diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/bioperl/Makefile | 21 | ||||
| -rw-r--r-- | biology/bioperl/files/md5 | 4 | ||||
| -rw-r--r-- | biology/bioperl/files/patch-sum | 9 | ||||
| -rw-r--r-- | biology/bioperl/patches/patch-aa | 16 | ||||
| -rw-r--r-- | biology/bioperl/patches/patch-ab | 20 | ||||
| -rw-r--r-- | biology/bioperl/patches/patch-ac | 13 | ||||
| -rw-r--r-- | biology/bioperl/pkg/PLIST | 50 |
7 files changed, 40 insertions, 93 deletions
diff --git a/biology/bioperl/Makefile b/biology/bioperl/Makefile index 1b46c91af2c..fcea148fbb7 100644 --- a/biology/bioperl/Makefile +++ b/biology/bioperl/Makefile @@ -1,32 +1,21 @@ -# $NetBSD: Makefile,v 1.3 2001/02/16 13:41:26 wiz Exp $ +# $NetBSD: Makefile,v 1.4 2001/04/05 21:48:40 jtb Exp $ # -DISTNAME= bioperl-0.04.4 +DISTNAME= bioperl-0.7.0 CATEGORIES= biology -MASTER_SITES= ftp://bio.perl.org/pub/DIST/ +MASTER_SITES= http://bioperl.org/Core/Latest/ MAINTAINER= packages@netbsd.org -HOMEPAGE= http://bio.perl.org/ +HOMEPAGE= http://bioperl.org/ COMMENT= Perl tools for computational molecular biology USE_PERL5= # defined PERL5_PACKLIST= ${PERL5_SITEARCH}/auto/Bio/.packlist -PERL5_PACKLIST+= ${PERL5_SITEARCH}/auto/bp_sw/.packlist do-configure: - cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL - cd ${WRKSRC}/Compile/SW; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL - -pre-build: - cd ${WRKSRC}/Compile/SW/libs; ${MAKE_PROGRAM} - -post-build: - cd ${WRKSRC}/Compile/SW; ${MAKE_PROGRAM} - cd ${WRKSRC}; ${MAKE_PROGRAM} test - cd ${WRKSRC}/Compile/SW; ${MAKE_PROGRAM} test + @cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL post-install: - cd ${WRKSRC}/Compile/SW; ${MAKE_PROGRAM} install ${INSTALL_DATA_DIR} ${PREFIX}/share/examples/bioperl cd ${WRKSRC}/examples; ${GTAR} cf - . \ | (cd ${PREFIX}/share/examples/bioperl; ${GTAR} xf -) diff --git a/biology/bioperl/files/md5 b/biology/bioperl/files/md5 index 41efd041385..d97ecad284c 100644 --- a/biology/bioperl/files/md5 +++ b/biology/bioperl/files/md5 @@ -1,3 +1,3 @@ -$NetBSD: md5,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $ +$NetBSD: md5,v 1.2 2001/04/05 21:48:40 jtb Exp $ -MD5 (bioperl-0.04.4.tar.gz) = e131dfd837423ec0fc746a3b83e68020 +SHA1 (bioperl-0.7.0.tar.gz) = c86abeeb5f2e2b98d1577d9cefd51ce15bbcb6b6 diff --git a/biology/bioperl/files/patch-sum b/biology/bioperl/files/patch-sum index 1cfc5723524..24b54b7806f 100644 --- a/biology/bioperl/files/patch-sum +++ b/biology/bioperl/files/patch-sum @@ -1,5 +1,6 @@ -$NetBSD: patch-sum,v 1.2 2000/08/26 03:36:38 jlam Exp $ +$NetBSD: patch-sum,v 1.3 2001/04/05 21:48:40 jtb Exp $ -MD5 (patch-aa) = c18e708c55eeae44ac7ec7a860d67f00 -MD5 (patch-ab) = cf3fd5491b9aac607ed516ce4cf0213c -MD5 (patch-ac) = 4de5755319b2d54ce180633847275c92 +This placeholder file is generated by the ``makepatchsum'' target +whenever the patches directory is empty or missing. Its purpose +is to ensure that the presence of any obsolete patches will cause +the proper error to be emitted at build time. diff --git a/biology/bioperl/patches/patch-aa b/biology/bioperl/patches/patch-aa deleted file mode 100644 index 704b8fdc216..00000000000 --- a/biology/bioperl/patches/patch-aa +++ /dev/null @@ -1,16 +0,0 @@ -$NetBSD: patch-aa,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $ - ---- Compile/SW/Makefile.PL.orig Fri Dec 11 08:24:25 1998 -+++ Compile/SW/Makefile.PL Mon Mar 1 11:37:15 1999 -@@ -13,9 +13,9 @@ - - sub MY::postamble{ - ' --$(MYEXTLIB): libs/libsw$(LIB_EXT) -+$(MYEXTLIB): - DEFINE=\'$(DEFINE)\'; CC=\'$(PERLMAINCC)\'; export DEFINE INC CC; \ -- cd libs && $(MAKE) libsw.a -e -+ cd libs && $(MAKE) libsw$(LIB_EXT) -e - - '; - } diff --git a/biology/bioperl/patches/patch-ab b/biology/bioperl/patches/patch-ab deleted file mode 100644 index b76fbbaa9b0..00000000000 --- a/biology/bioperl/patches/patch-ab +++ /dev/null @@ -1,20 +0,0 @@ -$NetBSD: patch-ab,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $ - ---- Compile/SW/libs/makefile.orig Fri Dec 11 16:24:29 1998 -+++ Compile/SW/libs/makefile Sat Apr 10 21:45:14 1999 -@@ -1,5 +1,4 @@ -- -- -+CFLAGS+=-fPIC - - OBJS = aln.o\ - alnconvert.o\ -@@ -52,7 +51,5 @@ - ar ru libsw.a $(OBJS) - - wisefile.o : wisefile.c -- $(CC) $(CFLAGS) -DNOERROR wisefile.c -+ ${CC} ${CFLAGS} -c -DNOERROR wisefile.c - --CFLAGS = -c -O --CC = cc diff --git a/biology/bioperl/patches/patch-ac b/biology/bioperl/patches/patch-ac deleted file mode 100644 index 064961c8ae6..00000000000 --- a/biology/bioperl/patches/patch-ac +++ /dev/null @@ -1,13 +0,0 @@ -$NetBSD: patch-ac,v 1.1 2000/08/26 03:36:45 jlam Exp $ - ---- Bio/Root/Err.pm.orig Thu Feb 4 03:06:35 1999 -+++ Bio/Root/Err.pm -@@ -984,7 +984,7 @@ - : This method is an alternative to Bio::Root::Object::throw() - : and is not as well developed or documented as that method. - --See Also : L<warning>(), B<Bio::Root::Object::throw()>, B<Bio::Root::Global::strictness() -+See Also : L<warning>(), B<Bio::Root::Object::throw()>, B<Bio::Root::Global::strictness()> - - =cut - diff --git a/biology/bioperl/pkg/PLIST b/biology/bioperl/pkg/PLIST index 4e429081653..99571fe9ec6 100644 --- a/biology/bioperl/pkg/PLIST +++ b/biology/bioperl/pkg/PLIST @@ -1,9 +1,4 @@ -@comment $NetBSD: PLIST,v 1.2 2000/08/27 07:10:59 jlam Exp $ -share/examples/bioperl/blast/blast_config.pl -share/examples/bioperl/blast/blast_seq.pl -share/examples/bioperl/blast/example.table1 -share/examples/bioperl/blast/example.table2 -share/examples/bioperl/blast/html.pl +@comment $NetBSD: PLIST,v 1.3 2001/04/05 21:48:41 jtb Exp $ share/examples/bioperl/blast/out/blastn.2.gz share/examples/bioperl/blast/out/blastn.2.wu.gz share/examples/bioperl/blast/out/blastp.1.gcg.gz @@ -19,26 +14,44 @@ share/examples/bioperl/blast/out/blastx.2 share/examples/bioperl/blast/out/blastx.2.email.gz share/examples/bioperl/blast/out/blastx.208.gz share/examples/bioperl/blast/out/tblastn.206.out.gz -share/examples/bioperl/blast/parse.pl -share/examples/bioperl/blast/parse2.pl -share/examples/bioperl/blast/parse_multi.pl -share/examples/bioperl/blast/parse_positions.pl -share/examples/bioperl/blast/parse_stream.pl -share/examples/bioperl/blast/print_blasts.pl -share/examples/bioperl/blast/run.pl share/examples/bioperl/blast/seq/acc1.dna.fasta share/examples/bioperl/blast/seq/seqs.fasta share/examples/bioperl/blast/seq/yal011w.dna.fasta share/examples/bioperl/blast/seq/yel009c.fasta share/examples/bioperl/blast/seq/ymr284w.fasta +share/examples/bioperl/blast/blast_config.pl +share/examples/bioperl/blast/blast_seq.pl +share/examples/bioperl/blast/example.table1 +share/examples/bioperl/blast/example.table2 +share/examples/bioperl/blast/html.pl +share/examples/bioperl/blast/parse_blast.pl +share/examples/bioperl/blast/parse_blast2.pl +share/examples/bioperl/blast/parse_multi.pl +share/examples/bioperl/blast/parse_positions.pl +share/examples/bioperl/blast/print_blasts.pl +share/examples/bioperl/blast/retrieve_blast.pl +share/examples/bioperl/blast/run_blast_remote.pl share/examples/bioperl/blosum62.bla +share/examples/bioperl/change_gene.pl +share/examples/bioperl/clustalw.pl +share/examples/bioperl/getGenBank.pl share/examples/bioperl/gon250.bla +share/examples/bioperl/gsequence +share/examples/bioperl/hitdisplay.pl share/examples/bioperl/psw.pl share/examples/bioperl/restriction.pl share/examples/bioperl/rev_and_trans.pl +share/examples/bioperl/seq_pattern.pl +share/examples/bioperl/simplealign.pl +share/examples/bioperl/standaloneblast.pl +share/examples/bioperl/test-genscan.pl +share/examples/bioperl/root_object/Outer.pm share/examples/bioperl/root_object/Bar.pm share/examples/bioperl/root_object/Foo.pm -share/examples/bioperl/root_object/Outer.pm +share/examples/bioperl/root_object/vector/Person.pm +share/examples/bioperl/root_object/vector/PersonManager.pm +share/examples/bioperl/root_object/vector/vector.out +share/examples/bioperl/root_object/vector/vector.pl share/examples/bioperl/root_object/destroy.pl share/examples/bioperl/root_object/error.out share/examples/bioperl/root_object/error.pl @@ -51,21 +64,14 @@ share/examples/bioperl/root_object/read.test share/examples/bioperl/root_object/read.test2 share/examples/bioperl/root_object/read.test3 share/examples/bioperl/root_object/utilities.pl -share/examples/bioperl/root_object/vector/Person.pm -share/examples/bioperl/root_object/vector/PersonManager.pm -share/examples/bioperl/root_object/vector/vector.out -share/examples/bioperl/root_object/vector/vector.pl -share/examples/bioperl/seq/id.list share/examples/bioperl/seq/seq.fasta.gz +share/examples/bioperl/seq/id.list share/examples/bioperl/seq/seq1.fasta share/examples/bioperl/seq/seq2.fasta share/examples/bioperl/seq/seqs1.pl share/examples/bioperl/seq/seqs2.pl share/examples/bioperl/seq/seqs3.pl -share/examples/bioperl/seq/seqs4.pl share/examples/bioperl/seq/seqtools.pl -share/examples/bioperl/seq_pattern.pl -share/examples/bioperl/simplealign.pl @dirrm share/examples/bioperl/seq @dirrm share/examples/bioperl/root_object/vector @dirrm share/examples/bioperl/root_object |