perlPackages.BioExtAlign: bug fix and add test (#380488)

pkgs/by-name/ke/kent/package.nix

@@ -53,7 +53,7 @@ stdenv.mkDerivation rec {
     export HOME=$TMPDIR
     export DESTBINDIR=$HOME/bin
 
-    mkdir -p $HOME/lib $HOME/bin/x86_64
+    mkdir -p $HOME/lib $HOME/bin/${stdenv.hostPlatform.parsed.cpu.name}
 
     cd ./src
     chmod +x ./checkUmask.sh
@@ -63,8 +63,8 @@ stdenv.mkDerivation rec {
     cd jkOwnLib
     make
 
-    cp ../lib/x86_64/jkOwnLib.a $HOME/lib
-    cp ../lib/x86_64/jkweb.a $HOME/lib
+    cp ../lib/${stdenv.hostPlatform.parsed.cpu.name}/jkOwnLib.a $HOME/lib
+    cp ../lib/${stdenv.hostPlatform.parsed.cpu.name}/jkweb.a $HOME/lib
     cp -r ../inc  $HOME/
 
     cd ../utils
@@ -79,7 +79,7 @@ stdenv.mkDerivation rec {
     mkdir -p $out/bin $out/lib $out/inc
     cp $HOME/lib/jkOwnLib.a $out/lib
     cp $HOME/lib/jkweb.a $out/lib
-    cp $HOME/bin/x86_64/* $out/bin
+    cp $HOME/bin/${stdenv.hostPlatform.parsed.cpu.name}/* $out/bin
     cp -r $HOME/inc/* $out/inc/
 
     runHook postInstall

pkgs/development/perl-modules/Bio-Ext-Align/default.nix

@@ -8,10 +8,7 @@ buildPerlPackage rec {
   pname = "BioExtAlign";
   version = "1.5.1";
 
-  outputs = [
-    "out"
-    "dev"
-  ];
+  outputs = [ "out" ];
 
   src = fetchFromGitHub {
     owner = "bioperl";
@@ -20,7 +17,15 @@ buildPerlPackage rec {
     sha256 = "sha256-+0tZ6q3PFem8DWa2vq+njOLmjDvMB0JhD0FGk00lVMA=";
   };
 
-  patches = [ ./fprintf.patch ];
+  patches = [
+    # Starting for Perl 5.6, implicit function declaration are treated as errors
+    # There may be an error but ensembl-vep (the main package for this dependency)
+    # runs
+    ./no-implicit-function.patch
+    # Tests need other parts of BioExt, disabling them
+    ./disable-other-tests.patch
+    ./fprintf.patch
+  ];
 
   # Do not install other Bio-ext packages
   preConfigure = ''
@@ -32,6 +37,14 @@ buildPerlPackage rec {
     make
   '';
 
+  checkPhase = ''
+    runHook preCheck
+
+    make test
+
+    runHook postCheck
+  '';
+
   meta = {
     homepage = "https://github.com/bioperl/bioperl-ext";
     description = "Write Perl Subroutines in Other Programming Languages";
@@ -39,5 +52,6 @@ buildPerlPackage rec {
       Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions.
     '';
     license = with lib.licenses; [ artistic1 ];
+    maintainers = with lib.maintainers; [ apraga ];
   };
 }

pkgs/development/perl-modules/Bio-Ext-Align/disable-other-tests.patch

@@ -0,0 +1,84 @@
+diff --git a/Bio/Ext/Align/test.pl b/Bio/Ext/Align/test.pl
+index 72411f3..1deb77b 100755
+--- a/Bio/Ext/Align/test.pl
++++ b/Bio/Ext/Align/test.pl
+@@ -8,13 +8,10 @@ my $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
+ BEGIN {
+     eval { require Test; };
+     use Test;
+-    plan tests => 9;
++    plan tests => 4;
+ }
+ 
+ use Bio::Ext::Align;
+-use Bio::Tools::dpAlign;
+-use Bio::Seq;
+-use Bio::AlignIO;
+ 
+ $loaded = 1;
+ ok(1); # modules loaded
+@@ -34,64 +31,3 @@ $alb = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($seq1,$seq2,
+ 					 $seq2->seq,15,50,STDERR) if $DEBUG;
+ 
+ 
+-warn( "Testing Local Alignment case...\n") if $DEBUg;
+-
+-$alnout = new Bio::AlignIO(-format => 'pfam', -fh => \*STDERR);
+-$aln = &Bio::Ext::Align::Align_DNA_Sequences("AATGCCATTGACGG",
+-					     "CAGCCTCGCTTAG",3,-1,3,1,
+-		      Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);
+-
+-$out = Bio::SimpleAlign->new();
+-
+-$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln1,
+-				     -start => $aln->start1,
+-				     -end   => $aln->end1,
+-				     -id    => "one"));
+-
+-$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln2,
+-				     -start => $aln->start2,
+-				     -end   => $aln->end2,
+-				     -id    => "two"));
+-$alnout->write_aln($out) if $DEBUG;
+-
+-$aln = &Bio::Ext::Align::Align_Protein_Sequences("WLGQRNLVSSTGGNLLNVWLKDW","WMGNRNVVNLLNVWFRDW",0,
+-						 Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);
+-$out = Bio::SimpleAlign->new();
+-ok($aln);
+-
+-$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln1,
+-				     -start => $aln->start1,
+-				     -end   => $aln->end1,
+-				     -id    => "one"));
+-
+-$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln2,
+-				     -start => $aln->start2,
+-				     -end   => $aln->end2,
+-				     -id    => "two"));
+-$alnout->write_aln($out) if $DEBUG;
+-ok(1);
+-
+-warn( "Testing Global Alignment case...\n") if $DEBUG;
+-
+-$factory = new Bio::Tools::dpAlign('-alg' => Bio::Tools::dpAlign::DPALIGN_GLOBAL_MILLER_MYERS);
+-$s1 = new Bio::Seq(-id => "one", -seq => "AATGCCATTGACGG", -alphabet => 'dna');
+-$s2 = new Bio::Seq(-id => "two", -seq => "CAGCCTCGCTTAG", -alphabet => 'dna');
+-$aln = $factory->pairwise_alignment($s1, $s2);
+-$alnout->write_aln($aln) if $DEBUG;
+-$factory->align_and_show($s1, $s2) if $DEBUG;
+-
+-ok(1);
+-
+-$s1 = new Bio::Seq(-id => "one", -seq => "WLGQRNLVSSTGGNLLNVWLKDW", 
+-		   -alphabet => 'protein');
+-$s2 = new Bio::Seq(-id => "two", -seq => "WMGNRNVVNLLNVWFRDW", 
+-		   -alphabet => 'protein');
+-$aln = $factory->pairwise_alignment($s1, $s2);
+-$alnout->write_aln($aln) if $DEBUG;
+-$factory->align_and_show($s1, $s2) if $DEBUG;
+-ok(1);
+-
+-$prof = $factory->sequence_profile($s1);
+-warn( "Optimal Alignment Score = %d\n", $factory->pairwise_alignment_score($prof, $s2)) if $DEBUG;
+-
+-ok($factory->pairwise_alignment_score($prof,$s2),77);

pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch

@@ -7,7 +7,7 @@ index 0e07b67..0eab932 100644
  dpAlign_fatal(char * s)
  {
 -    fprintf(stderr, s);
-+    fputs(stderr, s);
++    fputs(s, stderr);
      exit(-1);
  }
  

pkgs/development/perl-modules/Bio-Ext-Align/no-implicit-function.patch

@@ -0,0 +1,13 @@
+diff --git a/Bio/Ext/Align/Makefile.PL b/Bio/Ext/Align/Makefile.PL
+index cc6c343..ea5cffa 100755
+--- a/Bio/Ext/Align/Makefile.PL
++++ b/Bio/Ext/Align/Makefile.PL
+@@ -5,7 +5,7 @@ WriteMakefile(
+     'NAME'	=> 'Bio::Ext::Align',
+     'VERSION'	=> '1.5.1',
+     'LIBS'	=> ['-lm'],   # e.g., '-lm' 
+-    'DEFINE'	=> '-DPOSIX -DNOERROR',     # e.g., '-DHAVE_SOMETHING' 
++    'DEFINE'	=> '-DPOSIX -DNOERROR -Wno-implicit-function-declaration',     # e.g., '-DHAVE_SOMETHING'
+     'INC'	=> '-I./libs',     # e.g., '-I/usr/include/other'
+     'MYEXTLIB'  => 'libs/libsw$(LIB_EXT)',
+     'clean'     => { 'FILES' => 'libs/*.o libs/*.a' }