Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv1598
Modified Files:
freehelix.info freehelix.patch
Log Message:
move newer freehelix to stable. uses gfortran instead of fort77
Index: freehelix.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/freehelix.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- freehelix.patch 25 Jan 2006 06:20:10 -0000 1.1
+++ freehelix.patch 14 Jun 2011 11:34:21 -0000 1.2
@@ -1,26 +1,178 @@
---- ./freehel98.for Thu Nov 4 12:42:00 1999
-+++ .-patched/freehel98.for Mon Sep 23 11:35:32 2002
-@@ -2349,8 +2349,7 @@
- DATA NMAX/2000/,IBL/' '/,ZER/'0'/,O1/'O1'''/,FOUR/'4'/
+diff -Naur ../freehelix98old/freehel98.for ./freehel98.for
+--- ../freehelix98old/freehel98.for 2006-07-28 00:00:00.000000000 +0200
++++ ./freehel98.for 2009-09-12 11:53:38.000000000 +0200
+@@ -2350,7 +2350,7 @@
DATA IST/'*'/
READ(*,'(A80)') INP
-- OPEN(UNIT=L11,FILE=INP(1:(index(INP,' ')-1)),STATUS='OLD',
+ OPEN(UNIT=L11,FILE=INP(1:(index(INP,' ')-1)),STATUS='OLD',
- * READONLY)
-+ OPEN(UNIT=L11,FILE=INP(1:(index(INP,' ')-1)),STATUS='OLD')
++ * action='read')
C OPEN(UNIT=L11,STATUS='OLD',READONLY)
IB=3
NOCH=6
-
---- ./test.com Thu Nov 4 12:42:00 1999
-+++ .-patched/test.com Tue Oct 15 21:21:54 2002
-@@ -3,8 +3,8 @@
+diff -Naur ../freehelix98old/freehelix.patch ./freehelix.patch
+--- ../freehelix98old/freehelix.patch 1970-01-01 01:00:00.000000000 +0100
++++ ./freehelix.patch 2009-09-12 12:36:51.000000000 +0200
+@@ -0,0 +1,12 @@
++diff -Naur ../freehelix98old/freehel98.for ./freehel98.for
++--- ../freehelix98old/freehel98.for 2006-07-28 00:00:00.000000000 +0200
+++++ ./freehel98.for 2009-09-12 11:53:38.000000000 +0200
++@@ -2350,7 +2350,7 @@
++ DATA IST/'*'/
++ READ(*,'(A80)') INP
++ OPEN(UNIT=L11,FILE=INP(1:(index(INP,' ')-1)),STATUS='OLD',
++- * READONLY)
+++ * action='read')
++ C OPEN(UNIT=L11,STATUS='OLD',READONLY)
++ IB=3
++ NOCH=6
+diff -Naur ../freehelix98old/sel98.for ./sel98.for
+--- ../freehelix98old/sel98.for 2006-07-28 00:00:00.000000000 +0200
++++ ./sel98.for 2009-09-12 12:17:40.000000000 +0200
+@@ -59,9 +59,9 @@
+ C
+ 102 READ(*,1)TNAME
+ IF(TNAME.NE.' BASE PAIR N')GO TO 102
+- READ(*,3)
+- READ(*,3)
+- READ(*,3)
++ READ(*,333)
++ READ(*,333)
++ READ(*,333)
+ C
+ C READ IN X,Y NORMAL COSINES
+ C
+@@ -81,12 +81,12 @@
+ C
+ C READ IN NORMAL ANGLE MATRIX
+ C
+- READ(*,3)
+- READ(*,3)
+- READ(*,3)
++ READ(*,333)
++ READ(*,333)
++ READ(*,333)
+ READ(*,452)(NJAY(J),J=1,NBPR)
+ 452 FORMAT(8X,50I4)
+- READ(*,3)
++ READ(*,333)
+ DO 453 I=1,NBPR
+ READ(*,452)(IANGALL(I,J),J=1,NBPR)
+ 453 CONTINUE
+@@ -101,12 +101,12 @@
+ C
+ C READ IN 1ST HALF OF NORMAL ANGLE MATRIX
+ C
+- READ(*,3)
+- READ(*,3)
+- READ(*,3)
++ READ(*,333)
++ READ(*,333)
++ READ(*,333)
+ READ(*,852)(NJAY(J),J=1,25)
+ 852 FORMAT(8X,50I4)
+- READ(*,3)
++ READ(*,333)
+ DO 853 I=1,NBPR
+ READ(*,852)(IANGALL(I,J),J=1,25)
+ 853 CONTINUE
+@@ -120,12 +120,12 @@
+ C
+ C READ IN 2ND HALF OF NORMAL ANGLE MATRIX
+ C
+- READ(*,3)
+- READ(*,3)
+- READ(*,3)
++ READ(*,333)
++ READ(*,333)
++ READ(*,333)
+ READ(*,952)(NJAY(J),J=26,NBPR)
+ 952 FORMAT(8X,50I4)
+- READ(*,3)
++ READ(*,333)
+ DO 953 I=1,NBPR
+ READ(*,952)(IANGALL(I,J),J=26,NBPR)
+ 953 CONTINUE
+@@ -138,8 +138,9 @@
+ 1 FORMAT(A12)
+ IF(TNAME.NE.' BEST PLANE')GO TO 2
+ DO 10 J=1,3
+-10 READ(*,3)
++10 READ(*,333)
+ 3 FORMAT(1H )
++333 FORMAT(1X)
+ C
+ C READ IN TABLES OF BASE STEPS AND BASE PAIRS FROM BROLL
+ C
+@@ -158,7 +159,7 @@
+ 6 READ(*,1)TNAME
+ IF(TNAME.NE.' ROTATION ')GO TO 6
+ DO 7 K=1,5
+-7 READ(*,3)
++7 READ(*,333)
+ C
+ C READ IN FIRST TABLES FROM CYLIN
+ C
+@@ -171,7 +172,7 @@
+ C
+ 11 READ(*,1)TNAME
+ IF(TNAME.NE.' STRAND 2')GO TO 11
+- READ(*,3)
++ READ(*,333)
+ C
+ C READ IN SECOND TABLES FROM CYLIN
+ C
+@@ -186,7 +187,7 @@
+ C
+ 14 READ(*,1)TNAME
+ IF(TNAME.NE.' ALPHA ')GO TO 14
+- READ(*,3)
++ READ(*,333)
+ C
+ C READ FIRST TORAN LIST
+ C
+@@ -199,7 +200,7 @@
+ C
+ 47 READ(*,1)TNAME
+ IF(TNAME.NE.' ALPHA ')GO TO 47
+- READ(*,3)
++ READ(*,333)
+ C
+ C READ SECOND TORAN LIST
+ C
+@@ -212,7 +213,7 @@
+ C
+ 50 READ(*,1)TNAME
+ IF(TNAME.NE.' V0 ')GO TO 50
+- READ(*,3)
++ READ(*,333)
+ C
+ C READ FIRST PSEUDO VALUES
+ C
+@@ -225,7 +226,7 @@
+ C
+ 60 READ(*,1)TNAME
+ IF(TNAME.NE.' V0 ')GO TO 60
+- READ(*,3)
++ READ(*,333)
+ C
+ C READ SECOND PSEUDO VALUES
+ C
+diff -Naur ../freehelix98old/test.com ./test.com
+--- ../freehelix98old/test.com 2006-07-28 00:00:00.000000000 +0200
++++ ./test.com 2009-09-12 11:27:44.000000000 +0200
+@@ -1,10 +1,10 @@
+-#command file for freehel97 on UNIX machines tkc 1/23/98
+-#for meaning of keywords, refer to freehel98.tex
++#command file for freehel98 on UNIX machines tkc 1/23/98
++#for meaning of keywords, refer to freehel98.txt
#*.dat, *.PDB, & *.po4 files have the pdb filename (represented as *) as
prefix
#******* enter the pdb file name on the line after the 'END' keyword *******
#
-echo "Executing newhel98 ..."
-freehel97.exe<<eof>test.freehelix
+echo "Executing freehel98 ..."
-+@prefix@/bin/freehel98<<eof>test.freehelix
++freehel98 <<eof >test.freehelix
TITL TBPJ C-G-T-A-T-A-T-A-T-A-C-G Juo & Dickerson--Human TBP/DNA
CELL 1., 1., 1., 90., 90., 90.
BRKH
@@ -32,6 +184,5 @@
+echo "freehel98 finished and output as *.out, *.PDB, *.dat, and *.po4 "
echo "Executing sel98 ..."
-sel98.exe <test.freehelix >test.sel
-+@prefix@/bin/sel98 <test.freehelix >test.sel
++sel98 <test.freehelix >test.sel
echo "sel98 finished. "
-
Index: freehelix.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/freehelix.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- freehelix.info 29 Mar 2009 08:30:33 -0000 1.2
+++ freehelix.info 14 Jun 2011 11:34:21 -0000 1.3
@@ -1,52 +1,74 @@
Package: freehelix
Version: 98
-Revision: 11
-Maintainer: None <[email protected]>
-BuildDepends: fort77 (>= 1.18-15), fink (>= 0.24.12-1)
+Revision: 12
+Description: Nucleic acid helix analysis program
+License: Restrictive
+
+DescDetail: <<
+Freehelix is a substantially modified version of Newhelix, designed
+specifically for the analysis of radically bent and kinked DNA double
+helices.
+<<
+
+BuildDepends: gcc44, fink (>= 0.24.12-1)
+
Source: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/freehel%v.for
Source2: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/sel%v.for
Source3: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/freehel.tex
Source4: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/test.com
Source5: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/test.inp
+Source6: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/README
Source-MD5: 6bd8ecb84a087dfad0d3464e204e1a3f
Source2-MD5: 559cc8a1804a7f583766749bd92bb6f5
Source3-MD5: 2e79bba04111965eb6bf5f0917a6736d
Source4-MD5: 718841fe4ef3a6dce5ab55a60b766b5c
Source5-MD5: e8d854a995ff8cb90c4c49d00b498b1b
+Source6-MD5: 655b85d66b4d06de8d6b61393fa444c7
+
SourceDirectory: .
PatchFile: %n.patch
-PatchFile-MD5: f6214caa512d76181825b607bc727427
-PatchScript: sed 's|@prefix@|%p|g' <%{PatchFile} | patch -p1
+PatchFile-MD5: 61f00f63de1bb8d794329243259447b9
+
+PatchScript: <<
+ sed 's|@prefix@|%p|g' <%{PatchFile} | patch -p1
+ chmod -x README
+ chmod +x test.com
+<<
+
CompileScript: <<
-cp freehel98.for freehel98.f
-cp sel98.for sel98.f
-fort77 -O3 -w -o freehel98 freehel98.f
-fort77 -O3 -o sel98 sel98.f
+ gfortran -O3 -ffixed-form -w -o freehel98 freehel98.for
+ gfortran -O3 -ffixed-form -o sel98 sel98.for
<<
+
InstallScript: <<
-mkdir -p %i/bin
-mkdir -p %i/share/freehelix/examples
-install -c -m 755 freehel98 sel98 %i/bin
-install -c -m 755 test.com test.inp %i/share/freehelix/examples
+ mkdir -p %i/bin
+ mkdir -p %i/share/freehelix/examples
+ install -c -m 755 freehel98 sel98 %i/bin
+ install -c -m 755 test.com test.inp %i/share/freehelix/examples
<<
-DocFiles: freehel.tex
-Description: Nucleic acid helix analysis program
-DescDetail: <<
- Freehelix is a substantially modified version of Newhelix, designed
-specifically for the analysis of radically bent and kinked DNA double
-helices.
+
+DocFiles: freehel.tex:freehel.txt README
+
+InfoTest: <<
+TestScript: ./test.com || exit 2
<<
-Descusage: <<
- For instructions on how to use refer to the document 'freehel.tex' found
+
+DescUsage: <<
+For instructions on how to use refer to the document 'freehel.txt' found
in your finkdirectory/share/doc/freehelix. There is an example script
installed in your finkdirectory/share/freehelix/examples.
<<
+
DescPort: <<
- Use fort77 instead of g77 to build due to sel98 crashing with a bus error
+2009-09-12
+- Patches and fixes to enable compilation with gfortran
+- enable testscript
+- README added to DocFiles
+????-??-??
+Use fort77 instead of g77 to build due to sel98 crashing with a bus error
when compiled with g77.
<<
-DescPackaging: <<
- Originally packaged by Matt Stephenson.
-<<
-License: Restrictive
+
+DescPackaging: Originally packaged by Matt Stephenson.
Homepage:
http://www.csb.yale.edu/userguides/datamanip/freehelix/freehelix_descrip.html
+Maintainer: Karl-Michael Schindler <[email protected]>
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