rpms/elph/FC-5 elph-chris.patch, NONE, 1.1 elph.spec, NONE, 1.1 .cvsignore, 1.1, 1.2 sources, 1.1, 1.2

[Christian Iseli (c4chris)]

Author: c4chris

Update of /cvs/extras/rpms/elph/FC-5
In directory cvs-int.fedora.redhat.com:/tmp/cvs-serv15964

Modified Files:
	.cvsignore sources 
Added Files:
	elph-chris.patch elph.spec 
Log Message:
Import elph.spec elph-chris.patch.

elph-chris.patch:

--- NEW FILE elph-chris.patch ---
--- ELPH/sources/elph.cc.chris	2007-02-09 23:29:11.000000000 +0100
+++ ELPH/sources/elph.cc	2007-02-09 23:29:26.000000000 +0100
@@ -43,7 +43,7 @@
                    default = 500\n\
   SGFNO=n        : n = no of iterations to compute significance of motif;\n\
                    default = 1000\n\
- "
+"
 
 /* I am eliminating the following option from help file because it has no effect because I am never shuffling the file
   -z             : when using the makov chain file generation, don't exhaust\n\
--- ELPH/sources/GBase.h.chris	2006-09-28 19:07:25.000000000 +0200
+++ ELPH/sources/GBase.h	2007-02-09 23:21:52.000000000 +0100
@@ -61,13 +61,16 @@
 typedef void GFreeProc(pointer item); //usually just delete,
       //but may also support structures with embedded dynamic members
 
-#define GMALLOC(ptr,size)  if (!GMalloc((pointer*)(&ptr),size)) \
-                                     GError(ERR_ALLOC)
-#define GCALLOC(ptr,size)  if (!GCalloc((pointer*)(&ptr),size)) \
-                                     GError(ERR_ALLOC)
-#define GREALLOC(ptr,size) if (!GRealloc((pointer*)(&ptr),size)) \
-                                     GError(ERR_ALLOC)
-#define GFREE(ptr)       GFree((pointer*)(&ptr))
+#define GMALLOC(ptr,size) \
+  if ((ptr = static_cast<typeof(ptr)>(malloc(size))) == NULL) \
+    GError(ERR_ALLOC)
+#define GCALLOC(ptr,size) \
+  if ((ptr = static_cast<typeof(ptr)>(calloc(size, 1))) == NULL) \
+    GError(ERR_ALLOC)
+#define GREALLOC(ptr,size) \
+  if ((ptr = static_cast<typeof(ptr)>(realloc(ptr,size))) == NULL && size != 0) \
+    GError(ERR_ALLOC)
+#define GFREE(ptr)       free(ptr)
 
 
 


--- NEW FILE elph.spec ---
Name:           elph
Version:        1.0.1
Release:        1%{?dist}
Summary:        Tool to find motifs in a set of DNA or protein sequences

Group:          Applications/Engineering
License:        Artistic
URL:            http://www.cbcb.umd.edu/software/ELPH/
Source0:        ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-1.0.1.tar.gz
Patch0:         %{name}-chris.patch
BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)

%description
ELPH is a general-purpose Gibbs sampler for finding motifs in a set of
DNA or protein sequences. The program takes as input a set containing
anywhere from a few dozen to thousands of sequences, and searches
through them for the most common motif, assuming that each sequence
contains one copy of the motif.


%prep
%setup -q -n ELPH
%patch0 -p 1 -b .chris


%build
make -C sources %{?_smp_mflags} \
  CFLAGS="$RPM_OPT_FLAGS -fno-exceptions -fno-rtti -D_REENTRANT"


%check


%install
rm -rf $RPM_BUILD_ROOT
mkdir -p $RPM_BUILD_ROOT%{_bindir}
install -m 755 sources/elph $RPM_BUILD_ROOT/%{_bindir}


%clean
rm -rf $RPM_BUILD_ROOT


%files
%defattr(-,root,root,-)
%doc COPYRIGHT LICENSE README Readme.ELPH VERSION
%{_bindir}/elph


%changelog
* Thu Feb 22 2007 Christian Iseli <Christian.Iseli at licr.org> 1.0.1-1
 - Import in FC-5.

* Fri Feb  9 2007 Christian Iseli <Christian.Iseli at licr.org> 1.0.1-0
 - Create spec file.


Index: .cvsignore
===================================================================
RCS file: /cvs/extras/rpms/elph/FC-5/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- .cvsignore	22 Feb 2007 13:36:21 -0000	1.1
+++ .cvsignore	22 Feb 2007 16:24:47 -0000	1.2
@@ -0,0 +1 @@
+ELPH-1.0.1.tar.gz


Index: sources
===================================================================
RCS file: /cvs/extras/rpms/elph/FC-5/sources,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- sources	22 Feb 2007 13:36:21 -0000	1.1
+++ sources	22 Feb 2007 16:24:47 -0000	1.2
@@ -0,0 +1 @@
+eb96b4dde3ab12ba1f31a4230a829ff3  ELPH-1.0.1.tar.gz