[med-svn] [Git][med-team/phipack][master] Force signed char on every architecture
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 9 07:23:11 BST 2020
Andreas Tille pushed to branch master at Debian Med / phipack
Commits:
92c7e22b by Andreas Tille at 2020-09-09T08:14:52+02:00
Force signed char on every architecture
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/phipack.unsigned.char.fixes.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -3,6 +3,9 @@ phipack (0.0.20160614-5) UNRELEASED; urgency=medium
* Add salsa-ci file (routine-update)
* Fix compiler variable to enable cross building
Closes: #968242
+ * Force signed char on every architecture (Thanks a lot to
+ Lennart Sorensen)
+ Closes: #969552
-- Andreas Tille <tille at debian.org> Tue, 08 Sep 2020 22:29:16 +0200
=====================================
debian/patches/phipack.unsigned.char.fixes.patch
=====================================
@@ -0,0 +1,188 @@
+Date: Tue, 8 Sep 2020 19:23:15 -0400
+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 @@
+ void read_sequence_name(FILE *in_file,char *name, int capacity)
+ {
+ int i=0;
+- char ch='\0';
++ signed char ch='\0';
+
+ ch=fgetc(in_file);
+ if(ch != '>')
+@@ -97,7 +97,7 @@
+ {
+ int bases_read=0;
+ int new_limit;
+- char ch;
++ signed char ch;
+ char s[250];
+
+ ch=fgetc(in_file);
+@@ -175,7 +175,7 @@
+ int *seq_counter;
+ int i;
+
+- char ch;
++ signed char ch;
+
+ 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 @@
+ const int AA_AMBIG_SIZE =2;
+
+ const char GAP[] = {'-'};
+-const int GAP_SIZE=2;
++const int GAP_SIZE=1;
+
+ cbool memberOf(const char *set, const int num, char ch)
+ {
+@@ -79,10 +79,10 @@
+ switch(alignKind)
+ {
+ case DNA:
+- return (memberOf(DNA_MISSING,DNA_MISSING_SIZE,ch) || memberOf(DNA_AMBIG,DNA_AMBIG_SIZE,ch));
++ return (memberOf(DNA_MISSING,DNA_MISSING_SIZE,ch) || memberOf(DNA_AMBIG,DNA_AMBIG_SIZE,ch)) ? TRUE : FALSE;
+ break;
+ case AA:
+- return (memberOf(AA_MISSING,AA_MISSING_SIZE,ch) || memberOf(AA_AMBIG,AA_AMBIG_SIZE,ch));
++ return (memberOf(AA_MISSING,AA_MISSING_SIZE,ch) || memberOf(AA_AMBIG,AA_AMBIG_SIZE,ch)) ? TRUE : FALSE;
+ 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 @@
+
+ void get_params(int argc, char**argv, options *opt)
+ {
+- char *cur,ch,nextch;
++ char *cur;
++ signed char ch,nextch;
+ 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 @@
+
+ char ffclose(FILE *handle)
+ {
+- char f;
++ signed char f;
+ 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 @@
+
+ char skip_all_space(FILE *in_file)
+ {
+- char ch;
++ signed char ch;
+
+ ch=fgetc(in_file);
+ while((ch != EOF) && isspace(ch))
+@@ -61,7 +61,7 @@
+
+ char skip_newlines(FILE *in_file)
+ {
+- char ch;
++ signed char ch;
+
+ ch=fgetc(in_file);
+ while((ch != EOF) && (ch == '\n'))
+@@ -76,7 +76,7 @@
+
+ char skip_non_newline(FILE *in_file)
+ {
+- char ch;
++ signed char ch;
+
+ ch=fgetc(in_file);
+ while((ch != EOF) && (ch != '\n'))
+@@ -90,7 +90,7 @@
+
+ char skip_non_newline_space(FILE *in_file)
+ {
+- char ch;
++ signed char ch;
+
+ 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
+@@ -30,7 +30,7 @@
+ void read_strict_name(FILE *in_file,char *name, int capacity)
+ {
+ int i;
+- char ch='\0';
++ signed char ch='\0';
+ for(i=0;(i<PHYLIP_SIZE) && (ch!=EOF);i++)
+ {
+ ch=fgetc(in_file);
+@@ -51,7 +51,7 @@
+ void read_relaxed_name(FILE *in_file,char *name, int capacity)
+ {
+ int i=0;
+- char ch='\0',next_ch;
++ signed char ch='\0',next_ch;
+ cbool double_space=FALSE;
+
+ while((i<capacity) && (ch!=EOF) && (double_space == FALSE))
+@@ -129,7 +129,7 @@
+ int read_seq_bit(FILE *in_file, int base_limit, align_type* states, int index, int *num_bases)
+ {
+ int bases_read=num_bases[index];
+- char ch;
++ signed char ch;
+ char s[250];
+
+ ch=fgetc(in_file);
+@@ -213,7 +213,7 @@
+ int *seq_counter;
+ int i;
+ int cur_seq=0;
+- char ch;
++ signed char ch;
+
+ 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 @@
+
+ void get_params(int argc, char**argv, options *opt)
+ {
+- char *cur,ch,nextch;
++ char *cur;
++ signed char ch,nextch;
+ 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 @@
+ cbool validate_alignment(align_type **alignment, alignmentClass alignKind,int num_taxa, int num_sites)
+ {
+ int i,j;
+- char ch;
++ signed char ch;
+ char s[MAX_SIZE+1];
+
+ for(i=0;i<num_taxa;i++)
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
hardening.patch
cross.patch
+phipack.unsigned.char.fixes.patch
View it on GitLab: https://salsa.debian.org/med-team/phipack/-/commit/92c7e22b94873f3cb4a1cdff83b5ebb1e277bd35
--
View it on GitLab: https://salsa.debian.org/med-team/phipack/-/commit/92c7e22b94873f3cb4a1cdff83b5ebb1e277bd35
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