE_BUILD_TYPE MATCHES Debug)
- 
+-endif(COMPILATION_ARCH MATCHES "OFF")
+-
+-if(ENABLE_AVX2 MATCHES "OFF")
+-      message("Disabling AVX2 instructions")
+-      set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mno-avx2")
+-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mno-avx2")
+-endif(ENABLE_AVX2 MATCHES "OFF")
+-
+ # Manages build types
+ if(NOT CMAKE_BUILD_TYPE)
+   set(CMAKE_BUILD_TYPE "Release")
Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp
diff -u pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp:1.1 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp:1.2
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp:1.1  Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp      Sat Jul 27 12:22:54 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-ext_bifrost_src_BitContainer.cpp,v 1.1 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-ext_bifrost_src_BitContainer.cpp,v 1.2 2024/07/27 12:22:54 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:1.1 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp:1.2
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp:1.1      Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp  Sat Jul 27 12:22:54 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-ext_bifrost_src_ColorSet.cpp,v 1.1 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-ext_bifrost_src_ColorSet.cpp,v 1.2 2024/07/27 12:22:54 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:1.1 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h:1.2
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h:1.1       Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h   Sat Jul 27 12:22:54 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-ext_bifrost_src_libpopcnt.h,v 1.1 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-ext_bifrost_src_libpopcnt.h,v 1.2 2024/07/27 12:22:54 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:1.1 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp:1.2
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp:1.1       Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp   Sat Jul 27 12:22:54 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-ext_bifrost_src_strict__fstream.hpp,v 1.1 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-ext_bifrost_src_strict__fstream.hpp,v 1.2 2024/07/27 12:22:54 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h
diff -u pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h:1.1 pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h:1.2
--- pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h:1.1   Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-src_Bootstrap.h       Sat Jul 27 12:22:54 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_Bootstrap.h,v 1.1 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-src_Bootstrap.h,v 1.2 2024/07/27 12:22:54 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/kallisto/patches/patch-src_main.cpp
diff -u pkgsrc/biology/kallisto/patches/patch-src_main.cpp:1.1 pkgsrc/biology/kallisto/patches/patch-src_main.cpp:1.2
--- pkgsrc/biology/kallisto/patches/patch-src_main.cpp:1.1      Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-src_main.cpp  Sat Jul 27 12:22:54 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_main.cpp,v 1.1 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-src_main.cpp,v 1.2 2024/07/27 12:22:54 bacon Exp $
 
 # Portability
 

Index: pkgsrc/biology/kallisto/patches/patch-src_kseq.h
diff -u pkgsrc/biology/kallisto/patches/patch-src_kseq.h:1.2 pkgsrc/biology/kallisto/patches/patch-src_kseq.h:1.3
--- pkgsrc/biology/kallisto/patches/patch-src_kseq.h:1.2        Sat Nov  4 14:35:07 2023
+++ pkgsrc/biology/kallisto/patches/patch-src_kseq.h    Sat Jul 27 12:22:54 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_kseq.h,v 1.2 2023/11/04 14:35:07 bacon Exp $
+$NetBSD: patch-src_kseq.h,v 1.3 2024/07/27 12:22:54 bacon Exp $
 
 # Portability

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