some fixes for md5 cross-version compatibility

gjospin · Aug 15, 2013 · e90c89d · e90c89d
1 parent d35f8a9
commit e90c89d
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Showing 3 changed files with 17 additions and 15 deletions.
diff --git a/lib/Phylosift/FastSearch.pm b/lib/Phylosift/FastSearch.pm
@@ -11,11 +11,20 @@ use Phylosift::Utilities qw(:all);
 use Phylosift::MarkerAlign;
 use Phylosift::Settings;
 use File::Basename;
-use Digest::MD5 qw(md5_hex);
 use POSIX qw(ceil floor);
 
 use version; our $VERSION = version->declare("v1.0.0_01");
 
+# try to load the system's MD5 lib, but if that fails, load our own
+eval {
+	require Digest::MD5;
+	Digest::MD5->import();
+} or do {
+	unshift( @INC, "$FindBin::Bin/../legacy/md5lib" );
+	use Digest::MD5;
+};
+
+
 =head1 NAME
 
 Phylosift::FastSearch - Subroutines to perform fast sequence identity searches between reads and marker genes.

diff --git a/lib/Phylosift/Utilities.pm b/lib/Phylosift/Utilities.pm
@@ -419,7 +419,6 @@ sub marker_update_check {
 	eval {
 		require LWP::Simple;
 		LWP::Simple->import();
-		1;
 	};
 	my $result          = $@;
 	my $get_new_markers = 0;
@@ -598,7 +597,6 @@ sub ncbi_update_check {
 		LWP::Simple->import();
 		$have_lwp = 1;
 		@lwp_result = LWP::Simple::head("$url");
-		1;
 	} or do {
 		warn "Unable to load LWP::Simple, unable to check for updates to or download the NCBI taxonomy." unless $skip_lock;
 	};

diff --git a/tools/package_standalone.pl b/tools/package_standalone.pl
@@ -64,34 +64,29 @@
 `mv blib/lib/Locale/ $prefix/lib/`;
 chdir("..");
 
-# Digest::MD5
-add_package(url=>"http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Digest-MD5-2.52.tar.gz");
-
 # Locale::Maketext::Simple 
 add_package(url=>"http://search.cpan.org/CPAN/authors/id/J/JE/JESSE/Locale-Maketext-Simple-0.21.tar.gz", mv_cmd=>"mv blib/lib/Locale/Maketext/* $prefix/lib/Locale/Maketext/");
 
 # XML::Writer
 add_package(url=>"http://search.cpan.org/CPAN/authors/id/J/JO/JOSEPHW/XML-Writer-0.615.tar.gz");
 
-# libwww-perl (for LWP::Simple)
-add_package(url=>"http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/libwww-perl-6.04.tar.gz");
-add_package(url=>"http://search.cpan.org/CPAN/authors/id/C/CJ/CJM/IO-HTML-1.00.tar.gz");
-add_package(url=>"http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/URI-1.60.tar.gz");
-add_package(url=>"http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Message-6.06.tar.gz");
-add_package(url=>"http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Date-6.02.tar.gz", mv_cmd=>"mv blib/lib/HTTP/* $prefix/lib/HTTP");
-#add NSFLock.pm
+# File::NSFLock
 add_package(url=>"http://search.cpan.org/CPAN/authors/id/B/BB/BBB/File-NFSLock-1.21.tar.gz");
 
-add_package(url=>"http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Data-OptList-0.108.tar.gz");
-
 # add Version.pm
 #`mkdir -p $prefix/legacy`; #prefix is not right here as we are in the top level directory
 `mkdir -p PhyloSift/legacy`;
 add_package(url=>"http://search.cpan.org/CPAN/authors/id/J/JP/JPEACOCK/version-0.9902.tar.gz", make_opts=>"--perl_only", mv_cmd=>"mv blib/lib/* $prefix/legacy/");
 
+# Digest::MD5
+`mkdir -p PhyloSift/legacy/md5lib`;
+add_package(url=>"http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Digest-MD5-2.52.tar.gz", mv_cmd=>"mv blib/lib/* $prefix/legacy/md5lib/");
+
+
 # support for App::Cmd
 add_package(url=>"http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/List-MoreUtils-0.33.tar.gz");
 add_package(url=>"http://search.cpan.org/CPAN/authors/id/D/DO/DOY/Package-Stash-0.35.tar.gz");
+add_package(url=>"http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Data-OptList-0.108.tar.gz");
 add_package(url=>"http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Getopt-Long-Descriptive-0.092.tar.gz");
 add_package(url=>"http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/String-RewritePrefix-0.006.tar.gz");
 add_package(url=>"http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/App-Cmd-0.318.tar.gz");