Update of /cvsroot/fink/dists/10.3/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32338
Modified Files:
ccp4.info ccp4.patch
Log Message:
ccp4 upgrade to Jan15 2005 patch release unstable/sci 10.3
Index: ccp4.info
===================================================================
RCS file: /cvsroot/fink/dists/10.3/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -d -r1.23 -r1.24
--- ccp4.info 15 Jan 2005 03:31:50 -0000 1.23
+++ ccp4.info 18 Jan 2005 05:51:32 -0000 1.24
@@ -1,15 +1,15 @@
Package: ccp4
Version: 5.0.2
-Revision: 11
+Revision: 12
#
-# Revision 10 includes these post-release patches obtained from CCP4 web site
Jan. 10, 2005.
+# Revision 12 includes these post-release patches obtained from CCP4 web site
Jan. 17, 2005.
#
# CCP4_utils-25Aug2004.tcl.diff cmtzlib_f-10Aug2004.c.diff
lsqkab-9Aug2004.f.diff
# abs.f-18Aug2004.f dmmulti-12Aug2004.f.diff
refmac5-13Aug2004.tcl.diff
# ccp4_parser-25Aug2004.c.diff dmmulti_dmlib-12Aug2004.f.diff
unsupported-Makefile.in-11Aug2004.diff
# pdb_utils-17Sep2004.tcl maprot-20Sep2004.f
mapmask-20Sep2004.f
# ccp4i/templates/mapmask.com ccp4i mail interface fixed to work with OSX
Mail.app
-# autosnd-15Nov2004.f cmtzlib_f-24Dec2004.c.diff
+# autosnd-15Nov2004.f cmtzlib_f-24Dec2004.c.diff
cmtzlib_f-14Jan2005.c
#
#
Source: ftp://ftp.%n.ac.uk/%n/current/packed/%n-%v.tar.gz
@@ -128,7 +128,7 @@
License agreement is part of configure file -- print out form and mail in,
additional comments at http://chemistry.ucsc.edu/~wgscott/xtal/page5.html
CCP4 files will be installed under /sw/share/xtal/ccp4-5.0.2
-This revision includes all available CCP4 patches as of Jan. 10, 2005,
+This revision includes all available CCP4 patches as of Jan. 17, 2005,
and new bash and zsh command completions specific to ccp4.
<<
DocFiles: README CHANGES COPYING PROBLEMS INSTALL INSTALL.html INSTALL.ps
ccp4i_installation.html academic_software_licence.pdf
academic_software_licence.ps.gz academic_software_licence.rtf
Index: ccp4.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.3/unstable/main/finkinfo/sci/ccp4.patch,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -d -r1.13 -r1.14
--- ccp4.patch 10 Jan 2005 18:20:13 -0000 1.13
+++ ccp4.patch 18 Jan 2005 05:51:32 -0000 1.14
@@ -753,7 +753,7 @@
This is not a number so get out now */
diff -ruN ccp4-5.0.2-orig/lib/src/cmtzlib_f.c ccp4-5.0.2/lib/src/cmtzlib_f.c
--- ccp4-5.0.2-orig/lib/src/cmtzlib_f.c 2004-07-05 06:23:54.000000000
-0700
-+++ ccp4-5.0.2/lib/src/cmtzlib_f.c 2005-01-10 04:05:27.000000000 -0800
++++ ccp4-5.0.2/lib/src/cmtzlib_f.c 2005-01-17 14:52:03.000000000 -0800
@@ -98,7 +98,7 @@
#include "csymlib.h"
#include "ccp4_program.h"
@@ -772,7 +772,97 @@
ccp4_file_seek(mtzdata[*mindx-1]->filein, respos, SEEK_SET);
}
}
-@@ -2358,6 +2358,7 @@
+@@ -2299,47 +2299,61 @@
+ (const int *mindx, fpstr lsprgo, const int *nlprgo, fpstr
ctprgo, int *iappnd),
+ (const int *mindx, fpstr lsprgo, int lsprgo_len, const int
*nlprgo,
+ fpstr ctprgo, int ctprgo_len, int *iappnd))
+-{int i,j,istart;
++{ int i,j,istart;
+ char *label;
+ char *type;
+ MTZCOL **colarray, *colsort[5];
+
+ CMTZLIB_DEBUG(puts("CMTZLIB_F: LWASSN");)
+
+- if (MtzCheckSubInput(*mindx,"LWASSN",2)) return;
++ if (MtzCheckSubInput(*mindx,"LWASSN",2)) return;
+
+ label = (char *) ccp4_utils_malloc((*nlprgo)*31*sizeof(char));
+ type = (char *) ccp4_utils_malloc((*nlprgo)*3*sizeof(char));
+
+- /* to retain primacy of read structure for copy/rename
+- the read assignments should be done first, then
+- column information should be updated
+- */
++ /* Construct label array to pass to ccp4_lwassn.
++ This has undergone several iterations. Watch out for
++ special cases:
++ output assignment is taken from LABIN e.g. revise
++ (same prog label in lsprgi and lsprgo, and iappnd = 0)
++ dm has same prog label FDM in lsprgi and lsprgo, and
++ iappnd = 1 so these are distinct columns
++ sfall has "labout allin" which should be sorted out by
++ sfall itself
++ */
+ for (i = 0; i < *nlprgo; ++i) {
+- for (j = 0; j != lsprgo_len && lsprgo[lsprgo_len*i+j] != ' ' ; ++j) {
+- label[i*31+j] = lsprgo[lsprgo_len*i+j];
+- }
+- label[i*31+j] = '\0';
+- for (j = 0; j < MCOLUMNS; ++j) {
+- if (strcmp(user_label_in[*mindx-1][j][1],"") &&
!strcmp(user_label_in[*mindx-1][j][0],label+i*31)) {
+- strcpy(label+i*31,user_label_in[*mindx-1][j][1]);
+- break;
+- } /* strcmp if */
+- } /* MCOLUMNS loop */
+-/* use invariance of j */
+- if (j == MCOLUMNS) {
+- if (strcmp(user_label_out[*mindx-1][i][1],"") != 0) {
+- strcpy(label+i*31,user_label_out[*mindx-1][i][1]);
+- }
+- }
+- /* check for duplicated labels */
+- for (j = 0; j < i; ++j)
+- if ( ! strncmp(label+i*31,label+j*31,31) ) {
+- printf("LWASSN: duplicate column labels in output file, columns
%d and %d both have the label %s \n",j,i,label+i*31);
+- ccperror(1,"Duplicate column labels in output file");
++
++ /* set label to program default */
++ for (j = 0; j != 30 && j != lsprgo_len && lsprgo[lsprgo_len*i+j] != ' '
; ++j) {
++ label[i*31+j] = lsprgo[lsprgo_len*i+j];
++ }
++ label[i*31+j] = '\0';
++
++ /* if there was a user output assignment (LABOUT), overwrite
++ with this */
++ if (strcmp(user_label_out[*mindx-1][i][1],"")) {
++ strcpy(label+i*31,user_label_out[*mindx-1][i][1]);
++ } else {
++
++ /* else check for input assignment (see e.g. revise.exam) */
++ for (j = 0; j < MCOLUMNS; ++j) {
++ if (strcmp(user_label_in[*mindx-1][j][1],"") &&
!strcmp(user_label_in[*mindx-1][j][0],label+i*31)) {
++ strcpy(label+i*31,user_label_in[*mindx-1][j][1]);
++ break;
+ }
++ }
++
++ }
++
++ /* check for duplicated labels */
++ for (j = 0; j < i; ++j)
++ if ( ! strncmp(label+i*31,label+j*31,31) ) {
++ printf("LWASSN: duplicate column labels in output file, columns %d
and %d both have the label %s \n",j,i,label+i*31);
++ ccperror(1,"Duplicate column labels in output file");
++ }
++
++ } /* end of labels loop */
+
+- } /* nlprgo for */
+ /* types loop */
+ for (i = 0; i < *nlprgo; ++i) {
+ for (j = 0; j < 2; ++j) {
+@@ -2358,6 +2372,7 @@
/* assign new columns for output */
colarray = ccp4_lwassn(mtzdata[*mindx-1],label,*nlprgo,type,*iappnd);
@@ -780,11 +870,16 @@
for (j = 0; j < 5; ++j)
colsort[j] = NULL;
for (i = 0; i < *nlprgo; ++i) {
-@@ -2367,7 +2368,12 @@
+@@ -2367,12 +2382,12 @@
if (sortorder[*mindx-1][j] == (i + 1))
colsort[j] = colarray[i];
}
- MtzSetSortOrder(mtzdata[*mindx-1],colsort);
+-
+- /* now must update col data for write */
+- for (i = 0; i < *nlprgo; ++i)
+- if (strcmp(user_label_out[*mindx-1][i][1],"") )
strcpy(colarray[i]->label,user_label_out[*mindx-1][i][1]);
+- /*should confirm ctype */
+
+ /* If LWSORT has been called, then sortorder[][] should be set, and we
make
+ sure sort order is up-to-date with output columns. If sortorder[][] not
@@ -792,9 +887,9 @@
+ if (sortorder[*mindx-1][0])
+ MtzSetSortOrder(mtzdata[*mindx-1],colsort);
- /* now must update col data for write */
- for (i = 0; i < *nlprgo; ++i)
-@@ -2435,6 +2441,7 @@
+ free(colarray);
+ free(label);
+@@ -2435,6 +2450,7 @@
/* assign new columns for output */
colarray = ccp4_lwassn(mtzdata[*mindx-1],label,*nlprgo,type,*iappnd);
@@ -802,7 +897,7 @@
for (j = 0; j < 5; ++j)
colsort[j] = NULL;
for (i = 0; i < *nlprgo; ++i) {
-@@ -2444,7 +2451,12 @@
+@@ -2444,7 +2460,12 @@
if (sortorder[*mindx-1][j] == (i + 1))
colsort[j] = colarray[i];
}
@@ -818,8 +913,8 @@
free(label);
diff -ruN ccp4-5.0.2-orig/lib/src/cmtzlib_f.c.orig
ccp4-5.0.2/lib/src/cmtzlib_f.c.orig
--- ccp4-5.0.2-orig/lib/src/cmtzlib_f.c.orig 1969-12-31 16:00:00.000000000
-0800
-+++ ccp4-5.0.2/lib/src/cmtzlib_f.c.orig 2005-01-10 04:04:38.000000000
-0800
-@@ -0,0 +1,3010 @@
++++ ccp4-5.0.2/lib/src/cmtzlib_f.c.orig 2005-01-17 14:51:52.000000000
-0800
+@@ -0,0 +1,3019 @@
+/*
+ cmtzlib_f.c: Fortran API to CMTZlib
+ Copyright (C) 2001 CCLRC, Martyn Winn
@@ -3121,47 +3216,61 @@
+ (const int *mindx, fpstr lsprgo, const int *nlprgo, fpstr
ctprgo, int *iappnd),
+ (const int *mindx, fpstr lsprgo, int lsprgo_len, const int
*nlprgo,
+ fpstr ctprgo, int ctprgo_len, int *iappnd))
-+{int i,j,istart;
++{ int i,j,istart;
+ char *label;
+ char *type;
+ MTZCOL **colarray, *colsort[5];
+
+ CMTZLIB_DEBUG(puts("CMTZLIB_F: LWASSN");)
+
-+ if (MtzCheckSubInput(*mindx,"LWASSN",2)) return;
++ if (MtzCheckSubInput(*mindx,"LWASSN",2)) return;
+
+ label = (char *) ccp4_utils_malloc((*nlprgo)*31*sizeof(char));
+ type = (char *) ccp4_utils_malloc((*nlprgo)*3*sizeof(char));
+
-+ /* to retain primacy of read structure for copy/rename
-+ the read assignments should be done first, then
-+ column information should be updated
-+ */
++ /* Construct label array to pass to ccp4_lwassn.
++ This has undergone several iterations. Watch out for
++ special cases:
++ output assignment is taken from LABIN e.g. revise
++ (same prog label in lsprgi and lsprgo, and iappnd = 0)
++ dm has same prog label FDM in lsprgi and lsprgo, and
++ iappnd = 1 so these are distinct columns
++ sfall has "labout allin" which should be sorted out by
++ sfall itself
++ */
+ for (i = 0; i < *nlprgo; ++i) {
-+ for (j = 0; j != lsprgo_len && lsprgo[lsprgo_len*i+j] != ' ' ; ++j) {
-+ label[i*31+j] = lsprgo[lsprgo_len*i+j];
-+ }
-+ label[i*31+j] = '\0';
-+ for (j = 0; j < MCOLUMNS; ++j) {
-+ if (strcmp(user_label_in[*mindx-1][j][1],"") &&
!strcmp(user_label_in[*mindx-1][j][0],label+i*31)) {
-+ strcpy(label+i*31,user_label_in[*mindx-1][j][1]);
-+ break;
-+ } /* strcmp if */
-+ } /* MCOLUMNS loop */
-+/* use invariance of j */
-+ if (j == MCOLUMNS) {
-+ if (strcmp(user_label_out[*mindx-1][i][1],"") != 0) {
-+ strcpy(label+i*31,user_label_out[*mindx-1][i][1]);
-+ }
-+ }
-+ /* check for duplicated labels */
-+ for (j = 0; j < i; ++j)
-+ if ( ! strncmp(label+i*31,label+j*31,31) ) {
-+ printf("LWASSN: duplicate column labels in output file, columns
%d and %d both have the label %s \n",j,i,label+i*31);
-+ ccperror(1,"Duplicate column labels in output file");
++
++ /* set label to program default */
++ for (j = 0; j != 30 && j != lsprgo_len && lsprgo[lsprgo_len*i+j] != ' '
; ++j) {
++ label[i*31+j] = lsprgo[lsprgo_len*i+j];
++ }
++ label[i*31+j] = '\0';
++
++ /* if there was a user output assignment (LABOUT), overwrite
++ with this */
++ if (strcmp(user_label_out[*mindx-1][i][1],"")) {
++ strcpy(label+i*31,user_label_out[*mindx-1][i][1]);
++ } else {
++
++ /* else check for input assignment (see e.g. revise.exam) */
++ for (j = 0; j < MCOLUMNS; ++j) {
++ if (strcmp(user_label_in[*mindx-1][j][1],"") &&
!strcmp(user_label_in[*mindx-1][j][0],label+i*31)) {
++ strcpy(label+i*31,user_label_in[*mindx-1][j][1]);
++ break;
+ }
++ }
++
++ }
++
++ /* check for duplicated labels */
++ for (j = 0; j < i; ++j)
++ if ( ! strncmp(label+i*31,label+j*31,31) ) {
++ printf("LWASSN: duplicate column labels in output file, columns %d
and %d both have the label %s \n",j,i,label+i*31);
++ ccperror(1,"Duplicate column labels in output file");
++ }
++
++ } /* end of labels loop */
+
-+ } /* nlprgo for */
+ /* types loop */
+ for (i = 0; i < *nlprgo; ++i) {
+ for (j = 0; j < 2; ++j) {
@@ -3197,11 +3306,6 @@
+ if (sortorder[*mindx-1][0])
+ MtzSetSortOrder(mtzdata[*mindx-1],colsort);
+
-+ /* now must update col data for write */
-+ for (i = 0; i < *nlprgo; ++i)
-+ if (strcmp(user_label_out[*mindx-1][i][1],"") )
strcpy(colarray[i]->label,user_label_out[*mindx-1][i][1]);
-+ /*should confirm ctype */
-+
+ free(colarray);
+ free(label);
+ free(type);
-------------------------------------------------------
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