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biology/seaview: Update version 5.0.4=>5.0.5

Browse Source 
Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES
This commit is contained in:
Muhammad Moinur Rahman 2021-12-05 16:44:15 -06:00
parent fe90667bc2
commit 908f72ff10
3 changed files with 4 additions and 77 deletions
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5
biology/seaview/Makefile
View File

@ -1,7 +1,7 @@
# Created by: frankch@waru.life.nthu.edu.tw # Created by: frankch@waru.life.nthu.edu.tw
PORTNAME= seaview PORTNAME= seaview
PORTVERSION= 5.0.4 PORTVERSION= 5.0.5
PORTEPOCH= 1 PORTEPOCH= 1
CATEGORIES= biology CATEGORIES= biology
MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/ MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
@ -37,9 +37,6 @@ post-patch:
${REINPLACE_CMD} -e \ ${REINPLACE_CMD} -e \
's|^\(CC\) |#\1 | ; s|-ldl || ; \ 's|^\(CC\) |#\1 | ; s|-ldl || ; \
s|^\(CXX\) |#\1 |' ${WRKSRC}/Makefile s|^\(CXX\) |#\1 |' ${WRKSRC}/Makefile
${REINPLACE_CMD} -E \
'/firstplotblock|javarun|\*progname/s,^,extern ,' \
${WRKSRC}/csrc/phylip.h ${WRKSRC}/csrc/protpars.c
${ECHO_CMD} 'boolean javarun;' >> ${WRKSRC}/csrc/phylip.c ${ECHO_CMD} 'boolean javarun;' >> ${WRKSRC}/csrc/phylip.c
do-install: do-install:

6
biology/seaview/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1592674569 TIMESTAMP = 1638663734
SHA256 (seaview_5.0.4.tar.gz) = e153e7fe1dd0b466ce7a00e8b78d5d232aa26063ab82f78eb43811780c41d727 SHA256 (seaview_5.0.5.tar.gz) = ce8f5e98ba47883bfa91e91bc79e4d3a26f158dd9983b5e78331a452a4b1f8f2
SIZE (seaview_5.0.4.tar.gz) = 472837 SIZE (seaview_5.0.5.tar.gz) = 471739

70
biology/seaview/files/patch-csrc_dnapars.c
View File

@ -1,70 +0,0 @@
--- csrc/dnapars.c.orig 2019-11-29 14:00:33 UTC
+++ csrc/dnapars.c
@@ -77,41 +77,44 @@ void load_tree(long treei);
/* function prototypes */
-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
+extern Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
weightfilename[FNMLNGTH];
char basechar[32]="ACMGRSVTWYHKDBNO???????????????";
-node *root;
-long chars, col, msets, ith, njumble, jumb, maxtrees;
+extern node *root;
+extern long chars, col, msets, ith, njumble, jumb;
+long maxtrees;
/* chars = number of sites in actual sequences */
-long inseed, inseed0;
-double threshold;
-boolean jumble, usertree, thresh, weights, thorough, rearrfirst,
- trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf,
- multf;
+extern long inseed, inseed0;
+extern double threshold;
+extern boolean jumble, usertree, thresh, weights,
+ trout, progress, stepbox, ancseq, mulsets, justwts, firstset;
+boolean thorough, rearrfirst, mulf, multf;
steptr oldweight;
-longer seed;
-pointarray treenode; /* pointers to all nodes in tree */
-long *enterorder;
+extern longer seed;
+extern pointarray treenode; /* pointers to all nodes in tree */
+extern long *enterorder;
long *zeros;
/* local variables for Pascal maketree, propagated globally for C version: */
-long minwhich;
+extern long minwhich;
static double like, minsteps, bestyet, bestlike, bstlike2;
-boolean lastrearr, recompute;
-double nsteps[maxuser];
-long **fsteps;
-node *there, *oldnufork;
-long *place;
-bestelm *bestrees;
-long *threshwt;
+extern boolean lastrearr, recompute;
+extern double nsteps[maxuser];
+extern long **fsteps;
+extern node *there;
+node *oldnufork;
+extern long *place;
+extern bestelm *bestrees;
+extern long *threshwt;
baseptr nothing;
-gbases *garbage;
-node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
+extern gbases *garbage;
+extern node *temp, *temp1;
+node *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
*tmp2, *tmp3, *tmprm, *tmpadd;
-boolean *names;
+extern boolean *names;
node *grbg;
-char *progname;
+extern char *progname;
static void getoptions(int arg_maxtrees, dnapars_S_option s_option)