Patches for Glimmer to work with gcc-4.3
Hi,
when packaging Glimmer for the Debian GNU/Linux distributions which
will have GCC 4.3 as the default compiler of the upcomming next
release I had to do some patches I would like to send you for your
personal comfort. Feel free to apply these to your source to be
safe, that it compiles nicely for every user. (10_gcc4.3.patch)
Moreover I created a very simple Makefile that simplifies to build
the package from the base directory of Glimmer whicm makes packaging
more handy if you uses the cdbs tool for Debian packaging. I have
no idea whether you want to use this - but in case you are interested
feel free to use it or adapt it to your purpose.
As a further remark I would like to add that I have the impression
that the documentation of the single tools inside the Glimmer suite
is not as good for version 3.x as it was for 2.x. I tried to help
myself to provide some man pages by using those that were written
by the former Debian maintainer of the package (namely Steffen Möller)
for version 2.x of Glimmer. I have no idea whether Steffen informed
you about his work on some man pages but if you like to include these
into your upstream source feel free to ask me. I would like to
be helpful to enhance the user documentation wherever possible.
Kind regards and thanks for your work on Glimmer which is a nice
enhancement for our Debian Med subproject
Andreas.
--
http://fam-tille.de
--- glimmer3.02.orig/src/Common/delcher.cc
+++ glimmer3.02/src/Common/delcher.cc
@@ -9,6 +9,7 @@
#include "delcher.hh"
+#include <cstring>
const int COMMATIZE_BUFF_LEN = 50;
// Length of buffer for creating string with commas
--- glimmer3.02.orig/src/Common/fasta.cc
+++ glimmer3.02/src/Common/fasta.cc
@@ -9,7 +9,7 @@
#include "fasta.hh"
-
+#include <cstring>
void Fasta_Print
(FILE * fp, const char * s, const char * hdr, int fasta_width)
--- glimmer3.02.orig/src/Common/gene.cc
+++ glimmer3.02/src/Common/gene.cc
@@ -10,6 +10,7 @@
#include "delcher.hh"
#include "gene.hh"
+#include <cstring>
static const char COMPLEMENT_TABLE []
= "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"
--- glimmer3.02.orig/src/Glimmer/anomaly.cc
+++ glimmer3.02/src/Glimmer/anomaly.cc
@@ -12,6 +12,7 @@
#include "anomaly.hh"
+#include <cstring>
// Global variables
--- glimmer3.02.orig/src/ICM/icm.cc
+++ glimmer3.02/src/ICM/icm.cc
@@ -15,6 +15,8 @@
#include "icm.hh"
+#include <cstring>
+
using namespace std;
extern int Verbose;
--- glimmer3.02.orig/src/Util/entropy-score.cc
+++ glimmer3.02/src/Util/entropy-score.cc
@@ -9,7 +9,7 @@
// regions in it by entropy distance. Results are output
// to stdout .
-
+#include <cstring>
#include "entropy-score.hh"
--- glimmer3.02.orig/src/Glimmer/glimmer3.cc
+++ glimmer3.02/src/Glimmer/glimmer3.cc
@@ -12,11 +12,10 @@
// Copyright (c) 2006 University of Maryland Center for Bioinformatics
// & Computational Biology
-
+#include <cstring>
#include "glimmer3.hh"
-
static int For_Edwin = 0;
--- glimmer3.02.orig/src/ICM/build-icm.cc
+++ glimmer3.02/src/ICM/build-icm.cc
@@ -13,6 +13,7 @@
#include "build-icm.hh"
+#include <cstring>
static int Genbank_Xlate_Code = 0;
// Holds the Genbank translation table number that determines
--- glimmer3.02.orig/src/Util/extract.cc
+++ glimmer3.02/src/Util/extract.cc
@@ -9,7 +9,7 @@
// sequences specified by coordinates. The resulting sequences
// are output (in multifasta or two-string format) to stdout.
-
+#include <cstring>
#include "extract.hh"
--- glimmer3.02.orig/src/Glimmer/glimmer2.cc
+++ glimmer3.02/src/Glimmer/glimmer2.cc
@@ -37,6 +37,7 @@
#include "delcher.h"
#include "gene.h"
+#include <cstring>
const int DEFAULT_MIN_GENE_LEN = 90;
const double DEFAULT_MIN_OLAP_PERCENT = 0.10;
--- glimmer3.02.orig/src/Glimmer/long-orfs.cc
+++ glimmer3.02/src/Glimmer/long-orfs.cc
@@ -15,7 +15,7 @@
#include "long-orfs.hh"
-
+#include <cstring>
// External variables
--- glimmer3.02.orig/src/ICM/build-fixed.cc
+++ glimmer3.02/src/ICM/build-fixed.cc
@@ -12,6 +12,7 @@
#include "build-fixed.hh"
+#include <cstring>
static FILE * Index_File_fp = NULL;
// File containing a list of subscripts of strings to train model
--- glimmer3.02.orig/src/ICM/score-fixed.cc
+++ glimmer3.02/src/ICM/score-fixed.cc
@@ -8,6 +8,7 @@
#include "score-fixed.hh"
+#include <cstring>
static char * Pos_Model_Path;
// Name of file containing the positive model
--- glimmer3.02.orig/src/Util/multi-extract.cc
+++ glimmer3.02/src/Util/multi-extract.cc
@@ -10,7 +10,7 @@
// resulting sequences are output (in multifasta or two-string format)
// to stdout.
-
+#include <cstring>
#include "multi-extract.hh"
--- glimmer3.02.orig/src/Util/start-codon-distrib.cc
+++ glimmer3.02/src/Util/start-codon-distrib.cc
@@ -17,6 +17,7 @@
#include "start-codon-distrib.hh"
+#include <cstring>
// External variables
--- glimmer3.02.orig/src/Util/uncovered.cc
+++ glimmer3.02/src/Util/uncovered.cc
@@ -10,7 +10,7 @@
// specified in the file named as the second command-line argument.
// Output is a multifasta file sent to stdout.
-
+#include <cstring>
#include "uncovered.hh"
--- /dev/null
+++ glimmer3.02/Makefile
@@ -0,0 +1,7 @@
+all:
+ cd src; make
+
+clean:
+ cd src; make clean
+ rm -f bin/* lib/* obj/*
+
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