[lilac] updated to 1.4.0-1

3 files changed, 12 insertions, 180 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 6b377721bd3f..0e556eb41eaa 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -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
diff --git a/PKGBUILD b/PKGBUILD
index e563cea518a4..2229f95e3429 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -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);