Homebrew · cho-m · May 29, 2022 · May 29, 2022 · May 29, 2022 · May 29, 2022
diff --git a/Aliases/perl@5.34 → Aliases/perl@5.36 b/Aliases/perl@5.34 → Aliases/perl@5.36
diff --git a/Formula/abricate.rb b/Formula/abricate.rb
@@ -4,6 +4,7 @@ class Abricate < Formula
   url "https://github.com/tseemann/abricate/archive/v1.0.1.tar.gz"
   sha256 "5edc6b45a0ff73dcb4f1489a64cb3385d065a6f29185406197379522226a5d20"
   license "GPL-2.0-only"
+  revision 1
   head "https://github.com/tseemann/abricate.git", branch: "master"
 
   bottle do
@@ -15,7 +16,6 @@ class Abricate < Formula
     sha256 cellar: :any_skip_relocation, x86_64_linux:  "1758175ec977b93b4d9c6ca271a7091d9d90817c74417d00c52ca46d6237e571"
   end
 
-  depends_on "cpanminus" => :build
   depends_on "bioperl"
   depends_on "blast"
   depends_on "openssl@1.1"
@@ -28,18 +28,111 @@ class Abricate < Formula
     sha256 "ed20e895c7a94d246163267d56fce99ab0de48784ddda2b3bf1246aa296bf249"
   end
 
+  # Perl dependencies originally installed via cpanminus.
+  # For `JSON Path::Tiny List::MoreUtils LWP::Simple` and dependencies.
+  resource "JSON" do
+    url "http://www.cpan.org/authors/id/I/IS/ISHIGAKI/JSON-4.09.tar.gz"
+    sha256 "6780a51f438c0932eec0534fc9cd2b1ad0d64817eda4add8ede5ec77d6d2c991"
+  end
+  resource "Path::Tiny" do
+    url "http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Path-Tiny-0.124.tar.gz"
+    sha256 "fa083144781e46817ec39d21962bbbb0533c201f3baf031d2999a785a2a013fd"
+  end
+  resource "List::MoreUtils::XS" do
+    url "http://www.cpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-XS-0.430.tar.gz"
+    sha256 "e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242"
+  end
+  resource "Exporter::Tiny" do
+    url "http://www.cpan.org/authors/id/T/TO/TOBYINK/Exporter-Tiny-1.004003.tar.gz"
+    sha256 "7c6852f18367af05f03912f007a1fac318471a870a457f0e502c11adcf9a457b"
+  end
+  resource "List::MoreUtils" do
+    url "http://www.cpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-0.430.tar.gz"
+    sha256 "63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527"
+  end
+  resource "URI" do
+    url "http://www.cpan.org/authors/id/O/OA/OALDERS/URI-5.12.tar.gz"
+    sha256 "66abe0eaddd76b74801ecd28ec1411605887550fc0a45ef6aa744fdad768d9b3"
+  end
+  resource "LWP::MediaTypes" do
+    url "http://www.cpan.org/authors/id/O/OA/OALDERS/LWP-MediaTypes-6.04.tar.gz"
+    sha256 "8f1bca12dab16a1c2a7c03a49c5e58cce41a6fec9519f0aadfba8dad997919d9"
+  end
+  resource "Encode::Locale" do
+    url "http://www.cpan.org/authors/id/G/GA/GAAS/Encode-Locale-1.05.tar.gz"
+    sha256 "176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1"
+  end
+  resource "Time::Zone" do
+    url "http://www.cpan.org/authors/id/A/AT/ATOOMIC/TimeDate-2.33.tar.gz"
+    sha256 "c0b69c4b039de6f501b0d9f13ec58c86b040c1f7e9b27ef249651c143d605eb2"
+  end
+  resource "HTTP::Date" do
+    url "http://www.cpan.org/authors/id/O/OA/OALDERS/HTTP-Date-6.05.tar.gz"
+    sha256 "365d6294dfbd37ebc51def8b65b81eb79b3934ecbc95a2ec2d4d827efe6a922b"
+  end
+  resource "IO::HTML" do
+    url "http://www.cpan.org/authors/id/C/CJ/CJM/IO-HTML-1.004.tar.gz"
+    sha256 "c87b2df59463bbf2c39596773dfb5c03bde0f7e1051af339f963f58c1cbd8bf5"
+  end
+  resource "HTTP::Request" do
+    url "http://www.cpan.org/authors/id/O/OA/OALDERS/HTTP-Message-6.37.tar.gz"
+    sha256 "0e59da0a85e248831327ebfba66796314cb69f1bfeeff7a9da44ad766d07d802"
+  end
+  resource "HTML::Tagset" do
+    url "http://www.cpan.org/authors/id/P/PE/PETDANCE/HTML-Tagset-3.20.tar.gz"
+    sha256 "adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2"
+  end
+  resource "HTML::HeadParser" do
+    url "http://www.cpan.org/authors/id/O/OA/OALDERS/HTML-Parser-3.78.tar.gz"
+    sha256 "22564002f206af94c1dd8535f02b0d9735125d9ebe89dd0ff9cd6c000e29c29d"
+  end
+  resource "Try::Tiny" do
+    url "http://www.cpan.org/authors/id/E/ET/ETHER/Try-Tiny-0.31.tar.gz"
+    sha256 "3300d31d8a4075b26d8f46ce864a1d913e0e8467ceeba6655d5d2b2e206c11be"
+  end
+  resource "HTTP::Cookies" do
+    url "http://www.cpan.org/authors/id/O/OA/OALDERS/HTTP-Cookies-6.10.tar.gz"
+    sha256 "e36f36633c5ce6b5e4b876ffcf74787cc5efe0736dd7f487bdd73c14f0bd7007"
+  end
+  resource "File::Listing" do
+    url "http://www.cpan.org/authors/id/P/PL/PLICEASE/File-Listing-6.15.tar.gz"
+    sha256 "46c4fb9f9eb9635805e26b7ea55b54455e47302758a10ed2a0b92f392713770c"
+  end
+  resource "WWW::RobotRules" do
+    url "http://www.cpan.org/authors/id/G/GA/GAAS/WWW-RobotRules-6.02.tar.gz"
+    sha256 "46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e"
+  end
+  resource "HTTP::Negotiate" do
+    url "http://www.cpan.org/authors/id/G/GA/GAAS/HTTP-Negotiate-6.01.tar.gz"
+    sha256 "1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016"
+  end
+  resource "Net::HTTP" do
+    url "http://www.cpan.org/authors/id/O/OA/OALDERS/Net-HTTP-6.22.tar.gz"
+    sha256 "62faf9a5b84235443fe18f780e69cecf057dea3de271d7d8a0ba72724458a1a2"
+  end
+  resource "LWP::Simple" do
+    url "http://www.cpan.org/authors/id/O/OA/OALDERS/libwww-perl-6.67.tar.gz"
+    sha256 "96eec40a3fd0aa1bd834117be5eb21c438f73094d861a1a7e5774f0b1226b723"
+  end
+
   def install
     resource("any2fasta").stage do
       bin.install "any2fasta"
     end
 
-    ENV.prepend "PERL5LIB", Formula["bioperl"].libexec/"lib/perl5"
+    ENV.prepend_path "PERL5LIB", Formula["bioperl"].opt_libexec/"lib/perl5"
     ENV.prepend_create_path "PERL5LIB", libexec/"perl5/lib/perl5"
-
+    ENV["PERL_MM_USE_DEFAULT"] = "1"
     ENV["OPENSSL_PREFIX"] = Formula["openssl@1.1"].opt_prefix # for Net::SSLeay
 
-    pms = %w[JSON Path::Tiny List::MoreUtils LWP::Simple]
-    system "cpanm", "--self-contained", "-l", libexec/"perl5", *pms
+    resources.each do |r|
+      next if r.name == "any2fasta"
+
+      r.stage do
+        system "perl", "Makefile.PL", "INSTALL_BASE=#{libexec}/perl5"
+        system "make", "install"
+      end
+    end
 
     libexec.install Dir["*"]
     %w[abricate abricate-get_db].each do |name|

diff --git a/Formula/asciiquarium.rb b/Formula/asciiquarium.rb
@@ -8,7 +8,7 @@ class Asciiquarium < Formula
   url "https://robobunny.com/projects/asciiquarium/asciiquarium_1.1.tar.gz"
   sha256 "1b08c6613525e75e87546f4e8984ab3b33f1e922080268c749f1777d56c9d361"
   license "GPL-2.0-or-later"
-  revision 3
+  revision 4
 
   livecheck do
     url "https://robobunny.com/projects/asciiquarium/"

diff --git a/Formula/biber.rb b/Formula/biber.rb
@@ -4,7 +4,7 @@ class Biber < Formula
   url "https://github.com/plk/biber/archive/refs/tags/v2.17.tar.gz"
   sha256 "1ee7efdd8343e982046f2301c1b0dcf09e1f9a997ac86ed1018dcb41d04c9e88"
   license "Artistic-2.0"
-  revision 1
+  revision 2
 
   bottle do
     sha256 cellar: :any,                 arm64_monterey: "f35f6be9f3e6ad82ace58f3cdd49717f6fad197f2ca783fd7367ccc47e4fd74e"
@@ -506,9 +506,13 @@ class Biber < Formula
     url "https://cpan.metacpan.org/authors/id/V/VP/VPIT/autovivification-0.18.tar.gz"
     sha256 "2d99975685242980d0a9904f639144c059d6ece15899efde4acb742d3253f105"
   end
-  resource "test.bcf" do
-    url "https://downloads.sourceforge.net/project/biblatex-biber/biblatex-biber/testfiles/test.bcf"
-    sha256 "7239ac502a8fc6d90fcaf9e9630d939a21e28456312ee7e041f6627ebb8fed24"
+
+  # Fix Perl 5.36.0 compatibility
+  # Remove in the next release
+  # See https://github.com/plk/biber/pull/411
+  patch do
+    url "https://github.com/plk/biber/commit/760e6e4ec08a3097f7e6136331541a7b8c1c9df7.patch?full_index=1"
+    sha256 "68586264731e1583331ada69151026333a48b53ab90786f43c36ecac0807d32e"
   end
 
   def install
@@ -518,8 +522,6 @@ def install
     ENV["OPENSSL_PREFIX"] = Formula["openssl@1.1"].opt_prefix
 
     resources.each do |r|
-      next if r.name == "test.bcf"
-
       r.stage do
         # fix libbtparse.so linkage failure on Linux
         if r.name == "Text::BibTeX" && OS.linux?
@@ -540,30 +542,27 @@ def install
       end
     end
 
+    bin_before = Dir[libexec/"bin/*"].to_set
     system "perl", "Build.PL", "--install_base", libexec
     system "./Build"
     system "./Build", "install"
-
-    bin.install Dir[libexec/"bin/*"]
-    bin.env_script_all_files(libexec/"bin", PERL5LIB: ENV["PERL5LIB"])
+    bin_after = Dir[libexec/"bin/*"].to_set
+    (bin_after - bin_before).each do |file|
+      basename = Pathname(file).basename
+      (bin/basename).write_env_script file, PERL5LIB: ENV["PERL5LIB"]
+    end
     man1.install libexec/"man/man1/biber.1"
+    (pkgshare/"test").install "t/tdata/annotations.bcf", "t/tdata/annotations.bib"
   end
 
   test do
     assert_match version.to_s, shell_output("#{bin}/biber --version")
 
-    resource("test.bcf").stage testpath
-    (testpath/"test.bib").write <<~EOS
-      @BOOK{test1,
-        AUTHOR = {Terrence Test},
-        TITLE = {Testing is Trying and Troubling},
-        YEAR = {1987},
-      }
-    EOS
-
-    assert_match "Output to test.bbl", shell_output("#{bin}/biber --validate-control --convert-control test")
-    assert_predicate testpath/"test.bcf.html", :exist?
-    assert_predicate testpath/"test.blg", :exist?
-    assert_predicate testpath/"test.bbl", :exist?
+    cp (pkgshare/"test").children, testpath
+    output = shell_output("#{bin}/biber --validate-control --convert-control annotations")
+    assert_match "Output to annotations.bbl", output
+    assert_predicate testpath/"annotations.bcf.html", :exist?
+    assert_predicate testpath/"annotations.blg", :exist?
+    assert_predicate testpath/"annotations.bbl", :exist?
   end
 end
diff --git a/Formula/clipsafe.rb b/Formula/clipsafe.rb
@@ -4,7 +4,7 @@ class Clipsafe < Formula
   url "https://waxandwane.org/download/clipsafe-1.1.tar.gz"
   sha256 "7a70b4f467094693a58814a42d272e98387916588c6337963fa7258bda7a3e48"
   license "GPL-2.0-or-later"
-  revision 1
+  revision 2
 
   livecheck do
     url :homepage

diff --git a/Formula/collectd.rb b/Formula/collectd.rb
@@ -2,7 +2,7 @@ class Collectd < Formula
   desc "Statistics collection and monitoring daemon"
   homepage "https://collectd.org/"
   license "MIT"
-  revision 4
+  revision 5
 
   stable do
     url "https://collectd.org/files/collectd-5.12.0.tar.bz2"

diff --git a/Formula/ddclient.rb b/Formula/ddclient.rb
@@ -2,6 +2,7 @@ class Ddclient < Formula
   desc "Update dynamic DNS entries"
   homepage "https://ddclient.net/"
   license "GPL-2.0-or-later"
+  revision 1
 
   # Remove `stable` block when resources are no longer needed.
   stable do

diff --git a/Formula/extract_url.rb b/Formula/extract_url.rb
@@ -4,6 +4,7 @@ class ExtractUrl < Formula
   url "https://github.com/m3m0ryh0l3/extracturl/archive/v1.6.2.tar.gz"
   sha256 "5f0b568d5c9449f477527b4077d8269f1f5e6d6531dfa5eb6ca72dbacab6f336"
   license "BSD-2-Clause"
+  revision 1
 
   bottle do
     sha256 cellar: :any_skip_relocation, arm64_monterey: "6695e1a5dc10ac46acf1420064c5822095bb658a90ca1b43a1b68e769998edeb"

diff --git a/Formula/feedgnuplot.rb b/Formula/feedgnuplot.rb
@@ -4,7 +4,7 @@ class Feedgnuplot < Formula
   url "https://github.com/dkogan/feedgnuplot/archive/v1.61.tar.gz"
   sha256 "4239fe61a03232ea47909edd59af767b98481b205f58910b2e30d2d41f9caa80"
   license any_of: ["GPL-1.0-or-later", "Artistic-1.0"]
-  revision 1
+  revision 2
 
   bottle do
     sha256 cellar: :any_skip_relocation, arm64_monterey: "d921d4a402bdf9ad1633bea40e99f12c746dc671c256c7cfbe54995e2923cb55"
@@ -46,7 +46,7 @@ def install
       end
     end
 
-    system "perl", "Makefile.PL", "prefix=#{prefix}"
+    system "perl", "Makefile.PL", "prefix=#{prefix}", "INSTALLSITEMAN1DIR=#{man1}"
     system "make"
     system "make", "install"
     prefix.install Dir[prefix/"local/*"]

diff --git a/Formula/freeradius-server.rb b/Formula/freeradius-server.rb
@@ -2,7 +2,7 @@ class FreeradiusServer < Formula
   desc "High-performance and highly configurable RADIUS server"
   homepage "https://freeradius.org/"
   license all_of: ["GPL-2.0-or-later", "LGPL-2.1-or-later"]
-  revision 2
+  revision 3
   head "https://github.com/FreeRADIUS/freeradius-server.git", branch: "master"
 
   stable do

diff --git a/Formula/get-flash-videos.rb b/Formula/get-flash-videos.rb
@@ -4,7 +4,7 @@ class GetFlashVideos < Formula
   url "https://github.com/monsieurvideo/get-flash-videos/archive/1.25.99.03.tar.gz"
   sha256 "37267b41c7b0c240d99ed1f5e7ba04d00f98a8daff82ac9edd2b12c3bca83d73"
   license "Apache-2.0"
-  revision 1
+  revision 2
 
   bottle do
     sha256 cellar: :any_skip_relocation, arm64_monterey: "7556fc02fefbb77d6af0abba77201d802f3cad9532e68e998231e0fc7fe63cf5"

diff --git a/Formula/get_iplayer.rb b/Formula/get_iplayer.rb
@@ -4,6 +4,7 @@ class GetIplayer < Formula
   url "https://github.com/get-iplayer/get_iplayer/archive/v3.30.tar.gz"
   sha256 "05a39d5447eecfc2f95a616bf8d4dcf59ca3b3a0ecda1f82882401e6d74e286c"
   license "GPL-3.0-or-later"
+  revision 1
   head "https://github.com/get-iplayer/get_iplayer.git", branch: "develop"
 
   bottle do

diff --git a/Formula/git-svn.rb b/Formula/git-svn.rb
@@ -4,7 +4,7 @@ class GitSvn < Formula
   url "https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.37.3.tar.xz"
   sha256 "814641d7f61659cfbc17825d0462499ca1403e39ff53d76a8512050e6483e87a"
   license "GPL-2.0-only"
-  revision 1
+  revision 2
   head "https://github.com/git/git.git", branch: "master"
 
   livecheck do

diff --git a/Formula/gnumeric.rb b/Formula/gnumeric.rb
@@ -4,6 +4,7 @@ class Gnumeric < Formula
   url "https://download.gnome.org/sources/gnumeric/1.12/gnumeric-1.12.53.tar.xz"
   sha256 "5568e4c8dceabb9028f1361d1045522f95f0a71daa59e973cbdd2d39badd4f02"
   license any_of: ["GPL-3.0-only", "GPL-2.0-only"]
+  revision 1
 
   bottle do
     sha256 arm64_monterey: "e0e9e6d7cb46c08b5cf72c98cfe4a06aa72d20da2e4b058c3e019e904edf5c8d"

diff --git a/Formula/grokj2k.rb b/Formula/grokj2k.rb
@@ -5,7 +5,7 @@ class Grokj2k < Formula
   url "https://github.com/GrokImageCompression/grok/archive/v9.7.1.tar.gz"
   sha256 "a7d433dca92b035349ef8203eb44cb6d0b2c9b41aecd2d12872a9ca2761e0606"
   license "AGPL-3.0-or-later"
-  revision 1
+  revision 2
   head "https://github.com/GrokImageCompression/grok.git", branch: "master"
 
   livecheck do

diff --git a/Formula/help2man.rb b/Formula/help2man.rb
@@ -5,6 +5,7 @@ class Help2man < Formula
   mirror "https://ftpmirror.gnu.org/help2man/help2man-1.49.2.tar.xz"
   sha256 "9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36"
   license "GPL-3.0-or-later"
+  revision 1
 
   bottle do
     sha256 cellar: :any_skip_relocation, arm64_monterey: "383b411c2f38bcc248ef62253135047fcdf62d9dc53f8204d8789648705750e2"

diff --git a/Formula/imapsync.rb b/Formula/imapsync.rb
@@ -5,6 +5,7 @@ class Imapsync < Formula
   # NOTE: The mirror will return 404 until the version becomes outdated.
   sha256 "553ce6d6535b954987a859fa0c3c74da446df74157d398ab09159c7f8ed8043d"
   license "NLPL"
+  revision 1
   head "https://github.com/imapsync/imapsync.git", branch: "master"
 
   livecheck do

diff --git a/Formula/innotop.rb b/Formula/innotop.rb
@@ -4,7 +4,7 @@ class Innotop < Formula
   url "https://github.com/innotop/innotop/archive/v1.13.0.tar.gz"
   sha256 "6ec91568e32bda3126661523d9917c7fbbd4b9f85db79224c01b2a740727a65c"
   license any_of: ["GPL-2.0-only", "Artistic-1.0-Perl"]
-  revision 2
+  revision 3
   head "https://github.com/innotop/innotop.git"
 
   bottle do

diff --git a/Formula/intltool.rb b/Formula/intltool.rb
@@ -4,6 +4,7 @@ class Intltool < Formula
   url "https://launchpad.net/intltool/trunk/0.51.0/+download/intltool-0.51.0.tar.gz"
   sha256 "67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd"
   license "GPL-2.0-or-later"
+  revision 1
 
   bottle do
     sha256 cellar: :any_skip_relocation, arm64_monterey: "273d2b13868310fda429c3fbf1ddc347de0cab3189bf47639fd6c64adb8ec0cb"

diff --git a/Formula/irssi.rb b/Formula/irssi.rb
@@ -4,7 +4,7 @@ class Irssi < Formula
   url "https://github.com/irssi/irssi/releases/download/1.2.3/irssi-1.2.3.tar.xz"
   sha256 "a647bfefed14d2221fa77b6edac594934dc672c4a560417b1abcbbc6b88d769f"
   license "GPL-2.0-or-later"
-  revision 2
+  revision 3
 
   # This formula uses a file from a GitHub release, so we check the latest
   # release version instead of Git tags.

diff --git a/Formula/kpcli.rb b/Formula/kpcli.rb
@@ -8,6 +8,7 @@ class Kpcli < Formula
   url "https://downloads.sourceforge.net/project/kpcli/kpcli-3.8.1.pl"
   sha256 "6c84f8639245799bf9b2d5ce297c41b5d4ec0789f7f5fa9e8767556816ea472c"
   license any_of: ["Artistic-1.0-Perl", "GPL-1.0-or-later"]
+  revision 1
 
   livecheck do
     url :stable

diff --git a/Formula/lanraragi.rb b/Formula/lanraragi.rb
@@ -6,6 +6,7 @@ class Lanraragi < Formula
   url "https://github.com/Difegue/LANraragi/archive/v.0.8.6.tar.gz"
   sha256 "074c97568d75fb07ed0eb49c83639f2a7548a3f0a3714a854100637ea8891f68"
   license "MIT"
+  revision 1
   head "https://github.com/Difegue/LANraragi.git", branch: "dev"
 
   bottle do

diff --git a/Formula/latexindent.rb b/Formula/latexindent.rb
@@ -4,6 +4,7 @@ class Latexindent < Formula
   url "https://github.com/cmhughes/latexindent.pl/archive/V3.18.tar.gz"
   sha256 "ac67f08c4deb8d75adc7704d17f1145e96131a87abda9b996b67a66bd27a3b7c"
   license "GPL-3.0-or-later"
+  revision 1
 
   bottle do
     sha256 cellar: :any_skip_relocation, arm64_monterey: "5597c888dce5c08018adc793b8d41241d3212dd81a01f83a1c31e0029339e959"

diff --git a/Formula/latexml.rb b/Formula/latexml.rb
@@ -4,6 +4,7 @@ class Latexml < Formula
   url "https://dlmf.nist.gov/LaTeXML/releases/LaTeXML-0.8.6.tar.gz"
   sha256 "9529c651b67f5e8ddef1fd1852f974e756a17b711c46d4118f0677ad0e6e9bb1"
   license :public_domain
+  revision 1
   head "https://github.com/brucemiller/LaTeXML.git", branch: "master"
 
   livecheck do