diff options
-rw-r--r-- | .SRCINFO | 15 | ||||
-rw-r--r-- | PKGBUILD | 22 | ||||
-rw-r--r-- | system-libs.patch | 155 |
3 files changed, 12 insertions, 180 deletions
@@ -1,29 +1,26 @@ pkgbase = r-rarr pkgdesc = Read Zarr Files in R - pkgver = 1.2.0 - pkgrel = 3 + pkgver = 1.4.0 + pkgrel = 1 url = https://bioconductor.org/packages/Rarr arch = x86_64 license = MIT checkdepends = r-mockery checkdepends = r-tinytest depends = blosc - depends = lz4 depends = r-httr depends = r-jsonlite depends = r-paws.storage depends = r-r.utils depends = r-stringr + depends = zstd optdepends = r-biocstyle optdepends = r-covr optdepends = r-knitr optdepends = r-mockery optdepends = r-tinytest - source = https://bioconductor.org/packages/release/bioc/src/contrib/Rarr_1.2.0.tar.gz - source = system-libs.patch - md5sums = 94af864ae3de3557840993a429944ea2 - md5sums = 83d4df5360e4cf2088753078dc2970b6 - b2sums = 1ed0ea1b9eb24b60fcbebcd56ebb49f149a82b3d3218d0f86214537836c051f07cfcceac84ac53711005249cbd5c157b55371c629510de7457f9054b1dee9d1c - b2sums = 137df7ed9d8504b913aebd2588a8d88651d6a46bb8985981f0aa3032244372fd163b48c691b1fd2918d8f9aa3834b2538f6a4901bb01538fa8a0875e0f771353 + source = https://bioconductor.org/packages/release/bioc/src/contrib/Rarr_1.4.0.tar.gz + md5sums = b4ccf32bada187fdbb1ce37b6c49b23f + b2sums = 1b13a23377f723ea5d33e2b832edf10b79c92b1a6eca513859b3307b334b5a686bfc64a409a43dececda5840e093facd105b8582310a3c160f87954eccf57112 pkgname = r-rarr @@ -1,22 +1,22 @@ # Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com> _pkgname=Rarr -_pkgver=1.2.0 +_pkgver=1.4.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} -pkgrel=3 +pkgrel=1 pkgdesc="Read Zarr Files in R" arch=(x86_64) url="https://bioconductor.org/packages/$_pkgname" license=('MIT') depends=( blosc - lz4 r-httr r-jsonlite r-paws.storage r-r.utils r-stringr + zstd ) checkdepends=( r-mockery @@ -29,19 +29,9 @@ optdepends=( r-mockery r-tinytest ) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz" - "system-libs.patch") -md5sums=('94af864ae3de3557840993a429944ea2' - '83d4df5360e4cf2088753078dc2970b6') -b2sums=('1ed0ea1b9eb24b60fcbebcd56ebb49f149a82b3d3218d0f86214537836c051f07cfcceac84ac53711005249cbd5c157b55371c629510de7457f9054b1dee9d1c' - '137df7ed9d8504b913aebd2588a8d88651d6a46bb8985981f0aa3032244372fd163b48c691b1fd2918d8f9aa3834b2538f6a4901bb01538fa8a0875e0f771353') - -prepare() { - cd "$_pkgname" - # use system blosc and lz4 - patch -Np1 -i ../system-libs.patch - autoconf -} +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('b4ccf32bada187fdbb1ce37b6c49b23f') +b2sums=('1b13a23377f723ea5d33e2b832edf10b79c92b1a6eca513859b3307b334b5a686bfc64a409a43dececda5840e093facd105b8582310a3c160f87954eccf57112') build() { mkdir build diff --git a/system-libs.patch b/system-libs.patch deleted file mode 100644 index bb0e84b50b9d..000000000000 --- a/system-libs.patch +++ /dev/null @@ -1,155 +0,0 @@ -diff --git a/configure.ac b/configure.ac -index a6d5842..c29cf85 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -30,98 +30,3 @@ AC_SUBST(AR) - - AC_CONFIG_FILES([src/Makevars]) - AC_OUTPUT -- --## check if we have an x86 CPU --machine=`uname -m` --AS_CASE([$machine], -- [*86*], [x86_CPU=true], -- [x86_CPU=false] --) -- --## see if -msse2 is a supported flag --AX_CHECK_COMPILE_FLAG([-msse2], [MSSE2=true], [MSSE2=false]) -- --if [ "${IS_BIOC_BUILD_MACHINE}" == true ]; then -- AC_MSG_NOTICE(Bioc build machine; disabling MAVX2) -- MAVX2=false --else -- ## see if -mavx2 is a supported flag -- AX_CHECK_COMPILE_FLAG([-mavx2], [MAVX2=true], [MAVX2=false]) --fi -- --AC_RUN_IFELSE( -- [AC_LANG_PROGRAM([#include <stdlib.h>], -- [__builtin_cpu_init ();]) -- ], -- [ax_cv_gcc_check_x86_cpu_init=true], -- [ax_cv_gcc_check_x86_cpu_init=false]) -- --## check CPU supports sse2 and avx2 --if [ "$x86_CPU" == true ] && [ "$ax_cv_gcc_check_x86_cpu_init" == true ]; then -- AX_GCC_X86_CPU_SUPPORTS(sse2, [SSE2_SUPPORTED=true], [SSE2_SUPPORTED=false]) -- if [ "$MAVX2" = true ]; then -- AX_GCC_X86_CPU_SUPPORTS(avx2, [AVX2_SUPPORTED=true], [AVX2_SUPPORTED=false]) -- fi --else -- SSE2_SUPPORTED=false -- AVX2_SUPPORTED=false --fi -- --if [ "$MSSE2" = true ] && [ "$SSE2_SUPPORTED" = true ] ; then -- SSE2="-DSHUFFLE_SSE2_ENABLED" -- MSSE2="-msse2" -- SSE2_BITSHUFFLE='bitshuffle-sse2.o: bitshuffle-sse2.c -- $(CC) $(FLAGS) -c bitshuffle-sse2.c' -- SSE2_BITSHUFFLE_OBJ='bitshuffle-sse2.o' -- SSE2_SHUFFLE='shuffle-sse2.o: shuffle-sse2.c -- $(CC) $(FLAGS) -c shuffle-sse2.c' -- SSE2_SHUFFLE_OBJ='shuffle-sse2.o' -- SSE2_OBJ_PATH='lib/blosc-1.20.1/' --else -- SSE2="" -- MSSE2="" -- SSE2_BITSHUFFLE="" -- SSE2_SHUFFLE="" -- SSE2_BITSHUFFLE_OBJ="" -- SSE2_SHUFFLE_OBJ="" -- SSE2_OBJ_PATH="" --fi -- --AC_SUBST(SSE2) --AC_SUBST(MSSE2) --AC_SUBST(SSE2_BITSHUFFLE) --AC_SUBST(SSE2_SHUFFLE) --AC_SUBST(SSE2_BITSHUFFLE_OBJ) --AC_SUBST(SSE2_SHUFFLE_OBJ) --AC_SUBST(SSE2_OBJ_PATH) -- --if [ "$MAVX2" = true ] && [ "$AVX2_SUPPORTED" = true ] ; then -- AVX2="-DSHUFFLE_AVX2_ENABLED" -- MAVX2="-mavx2" -- AVX2_BITSHUFFLE='bitshuffle-avx2.o: bitshuffle-avx2.c -- $(CC) $(FLAGS) -c bitshuffle-avx2.c' -- AVX2_BITSHUFFLE_OBJ='bitshuffle-avx2.o' -- AVX2_SHUFFLE='shuffle-avx2.o: shuffle-avx2.c -- $(CC) $(FLAGS) -c shuffle-avx2.c' -- AVX2_SHUFFLE_OBJ='shuffle-avx2.o' -- AVX2_OBJ_PATH='lib/blosc-1.20.1/' --else -- AVX2="" -- MAVX2="" -- AVX2_BITSHUFFLE="" -- AVX2_SHUFFLE="" -- AVX2_BITSHUFFLE_OBJ="" -- AVX2_SHUFFLE_OBJ="" -- AVX2_OBJ_PATH="" --fi -- --AC_SUBST(AVX2) --AC_SUBST(MAVX2) --AC_SUBST(AVX2_BITSHUFFLE) --AC_SUBST(AVX2_SHUFFLE) --AC_SUBST(AVX2_BITSHUFFLE_OBJ) --AC_SUBST(AVX2_SHUFFLE_OBJ) --AC_SUBST(AVX2_OBJ_PATH) -- --AC_CONFIG_FILES([src/compression_tools/blosc/lib/blosc-1.20.1/Makefile src/compression_tools/blosc/Makefile]) --AC_OUTPUT -diff --git a/src/Makevars.in b/src/Makevars.in -index bcb0b4f..91881df 100644 ---- a/src/Makevars.in -+++ b/src/Makevars.in -@@ -9,12 +9,10 @@ export PKG_R_CPPFLAGS=@R_CPPFLAGS@ - - COMPRESSION_LIBS=compression_tools/blosc/libblosc.a - --PKG_LIBS=$(COMPRESSION_LIBS) -+PKG_LIBS = -lblosc -llz4 - - all: $(SHLIB) - --$(SHLIB): compression_libs -- - compression_libs: $(COMPRESSION_LIBS) - - compression_tools/blosc/libblosc.a: -diff --git a/src/compress.h b/src/compress.h -index 573e203..72ddd98 100644 ---- a/src/compress.h -+++ b/src/compress.h -@@ -2,9 +2,9 @@ - - #ifndef _COMPRESSION_H - #define _COMPRESSION_H -- #include "compression_tools/blosc/lib/blosc-1.20.1/blosc.h" -- #include "compression_tools/blosc/lib/lz4-1.9.2/lz4.h" -- #include "compression_tools/blosc/lib/lz4-1.9.2/lz4hc.h" -+ #include <blosc.h> -+ #include <lz4.h> -+ #include <lz4hc.h> - #endif - - SEXP compress_chunk_BLOSC(SEXP input, SEXP type_size); -diff --git a/src/decompress.h b/src/decompress.h -index a13b390..3ed84e7 100644 ---- a/src/decompress.h -+++ b/src/decompress.h -@@ -2,9 +2,9 @@ - - #ifndef _COMPRESSION_H - #define _COMPRESSION_H -- #include "compression_tools/blosc/lib/blosc-1.20.1/blosc.h" -- #include "compression_tools/blosc/lib/lz4-1.9.2/lz4.h" -- #include "compression_tools/blosc/lib/lz4-1.9.2/lz4hc.h" -+ #include <blosc.h> -+ #include <lz4.h> -+ #include <lz4hc.h> - #endif - - SEXP decompress_chunk_BLOSC(SEXP input); |