[med-svn] [Git][med-team/phipack][master] Upload to unstable
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 9 07:33:11 BST 2020
Andreas Tille pushed to branch master at Debian Med / phipack
Commits:
cbfedf88 by Andreas Tille at 2020-09-09T08:31:56+02:00
Upload to unstable
- - - - -
2 changed files:
- debian/changelog
- debian/patches/phipack.unsigned.char.fixes.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-phipack (0.0.20160614-5) UNRELEASED; urgency=medium
+phipack (0.0.20160614-5) unstable; urgency=medium
* Add salsa-ci file (routine-update)
* Fix compiler variable to enable cross building
@@ -7,7 +7,7 @@ phipack (0.0.20160614-5) UNRELEASED; urgency=medium
Lennart Sorensen)
Closes: #969552
- -- Andreas Tille <tille at debian.org> Tue, 08 Sep 2020 22:29:16 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 09 Sep 2020 08:30:55 +0200
phipack (0.0.20160614-4) unstable; urgency=medium
=====================================
debian/patches/phipack.unsigned.char.fixes.patch
=====================================
@@ -3,10 +3,9 @@ From: Lennart Sorensen <lsorense at csclub.uwaterloo.ca>
Description: Force signed char on every architecture
Bug-Debian: https://bugs.debian.org/969552
-diff -ruN phipack-0.0.20160614/src/fasta.c phipack-0.0.20160614.arm64/src/fasta.c
---- phipack-0.0.20160614/src/fasta.c 2016-06-14 00:18:29.000000000 -0400
-+++ phipack-0.0.20160614.arm64/src/fasta.c 2020-09-08 19:08:06.672390326 -0400
-@@ -36,7 +36,7 @@
+--- a/src/fasta.c
++++ b/src/fasta.c
+@@ -36,7 +36,7 @@ along with PhiPack. If not, see <http:/
void read_sequence_name(FILE *in_file,char *name, int capacity)
{
int i=0;
@@ -15,7 +14,7 @@ diff -ruN phipack-0.0.20160614/src/fasta.c phipack-0.0.20160614.arm64/src/fasta.
ch=fgetc(in_file);
if(ch != '>')
-@@ -97,7 +97,7 @@
+@@ -97,7 +97,7 @@ char read_seq_part(FILE *in_file, int b
{
int bases_read=0;
int new_limit;
@@ -24,7 +23,7 @@ diff -ruN phipack-0.0.20160614/src/fasta.c phipack-0.0.20160614.arm64/src/fasta.
char s[250];
ch=fgetc(in_file);
-@@ -175,7 +175,7 @@
+@@ -175,7 +175,7 @@ void read_fasta(const char* file_name,
int *seq_counter;
int i;
@@ -33,10 +32,9 @@ diff -ruN phipack-0.0.20160614/src/fasta.c phipack-0.0.20160614.arm64/src/fasta.
int cur_seqs;
int num_seqs=1,new_num;
-diff -ruN phipack-0.0.20160614/src/global.c phipack-0.0.20160614.arm64/src/global.c
---- phipack-0.0.20160614/src/global.c 2016-06-13 22:33:15.000000000 -0400
-+++ phipack-0.0.20160614.arm64/src/global.c 2020-09-08 18:04:48.956444973 -0400
-@@ -34,7 +34,7 @@
+--- a/src/global.c
++++ b/src/global.c
+@@ -34,7 +34,7 @@ const char AA_AMBIG[] = {'B','Z'};
const int AA_AMBIG_SIZE =2;
const char GAP[] = {'-'};
@@ -45,7 +43,7 @@ diff -ruN phipack-0.0.20160614/src/global.c phipack-0.0.20160614.arm64/src/globa
cbool memberOf(const char *set, const int num, char ch)
{
-@@ -79,10 +79,10 @@
+@@ -79,10 +79,10 @@ cbool missing_ambig_State(alignmentClass
switch(alignKind)
{
case DNA:
@@ -58,10 +56,9 @@ diff -ruN phipack-0.0.20160614/src/global.c phipack-0.0.20160614.arm64/src/globa
break;
case OTHER:
if(ch == GLOBAL_MISSING)
-diff -ruN phipack-0.0.20160614/src/main.c phipack-0.0.20160614.arm64/src/main.c
---- phipack-0.0.20160614/src/main.c 2016-06-14 00:18:17.000000000 -0400
-+++ phipack-0.0.20160614.arm64/src/main.c 2020-09-08 19:17:18.230153542 -0400
-@@ -71,7 +71,8 @@
+--- a/src/main.c
++++ b/src/main.c
+@@ -71,7 +71,8 @@ void print_usage()
void get_params(int argc, char**argv, options *opt)
{
@@ -71,10 +68,9 @@ diff -ruN phipack-0.0.20160614/src/main.c phipack-0.0.20160614.arm64/src/main.c
char temp[MAX_SIZE+1];
int i;
cbool inFileFound=FALSE;
-diff -ruN phipack-0.0.20160614/src/mem.c phipack-0.0.20160614.arm64/src/mem.c
---- phipack-0.0.20160614/src/mem.c 2016-06-13 22:33:15.000000000 -0400
-+++ phipack-0.0.20160614.arm64/src/mem.c 2020-09-08 19:12:52.415278666 -0400
-@@ -96,7 +96,7 @@
+--- a/src/mem.c
++++ b/src/mem.c
+@@ -96,7 +96,7 @@ FILE *ffopen(char *name,char *mod)
char ffclose(FILE *handle)
{
@@ -83,10 +79,9 @@ diff -ruN phipack-0.0.20160614/src/mem.c phipack-0.0.20160614.arm64/src/mem.c
char s[MAX_SIZE+1];
f=fclose(handle);
-diff -ruN phipack-0.0.20160614/src/misc.c phipack-0.0.20160614.arm64/src/misc.c
---- phipack-0.0.20160614/src/misc.c 2016-06-13 22:33:15.000000000 -0400
-+++ phipack-0.0.20160614.arm64/src/misc.c 2020-09-08 19:08:28.352322441 -0400
-@@ -46,7 +46,7 @@
+--- a/src/misc.c
++++ b/src/misc.c
+@@ -46,7 +46,7 @@ char *strsub(char *s1, const char *s2, i
char skip_all_space(FILE *in_file)
{
@@ -95,7 +90,7 @@ diff -ruN phipack-0.0.20160614/src/misc.c phipack-0.0.20160614.arm64/src/misc.c
ch=fgetc(in_file);
while((ch != EOF) && isspace(ch))
-@@ -61,7 +61,7 @@
+@@ -61,7 +61,7 @@ char skip_all_space(FILE *in_file)
char skip_newlines(FILE *in_file)
{
@@ -104,7 +99,7 @@ diff -ruN phipack-0.0.20160614/src/misc.c phipack-0.0.20160614.arm64/src/misc.c
ch=fgetc(in_file);
while((ch != EOF) && (ch == '\n'))
-@@ -76,7 +76,7 @@
+@@ -76,7 +76,7 @@ char skip_newlines(FILE *in_file)
char skip_non_newline(FILE *in_file)
{
@@ -113,7 +108,7 @@ diff -ruN phipack-0.0.20160614/src/misc.c phipack-0.0.20160614.arm64/src/misc.c
ch=fgetc(in_file);
while((ch != EOF) && (ch != '\n'))
-@@ -90,7 +90,7 @@
+@@ -90,7 +90,7 @@ char skip_non_newline(FILE *in_file)
char skip_non_newline_space(FILE *in_file)
{
@@ -122,9 +117,8 @@ diff -ruN phipack-0.0.20160614/src/misc.c phipack-0.0.20160614.arm64/src/misc.c
ch=fgetc(in_file);
while((ch != EOF) && (ch != '\n') && isspace(ch))
-diff -ruN phipack-0.0.20160614/src/phylip.c phipack-0.0.20160614.arm64/src/phylip.c
---- phipack-0.0.20160614/src/phylip.c 2016-06-14 00:18:17.000000000 -0400
-+++ phipack-0.0.20160614.arm64/src/phylip.c 2020-09-08 19:10:06.483985652 -0400
+--- a/src/phylip.c
++++ b/src/phylip.c
@@ -30,7 +30,7 @@
void read_strict_name(FILE *in_file,char *name, int capacity)
{
@@ -134,7 +128,7 @@ diff -ruN phipack-0.0.20160614/src/phylip.c phipack-0.0.20160614.arm64/src/phyli
for(i=0;(i<PHYLIP_SIZE) && (ch!=EOF);i++)
{
ch=fgetc(in_file);
-@@ -51,7 +51,7 @@
+@@ -51,7 +51,7 @@ void read_strict_name(FILE *in_file,char
void read_relaxed_name(FILE *in_file,char *name, int capacity)
{
int i=0;
@@ -143,7 +137,7 @@ diff -ruN phipack-0.0.20160614/src/phylip.c phipack-0.0.20160614.arm64/src/phyli
cbool double_space=FALSE;
while((i<capacity) && (ch!=EOF) && (double_space == FALSE))
-@@ -129,7 +129,7 @@
+@@ -129,7 +129,7 @@ void write_phylip(FILE* cur_stream, cboo
int read_seq_bit(FILE *in_file, int base_limit, align_type* states, int index, int *num_bases)
{
int bases_read=num_bases[index];
@@ -152,7 +146,7 @@ diff -ruN phipack-0.0.20160614/src/phylip.c phipack-0.0.20160614.arm64/src/phyli
char s[250];
ch=fgetc(in_file);
-@@ -213,7 +213,7 @@
+@@ -213,7 +213,7 @@ void read_phylip(const char* file_name,
int *seq_counter;
int i;
int cur_seq=0;
@@ -161,10 +155,9 @@ diff -ruN phipack-0.0.20160614/src/phylip.c phipack-0.0.20160614.arm64/src/phyli
in_file=fopen(file_name,"r");
if(in_file == NULL)
-diff -ruN phipack-0.0.20160614/src/profile.c phipack-0.0.20160614.arm64/src/profile.c
---- phipack-0.0.20160614/src/profile.c 2016-06-14 00:18:17.000000000 -0400
-+++ phipack-0.0.20160614.arm64/src/profile.c 2020-09-08 19:16:45.274292568 -0400
-@@ -71,7 +71,8 @@
+--- a/src/profile.c
++++ b/src/profile.c
+@@ -71,7 +71,8 @@ void print_usage()
void get_params(int argc, char**argv, options *opt)
{
@@ -174,10 +167,9 @@ diff -ruN phipack-0.0.20160614/src/profile.c phipack-0.0.20160614.arm64/src/prof
char temp[MAX_SIZE+1];
int i;
cbool inFileFound=FALSE;
-diff -ruN phipack-0.0.20160614/src/seqManip.c phipack-0.0.20160614.arm64/src/seqManip.c
---- phipack-0.0.20160614/src/seqManip.c 2016-06-14 00:18:17.000000000 -0400
-+++ phipack-0.0.20160614.arm64/src/seqManip.c 2020-09-08 19:14:37.974830794 -0400
-@@ -190,7 +190,7 @@
+--- a/src/seqManip.c
++++ b/src/seqManip.c
+@@ -190,7 +190,7 @@ void get_informative( align_type **align
cbool validate_alignment(align_type **alignment, alignmentClass alignKind,int num_taxa, int num_sites)
{
int i,j;
View it on GitLab: https://salsa.debian.org/med-team/phipack/-/commit/cbfedf88cfe682fb8924e3a55f213ee775a250b9
--
View it on GitLab: https://salsa.debian.org/med-team/phipack/-/commit/cbfedf88cfe682fb8924e3a55f213ee775a250b9
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