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staden-io-lib 1.15.0 #1669

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Mar 2, 2024
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staden-io-lib 1.15.0 #1669

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staden-io-lib 1.15.0
YoshitakaMo Mar 2, 2024
18fb7bf
staden-io-lib 1.15.0
YoshitakaMo Mar 2, 2024
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18 changes: 16 additions & 2 deletions Formula/staden-io-lib.rb
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
class StadenIoLib < Formula
desc "Staden Package io_lib"
homepage "https://staden.sourceforge.io/"
url "https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-13/io_lib-1.14.13.tar.gz"
sha256 "5641c02f98342f689274ed9b71e57d26fbf8216730619bde3a663214ce2ae8b0"
url "https://github.com/jkbonfield/io_lib/archive/refs/tags/io_lib-1-15-0.tar.gz"
sha256 "7006ab127ec05649d1f1bceafb7953defc665408da24cf990804d2c65e510f39"
head "https://github.com/jkbonfield/io_lib.git"

bottle do
Expand All @@ -11,16 +11,30 @@
sha256 cellar: :any, x86_64_linux: "ec45d0b6f055089c5bc95c798e7be60e39699aa664fad44e9ea9dda862b26054"
end

depends_on "autoconf" => :build
depends_on "automake" => :build
depends_on "libtool" => :build
depends_on "libdeflate"
depends_on "xz"
depends_on "zstd"

uses_from_macos "bzip2"
uses_from_macos "curl"
uses_from_macos "zlib"

resource "htscodecs" do
url "https://github.com/samtools/htscodecs/archive/5aecc6e107db1c2ff59529a5aa034d28b799b7d1.tar.gz"
sha256 "32e630af98e1dd445ee9537c2ac5adbd3910195fd39a03e7912ee7ea201b5b74"
end

def install

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GitHub Actions / build-bottles (macos-14)

`brew install --verbose --build-bottle brewsci/bio/staden-io-lib` failed on macOS Sonoma (14) on Apple Silicon! 

 -g -O2 -o .libs/extract_fastq extract_fastq.o  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o index_tar index_tar.o  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -llzma -lbz2 -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -o scf_info scf_info.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -o scf_update scf_update.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/scf_dump scf_dump.o  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/scf_info scf_info.o  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/scf_update scf_update.o  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -o get_comment get_comment.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/get_comment get_comment.o  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/hash_tar hash_tar.o  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/hash_extract hash_extract.o  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -o hash_list hash_list.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib -o hash_sff hash_sff.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/hash_list hash_list.o  -L/opt/homebrew/opt/libdeflate/lib -L/opt/homebrew/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/trace_dump trace_dump.o  -L/opt/homebrew/opt/libde

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GitHub Actions / build-bottles (macos-13)

`brew install --verbose --build-bottle brewsci/bio/staden-io-lib` failed on macOS Ventura (13)! 

ct_fastq.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -o index_tar index_tar.o  -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/extract_qual extract_qual.o  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/extract_fastq extract_fastq.o  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o index_tar index_tar.o  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -llzma -lbz2 -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -o scf_info scf_info.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/scf_dump scf_dump.o  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -o scf_update scf_update.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -o get_comment get_comment.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/scf_info scf_info.o  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/scf_update scf_update.o  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/get_comment get_comment.o  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -o hash_list hash_list.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/hash_tar hash_tar.o  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lzstd -ldeflate -llzma -lbz2  -ldeflate -lzstd
libtool: link: clang -Wall -g -O2 -o .libs/hash_extract hash_extract.o  -L/usr/local/opt/libdeflate/lib -L/usr/local/opt/zstd/lib ../io_lib/.libs/libstaden-read.dylib -lz -lcurl -lm -lpthread -llzma -lbz2 -ldeflate -lzstd
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -g -O2  -L/usr/local/opt/libdeflate/lib -L/usr/loc
(buildpath/"htscodecs").install resource("htscodecs")
system "./bootstrap"
system "./configure", "--disable-debug",
"--disable-dependency-tracking",
"--disable-silent-rules",
"--with-libdeflate=#{Formula["libdeflate"].opt_prefix}",
"--with-zstd=#{Formula["zstd"].opt_prefix}",
"--prefix=#{prefix}"
system "make", "install"

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