[med-svn] [paml] 01/03: *.ctl files are pointing to existing data files in /usr/lib/paml/data, *.ctl files are symlinked to /etc/paml and found properly by the according code

[Andreas Tille]

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tille pushed a commit to branch master
in repository paml.

commit 62c6d22a7542dc3f5a7a09e50818ec920b7acb2b
Author: Andreas Tille <tille at debian.org>
Date:   Tue May 3 14:23:58 2016 +0200

    *.ctl files are pointing to existing data files in /usr/lib/paml/data, *.ctl files are symlinked to /etc/paml and found properly by the
        according code
---
 debian/changelog                      |  3 ++
 debian/patches/ctl_files_in_etc.patch | 96 +++++++++++++++++++++++++++++++++++
 debian/patches/series                 |  1 +
 3 files changed, 100 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 3bddab3..64804f0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,9 @@ paml (4.91+dfsg-1) UNRELEASED; urgency=medium
   * cme fix dpkg-control
   * Removed *.pdf files since there is no source for theses files
   * Add clean target to upstream Makefile
+  * *.ctl files are pointing to existing data files in /usr/lib/paml/data
+  * *.ctl files are symlinked to /etc/paml and found properly by the
+    according code
 
  -- Andreas Tille <tille at debian.org>  Mon, 02 May 2016 15:37:17 +0200
 
diff --git a/debian/patches/ctl_files_in_etc.patch b/debian/patches/ctl_files_in_etc.patch
new file mode 100644
index 0000000..6398d79
--- /dev/null
+++ b/debian/patches/ctl_files_in_etc.patch
@@ -0,0 +1,96 @@
+Description: Debian package symlinks *.ctl files to /etc/paml.  This patch
+ ensures that the code is seeking at the same location.
+Author: Andreas Tille <tille at debian.org>
+Last-Update Mon, 02 May 2016 15:37:17 +0200
+
+--- a/src/baseml.c
++++ b/src/baseml.c
+@@ -132,7 +132,7 @@ int main (int argc, char *argv[])
+ {
+    FILE *fout, *fseq=NULL, *fpair[6];
+    char pairfs[1][32]={"2base.t"};
+-   char rstf[512]="rst", ctlf[512]="baseml.ctl", timestr[64];
++   char rstf[512]="rst", ctlf[512]="/etc/paml/baseml.ctl", timestr[64];
+    char *Mgenestr[]={"diff. rate", "separate data", "diff. rate & pi", 
+                      "diff. rate & kappa", "diff. rate & pi & kappa"};
+    int getdistance=1, i, idata;
+--- a/src/basemlg.c
++++ b/src/basemlg.c
+@@ -83,7 +83,7 @@ int main (int argc, char *argv[])
+ {
+    FILE *fout, *fseq=NULL, *fpair[6];
+    char pairfs[1][32]={"2base.t"};
+-   char ctlf[96]="baseml.ctl";
++   char ctlf[512]="/etc/paml/baseml.ctl";
+    double  space[50000];
+ 
+    noisy=2;  com.cleandata=1;  /* works with clean data only */
+@@ -810,7 +810,7 @@ int GetOptions (char *ctlf)
+    if (com.alpha<=0) error2("init alpha..");
+    if (com.alpha==0 || com.Malpha || com.rho>0 || com.nhomo>0 || com.nparK>0 
+       || com.model>HKY85)
+-       error2 ("\noptions in file baseml.ctl inappropriate.. giving up..");
++       error2 ("\noptions in file /etc/paml/baseml.ctl inappropriate.. giving up..");
+    if (com.model==JC69 || com.model==F81) { com.fix_kappa=1; com.kappa=1; }
+    if(com.cleandata==0) { 
+       puts("cleandata set to 1, with ambiguity data removed. ");
+--- a/src/codeml.c
++++ b/src/codeml.c
+@@ -242,7 +242,7 @@ int main (int argc, char *argv[])
+ {
+    FILE *fseq=NULL, *fpair[6]; 
+    char pairfs[6][32]={"2NG.dS","2NG.dN","2NG.t", "2ML.dS","2ML.dN","2ML.t"};
+-   char ctlf[96]="codeml.ctl", *pmodel, timestr[64];
++   char ctlf[512]="/etc/paml/codeml.ctl", *pmodel, timestr[64];
+    char *seqtypestr[3]={"CODONML", "AAML", "CODON2AAML"};
+    char *Mgenestr[]={"diff. rate", "separate data", "diff. rate & pi", 
+                      "diff. rate & k&w", "diff. rate & pi & k&w"};
+@@ -1448,7 +1448,7 @@ void DetailOutput (FILE *fout, double x[
+ 
+ void ReadNSsitesModels(char *line)
+ {
+-/* This reads the line  NSsites = 0 1 2 3 7 8  in codeml.ctl.
++/* This reads the line  NSsites = 0 1 2 3 7 8  in /etc/paml/codeml.ctl.
+ */
+    char *pline;
+    int pop_digit;
+--- a/src/mcmctree.c
++++ b/src/mcmctree.c
+@@ -191,7 +191,7 @@ char *Btransform[]={"", "square root", "
+ 
+ int main (int argc, char *argv[])
+ {
+-   char ctlf[512] = "mcmctree.ctl";
++   char ctlf[512] = "/etc/paml/mcmctree.ctl";
+    int i, j, k=4;
+    FILE  *fout;
+ 
+--- a/src/pamp.c
++++ b/src/pamp.c
+@@ -1,5 +1,5 @@
+ /* PAMP.c, Copyright, Ziheng Yang, April 1995.
+-   Specify the sequence type in the file pamp.ctl.  Results go into mp.
++   Specify the sequence type in the file /etc/paml/pamp.ctl.  Results go into mp.
+ 
+                     gcc -o pamp pamp.c tools.o
+                     pamp <ControlFileName>
+@@ -68,7 +68,7 @@ int LASTROUND=0; /* no use for this */
+ int main (int argc, char *argv[])
+ {
+    FILE *ftree, *fout, *fseq;
+-   char ctlf[32]="pamp.ctl";
++   char ctlf[512]="/etc/paml/pamp.ctl";
+    char *Seqstr[]={"nucleotide", "", "amino-acid", "Binary"};
+    int itree, ntree, i, j, s3;
+    double *space, *Ft;
+--- a/src/yn00.c
++++ b/src/yn00.c
+@@ -74,7 +74,7 @@ int main(int argc, char *argv[])
+ {
+    char dsf[512]="2YN.dS", dnf[512]="2YN.dN", tf[512]="2YN.t";
+    FILE *fout, *fseq, *fds, *fdn, *ft;
+-   char ctlf[96]="yn00.ctl", timestr[64];
++   char ctlf[512]="/etc/paml/yn00.ctl", timestr[64];
+    int    n=com.ncode, is,js, j, idata, wname=20, sspace;
+    double t=0.4, dS=0.1,dN=0.1, S,N, SEdS, SEdN, f3x4[12], *space=NULL;
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 8135895..0727394 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 fix_format_security.patch
 hardening.patch
 add_clean_target.patch
+ctl_files_in_etc.patch

-- 
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