Index: head/biology/p5-AcePerl/Makefile =================================================================== --- head/biology/p5-AcePerl/Makefile (revision 385810) +++ head/biology/p5-AcePerl/Makefile (revision 385811) @@ -1,41 +1,41 @@ # Created by: Johann Visagie # $FreeBSD$ PORTNAME= AcePerl PORTVERSION= 1.92 PORTREVISION= 4 CATEGORIES= biology databases perl5 MASTER_SITES= CPAN/Ace PKGNAMEPREFIX= p5- -MAINTAINER= ports@FreeBSD.org +MAINTAINER= perl@FreeBSD.org COMMENT= Perl5 interface to the ACEDB genome database system LICENSE= ART10 GPLv1 LICENSE_COMB= dual BUILD_DEPENDS= p5-Cache-Cache>=0:${PORTSDIR}/devel/p5-Cache-Cache RUN_DEPENDS:= ${BUILD_DEPENDS} MAKE_JOBS_UNSAFE= yes USES= perl5 USE_PERL5= configure .include .if ${ARCH} == "amd64" || ${ARCH} == "ia64" CFLAGS+= -fPIC .endif post-patch: @${SED} -e 's|XX__CC__XX|${CC}|' < ${FILESDIR}/FREEBSD_DEF \ > ${WRKSRC}/acelib/wmake/FREEBSD_DEF post-install: .for f in Freesubs/Freesubs.so RPC/RPC.so ${CHMOD} u+w ${STAGEDIR}${PREFIX}/${SITE_ARCH_REL}/auto/Ace/${f} ${STRIP_CMD} ${STAGEDIR}${PREFIX}/${SITE_ARCH_REL}/auto/Ace/${f} ${CHMOD} u-w ${STAGEDIR}${PREFIX}/${SITE_ARCH_REL}/auto/Ace/${f} .endfor .include Index: head/biology/p5-AcePerl/files/patch-Makefile.PL =================================================================== --- head/biology/p5-AcePerl/files/patch-Makefile.PL (revision 385810) +++ head/biology/p5-AcePerl/files/patch-Makefile.PL (revision 385811) @@ -1,20 +1,20 @@ ---- Makefile.PL.orig Fri Sep 28 16:13:04 2001 -+++ Makefile.PL Fri Jan 25 14:11:26 2002 -@@ -2,7 +2,7 @@ - use ExtUtils::MakeMaker qw(prompt WriteMakefile); +--- Makefile.PL.orig 2006-01-04 15:18:10 UTC ++++ Makefile.PL +@@ -3,7 +3,7 @@ use ExtUtils::MakeMaker qw(prompt WriteM use File::Path; + require 5.8.0; -my $choice; +my $choice = 3; while (!$choice) { $reply = prompt( "\nWhat do you want to build?\n\n" . -@@ -22,8 +22,6 @@ +@@ -23,8 +23,6 @@ my @extlib = (); push @extlib,'Freesubs' if $choice >= 2; push @extlib,'RPC' if $choice >= 3; -print "\n"; -setup_sitedefs() if prompt("Do you want to install Ace::Browser? ","n") =~ /[yY]/; - my $headers = "./ace/wh"; + my $headers = "./acelib/wh"; WriteMakefile( Index: head/biology/p5-AcePerl/files/patch-RPC__RPC.xs =================================================================== --- head/biology/p5-AcePerl/files/patch-RPC__RPC.xs (revision 385810) +++ head/biology/p5-AcePerl/files/patch-RPC__RPC.xs (revision 385811) @@ -1,11 +1,11 @@ ---- ./RPC/RPC.xs.orig 2014-08-21 20:31:10.000000000 -0400 -+++ ./RPC/RPC.xs 2014-08-21 20:31:34.000000000 -0400 -@@ -153,7 +153,7 @@ +--- RPC/RPC.xs.orig 2000-06-13 17:17:19 UTC ++++ RPC/RPC.xs +@@ -153,7 +153,7 @@ int arg; break; case '_': if (strEQ(name, "_ACECLIENT_")) -#ifdef _ACECLIENT_ +#if 0 return _ACECLIENT_; #else goto not_there; Index: head/biology/p5-AcePerl/files/patch-acelib_memsubs.c =================================================================== --- head/biology/p5-AcePerl/files/patch-acelib_memsubs.c (revision 385810) +++ head/biology/p5-AcePerl/files/patch-acelib_memsubs.c (revision 385811) @@ -1,11 +1,11 @@ ---- acelib/memsubs.c.orig Mon Jan 11 02:01:29 1999 -+++ acelib/memsubs.c Thu Jul 27 17:18:45 2000 +--- acelib/memsubs.c.orig 2002-11-24 19:24:23 UTC ++++ acelib/memsubs.c @@ -21,7 +21,7 @@ #if defined(NEXT) || defined(HP) || defined(MACINTOSH) extern void* malloc(mysize_t size) ; #elif !defined(WIN32) && !defined(DARWIN) -#include /* normal machines */ +#include /* normal machines */ #endif /********** primary type definition **************/ Index: head/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h =================================================================== --- head/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h (revision 385810) +++ head/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h (revision 385811) @@ -1,11 +1,11 @@ ---- acelib/wh/mydirent.h.orig Mon Jul 16 23:04:45 2001 -+++ acelib/wh/mydirent.h Mon Aug 13 12:41:59 2001 +--- acelib/wh/mydirent.h.orig 2002-11-14 20:00:06 UTC ++++ acelib/wh/mydirent.h @@ -55,7 +55,7 @@ extern char *getwd(char *pathname) ; #endif /* HP || SOLARIS || WIN32 */ -#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined (INTEL_SOLARIS) +#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined (INTEL_SOLARIS) || defined (FREEBSD) #include typedef struct dirent MYDIRENT ; #endif Index: head/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h =================================================================== --- head/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h (revision 385810) +++ head/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h (revision 385811) @@ -1,12 +1,12 @@ ---- acelib/wh/mystdlib.h.orig Mon Jul 16 23:04:45 2001 -+++ acelib/wh/mystdlib.h Mon Aug 13 12:42:25 2001 -@@ -161,7 +161,8 @@ +--- acelib/wh/mystdlib.h.orig 2002-11-14 20:00:06 UTC ++++ acelib/wh/mystdlib.h +@@ -161,7 +161,8 @@ char *DosToPosix(char *path) ; /* define #endif #if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \ - defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS) + defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS) || \ + defined(FREEBSD) #ifdef WIN32 #include Index: head/biology/p5-Bio-ASN1-EntrezGene/Makefile =================================================================== --- head/biology/p5-Bio-ASN1-EntrezGene/Makefile (revision 385810) +++ head/biology/p5-Bio-ASN1-EntrezGene/Makefile (revision 385811) @@ -1,20 +1,22 @@ # Created by: Mauricio Herrera Cuadra # $FreeBSD$ PORTNAME= Bio-ASN1-EntrezGene PORTVERSION= 1.70 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= biology perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:CJFIELDS PKGNAMEPREFIX= p5- -MAINTAINER= ports@FreeBSD.org +MAINTAINER= perl@FreeBSD.org COMMENT= Regular expression-based Perl Parser for NCBI Entrez Gene -WRKSRC= ${WRKDIR}/Bio-ASN1-EntrezGene-${PORTVERSION} +BUILD_DEPENDS= p5-bioperl>=0:${PORTSDIR}/biology/p5-bioperl +RUN_DEPENDS:= ${BUILD_DEPENDS} USES= perl5 USE_PERL5= configure .include Index: head/biology/p5-bioperl/Makefile =================================================================== --- head/biology/p5-bioperl/Makefile (revision 385810) +++ head/biology/p5-bioperl/Makefile (revision 385811) @@ -1,85 +1,84 @@ # Created by: Johann Visagie # $FreeBSD$ PORTNAME= bioperl PORTVERSION= 1.6.924 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:CJFIELDS PKGNAMEPREFIX= p5- DISTNAME= BioPerl-${PORTVERSION} MAINTAINER= perl@FreeBSD.org COMMENT= Collection of Perl modules for bioinformatics LICENSE= ART10 GPLv1 LICENSE_COMB= dual BUILD_DEPENDS= p5-Algorithm-Munkres>=0:${PORTSDIR}/math/p5-Algorithm-Munkres \ p5-Array-Compare>=0:${PORTSDIR}/misc/p5-Array-Compare \ - p5-Bio-ASN1-EntrezGene>=0:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \ p5-Class-AutoClass>=0:${PORTSDIR}/devel/p5-Class-AutoClass \ p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \ p5-Convert-Binary-C>=0:${PORTSDIR}/converters/p5-Convert-Binary-C \ p5-Data-Stag>=0:${PORTSDIR}/devel/p5-Data-Stag \ p5-DBD-mysql>=0:${PORTSDIR}/databases/p5-DBD-mysql \ p5-Error>=0:${PORTSDIR}/lang/p5-Error \ p5-GD>=0:${PORTSDIR}/graphics/p5-GD \ p5-GD-SVG>=0:${PORTSDIR}/graphics/p5-GD-SVG \ p5-Graph>=0:${PORTSDIR}/math/p5-Graph \ p5-GraphViz>=0:${PORTSDIR}/graphics/p5-GraphViz \ p5-HTML-Parser>=0:${PORTSDIR}/www/p5-HTML-Parser \ p5-HTML-TableExtract>=2:${PORTSDIR}/www/p5-HTML-TableExtract \ p5-IO-stringy>=0:${PORTSDIR}/devel/p5-IO-stringy \ p5-IO-String>=0:${PORTSDIR}/devel/p5-IO-String \ p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \ p5-PostScript>=0:${PORTSDIR}/print/p5-PostScript \ p5-SOAP-Lite>=0:${PORTSDIR}/net/p5-SOAP-Lite \ p5-Set-Scalar>=0:${PORTSDIR}/devel/p5-Set-Scalar \ p5-Sort-Naturally>=1:${PORTSDIR}/textproc/p5-Sort-Naturally \ p5-Spreadsheet-ParseExcel>=0:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \ p5-SVG>=0:${PORTSDIR}/textproc/p5-SVG \ p5-SVG-Graph>=0:${PORTSDIR}/graphics/p5-SVG-Graph \ p5-Test-Most>=0:${PORTSDIR}/devel/p5-Test-Most \ p5-Text-Shellwords>=0:${PORTSDIR}/textproc/p5-Text-Shellwords \ p5-Text-Tabs+Wrap>=0:${PORTSDIR}/textproc/p5-Text-Tabs+Wrap \ p5-URI>=0:${PORTSDIR}/net/p5-URI \ p5-XML-DOM>=0:${PORTSDIR}/textproc/p5-XML-DOM \ p5-XML-DOM-XPath>=0:${PORTSDIR}/textproc/p5-XML-DOM-XPath \ p5-XML-LibXML>=0:${PORTSDIR}/textproc/p5-XML-LibXML \ p5-XML-Parser>=0:${PORTSDIR}/textproc/p5-XML-Parser \ p5-XML-SAX>=0:${PORTSDIR}/textproc/p5-XML-SAX \ p5-XML-SAX-Writer>=0:${PORTSDIR}/textproc/p5-XML-SAX-Writer \ p5-XML-Simple>=2:${PORTSDIR}/textproc/p5-XML-Simple \ p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \ p5-XML-Writer>=0:${PORTSDIR}/textproc/p5-XML-Writer \ p5-YAML>=0:${PORTSDIR}/textproc/p5-YAML \ p5-libwww>=0:${PORTSDIR}/www/p5-libwww \ p5-libxml>=0:${PORTSDIR}/textproc/p5-libxml RUN_DEPENDS:= ${BUILD_DEPENDS} USES= perl5 USE_PERL5= modbuild OPTIONS_DEFINE= DOCS PGTEST SQLITETEST PGTEST_DESC= Test PostGreSQL SQLITETEST_DESC= Test SQLite PGTEST_RUN_DEPENDS= p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg PGTEST_BUILD_DEPENDS= p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg SQLITETEST_RUN_DEPENDS= p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite SQLITETEST_BUILD_DEPENDS= p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite post-install: @${MKDIR} ${STAGEDIR}${DATADIR} ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR} @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} @${MKDIR} ${STAGEDIR}${DOCSDIR} .for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README ${INSTALL_MAN} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} .endfor ${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR} .include