From 827fd8ad5f48ce64008be64caea2c4b9c8fba38a Mon Sep 17 00:00:00 2001 From: Ying-Chieh Liao Date: Tue, 16 Jul 2002 06:18:16 +0000 Subject: upgrade to 4.4 PR: 40612 Submitted by: maintainer --- biology/nab/Makefile | 5 +++- biology/nab/distinfo | 2 +- biology/nab/files/config.h | 4 +-- biology/nab/files/patch-examples:program_7.nab | 19 ++++++++++++++ biology/nab/files/patch-src:database.c | 32 +++++++++++++++++++++++ biology/nab/files/patch-tleap:database.c | 35 ++++++++++++++++++++++++++ biology/nab/pkg-descr | 2 +- biology/nab/pkg-plist | 14 +++-------- 8 files changed, 97 insertions(+), 16 deletions(-) create mode 100644 biology/nab/files/patch-examples:program_7.nab create mode 100644 biology/nab/files/patch-src:database.c create mode 100644 biology/nab/files/patch-tleap:database.c (limited to 'biology') diff --git a/biology/nab/Makefile b/biology/nab/Makefile index 669b522af9c7..d87e52a8103f 100644 --- a/biology/nab/Makefile +++ b/biology/nab/Makefile @@ -4,7 +4,7 @@ # $FreeBSD$ PORTNAME= nab -PORTVERSION= 4.3.2 +PORTVERSION= 4.4 CATEGORIES= biology MASTER_SITES= ftp://ftp.scripps.edu/pub/case/ @@ -31,6 +31,9 @@ pre-patch: @${PERL} -pi -e 's,,,' \ ${WRKSRC}/cifparse/cifparse.c +post-patch: + @rm -f ${WRKSRC}/examples/program_7.nab.orig + pre-install: @cd ${WRKSRC}/src && \ ${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall diff --git a/biology/nab/distinfo b/biology/nab/distinfo index c32c9718676d..00bddf409b0e 100644 --- a/biology/nab/distinfo +++ b/biology/nab/distinfo @@ -1 +1 @@ -MD5 (nab-4.3.2.tar.gz) = 35a706bd124a212cc8310ca1327be227 +MD5 (nab-4.4.tar.gz) = c1fe516ab9aebff74fcadd61f874d474 diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h index 8166c22b49ce..1d2f9ebab0a8 100644 --- a/biology/nab/files/config.h +++ b/biology/nab/files/config.h @@ -97,8 +97,8 @@ CPP= ucpp -l # # Use these CFLAGS if AVS = 0 # -CFLAGS= -OCFLAGS= -O +CFLAGS= -O -pipe +OCFLAGS= -O -pipe NABFLAGS= # # Use these CFLAGS if AVS = 1 diff --git a/biology/nab/files/patch-examples:program_7.nab b/biology/nab/files/patch-examples:program_7.nab new file mode 100644 index 000000000000..4e6455533df4 --- /dev/null +++ b/biology/nab/files/patch-examples:program_7.nab @@ -0,0 +1,19 @@ +*** examples/program_7.nab Wed Mar 10 18:57:51 1999 +--- examples/program_7.nab Sun Jun 2 13:40:36 2002 +*************** +*** 9,15 **** + cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" ); + + m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb", +! "dna", 2.25, -4.96, 36.0, 4.38, "" ); + + b = newbounds(m, ""); + allocate xyz[ 4*m.natoms ]; +--- 9,15 ---- + cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" ); + + m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb", +! "dna", 2.25, -4.96, 36.0, 3.38, "" ); + + b = newbounds(m, ""); + allocate xyz[ 4*m.natoms ]; diff --git a/biology/nab/files/patch-src:database.c b/biology/nab/files/patch-src:database.c new file mode 100644 index 000000000000..fc36828b3bfd --- /dev/null +++ b/biology/nab/files/patch-src:database.c @@ -0,0 +1,32 @@ +*** src/database.c.orig Wed Nov 15 19:46:50 2000 +--- src/database.c Sun Jun 2 12:57:50 2002 +*************** +*** 67,72 **** +--- 67,79 ---- + + + ++ #if (defined(__unix__) || defined(unix)) && !defined(USG) ++ #include ++ #endif ++ ++ #if defined(BSD) ++ #include ++ #endif + + + #include "stdio.h" +*************** +*** 979,985 **** +--- 986,996 ---- + + sDBRemoveLeadingSpaces( sLine ); + sDBRemoveFirstString( sLine, sHead ); ++ #if defined (linux) || defined(BSD) ++ sscanf( sHead, "%lg", dPDbl ); ++ #else + sscanf( sHead, "%lG", dPDbl ); ++ #endif + + } + diff --git a/biology/nab/files/patch-tleap:database.c b/biology/nab/files/patch-tleap:database.c new file mode 100644 index 000000000000..bdb35b202fa7 --- /dev/null +++ b/biology/nab/files/patch-tleap:database.c @@ -0,0 +1,35 @@ +*** tleap/database.c.orig Wed Mar 27 15:41:01 2002 +--- tleap/database.c Sun Jun 2 12:59:14 2002 +*************** +*** 97,102 **** +--- 97,109 ---- + + + ++ #if (defined(__unix__) || defined(unix)) && !defined(USG) ++ #include ++ #endif ++ ++ #if defined(BSD) ++ #include ++ #endif + + + #include "basics.h" +*************** +*** 563,569 **** + + sRemoveLeadingSpaces( sLine ); + sRemoveFirstString( sLine, sHead ); +! #ifdef linux + sscanf( sHead, "%lg", dPDbl ); + #else + sscanf( sHead, "%lG", dPDbl ); +--- 570,576 ---- + + sRemoveLeadingSpaces( sLine ); + sRemoveFirstString( sLine, sHead ); +! #if defined(linux) || defined(BSD) + sscanf( sHead, "%lg", dPDbl ); + #else + sscanf( sHead, "%lG", dPDbl ); diff --git a/biology/nab/pkg-descr b/biology/nab/pkg-descr index 782bbe66c6a0..6b5bb0463a4b 100644 --- a/biology/nab/pkg-descr +++ b/biology/nab/pkg-descr @@ -1,4 +1,4 @@ -This is version 4.2 of nab (nucleic acid builder), a computer language that +This is version 4.4 of nab (nucleic acid builder), a computer language that is intended for use in creating, describing and modifying macromolecules, especially nucleic acids. Programs written in nab are translated into C, which in turn is compiled into machine code. diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist index f79f228b8b52..ba96f8b296ca 100644 --- a/biology/nab/pkg-plist +++ b/biology/nab/pkg-plist @@ -101,17 +101,6 @@ share/nab/test/write_sander_inp.nab share/nab/test/duplex.nab share/nab/test/ltest.out.check share/nab/test/dg_gyrate.out.check -share/nab/peptide/COPYING -share/nab/peptide/aaaa.pdb -share/nab/peptide/lprot.nab -share/nab/peptide/write_pdb.nab -share/nab/peptide/README -share/nab/peptide/Makefile -share/nab/peptide/conf.lib -share/nab/peptide/peptide.nab -share/nab/peptide/match_template.nab -share/nab/peptide/peptide.c -share/nab/peptide/fix_angles.nab share/nab/suppose/suppose.1 share/nab/suppose/suppose.nab share/nab/dgdb/adna.basepair.db @@ -131,6 +120,8 @@ share/nab/dgdb/trna.stack.db share/nab/dgdb/zdna.basepair.db share/nab/dgdb/zdna.nucleotide.db share/nab/dgdb/zdna.stack.db +share/nab/peptide/peptide.nab +share/nab/peptide/README share/nab/reslib/leap.log share/nab/reslib/hetatm.amber94/hetatm.amber94.chi share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd @@ -301,6 +292,7 @@ share/nab/fd_data/sbdna.dat share/nab/fd_data/abdna.dat share/nab/fd_data/aprna.dat share/nab/fd_data/lbdna.dat +share/nab/fd_data/abdna.dat.old share/nab/coords share/nab/lib/cifparse.a share/nab/lib/libnab.a -- cgit v1.2.3