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lastz: declare ch as type int (#15350)

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Adam J. Stewart 2020-03-05 15:06:20 -06:00 committed by GitHub
parent fde1b2088a
commit 28a75a4c35
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 247 additions and 72 deletions
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70
var/spack/repos/builtin/packages/lastz/cast_signed_char.patch
View file

@ -1,70 +0,0 @@
--- spack-src/src/sequences.c.org 2020-02-27 16:51:13.380985769 +0900
+++ spack-src/src/sequences.c 2020-02-27 16:55:38.641465062 +0900
@@ -5086,14 +5086,14 @@
// find the next header
ch = seq_getc (_seq);
- if (ch == EOF) goto failure;
+ if ((signed char)ch == EOF) goto failure;
if ((allowComments) && (ch == '#'))
{ // comment, skip to end-of-line and go back and try again
while (ch != '\n')
{
ch = seq_getc (_seq);
- if (ch == EOF) goto failure;
+ if ((signed char)ch == EOF) goto failure;
}
continue;
}
@@ -5117,12 +5117,12 @@
leadingWhite = 0;
ch = seq_getc (_seq);
- if (ch == EOF) goto failure;
+ if ((signed char)ch == EOF) goto failure;
while ((ch != '\n') && (isspace (ch)))
{
leadingWhite++;
ch = seq_getc (_seq);
- if (ch == EOF) goto failure;
+ if ((signed char)ch == EOF) goto failure;
}
if (ch == '\n')
@@ -5137,7 +5137,7 @@
break; // .. truncate the header)
*(s++) = ch;
ch = seq_getc (_seq);
- if (ch == EOF) goto failure;
+ if ((signed char)ch == EOF) goto failure;
}
*s = 0;
@@ -5231,7 +5231,7 @@
debugNamesFile_14;
ch = seq_getc (_seq);
- if (ch == EOF) goto failure;
+ if ((signed char)ch == EOF) goto failure;
if (ch != '@')
suicidef ("internal error in find_next_fastq_coi\n"
@@ -5241,7 +5241,7 @@
// read the header
ch = seq_getc (_seq);
- if (ch == EOF) goto failure;
+ if ((signed char)ch == EOF) goto failure;
s = buffer;
while ((ch != '\n') && (ch != '\r'))
@@ -5250,7 +5250,7 @@
break; // .. truncate the header)
*(s++) = ch;
ch = seq_getc (_seq);
- if (ch == EOF) goto failure;
+ if ((signed char)ch == EOF) goto failure;
}
*s = 0;

5
var/spack/repos/builtin/packages/lastz/package.py
View file

@ -12,10 +12,11 @@ class Lastz(MakefilePackage):
homepage = "https://lastz.github.io/lastz"
url = "https://github.com/lastz/lastz/archive/1.04.00.tar.gz"
version('1.04.03', sha256='c58ed8e37c4b0e82492b3a2b3e12447a3c40286fb8358906d19f10b0a713e9f4')
version('1.04.00', sha256='a4c2c7a77430387e96dbc9f5bdc75874334c672be90f5720956c0f211abf9f5a')
# cast from char to signed char
patch('cast_signed_char.patch')
# Ref: https://github.com/lastz/lastz/commit/20aa14f483265b4eac97f25aca666c708b9655e4
patch('sequences.c.patch', when='@:1.04.03')
# set compile commands for each compiler
def edit(self, spec, prefix):

244
var/spack/repos/builtin/packages/lastz/sequences.c.patch Normal file
View file

@ -0,0 +1,244 @@
--- spack-src/src/sequences.c.org 2020-03-05 13:34:15.764971874 +0900
+++ spack-src/src/sequences.c 2020-03-05 13:49:45.315370741 +0900
@@ -2180,7 +2180,7 @@
ch = skip_seq_whitespace (_seq);
- if (ch != '>') seq_ungetc (ch, _seq);
+ if (ch != '>') seq_ungetc ((char)ch, _seq);
else parse_fasta_header (_seq);
debugFastaFile_2;
@@ -2298,7 +2298,7 @@
if (ch == '\r') // handle possible DOS CR-LF line ending
{
ch = seq_getc (_seq);
- if (ch != '\n') seq_ungetc (ch, _seq);
+ if (ch != '\n') seq_ungetc ((char)ch, _seq);
}
}
@@ -2346,7 +2346,7 @@
while (ch != EOF)
{
if ((prevCh == '\n') && (ch == '>')) // (start of next sequence)
- { seq_ungetc (ch, _seq); break; }
+ { seq_ungetc ((char)ch, _seq); break; }
if ((_seq->separatorCh == 0) || (ch != _seq->separatorCh))
{
@@ -2445,7 +2445,7 @@
// while (ch != EOF)
// {
// if ((prevCh == '\n') && (ch == '>')) // (start of next sequence)
-// { seq_ungetc (ch, _seq); break; }
+// { seq_ungetc ((char)ch, _seq); break; }
//
// switch (char_to_fasta_type[(u8)ch])
// {
@@ -2627,7 +2627,7 @@
if (ch == '\r') // handle possible DOS CR-LF line ending
{
ch = seq_getc (_seq);
- if (ch != '\n') seq_ungetc (ch, _seq);
+ if (ch != '\n') seq_ungetc ((char)ch, _seq);
}
// copy from trueHeader into the header (unless the header is locked), then
@@ -2762,7 +2762,7 @@
if (ch == '\r') // handle possible DOS CR-LF line ending
{
ch = seq_getc (_seq);
- if (ch != '\n') seq_ungetc (ch, _seq);
+ if (ch != '\n') seq_ungetc ((char)ch, _seq);
}
_seq->v[_seq->len] = 0; // (set the terminating zero)
@@ -2834,7 +2834,7 @@
if (ch == '\r') // handle possible DOS CR-LF line ending
{
ch = seq_getc (_seq);
- if (ch != '\n') seq_ungetc (ch, _seq);
+ if (ch != '\n') seq_ungetc ((char)ch, _seq);
}
//////////
@@ -2877,7 +2877,7 @@
if (ch == '\r') // handle possible DOS CR-LF line ending
{
ch = seq_getc (_seq);
- if (ch != '\n') seq_ungetc (ch, _seq);
+ if (ch != '\n') seq_ungetc ((char)ch, _seq);
}
if (qualCount < nucCount) goto not_enough_qualities;
@@ -3061,7 +3061,7 @@
ch = seq_getc (_seq);
}
- if (ch != '>') seq_ungetc (ch, _seq);
+ if (ch != '>') seq_ungetc ((char)ch, _seq);
else parse_csfasta_header (_seq);
//////////
@@ -3166,7 +3166,7 @@
if (ch == '\r') // handle possible DOS CR-LF line ending
{
ch = seq_getc (_seq);
- if (ch != '\n') seq_ungetc (ch, _seq);
+ if (ch != '\n') seq_ungetc ((char)ch, _seq);
}
}
@@ -3223,7 +3223,7 @@
{
if ((prevCh == '\n')
&& ((ch == '#') || (ch == '>'))) // (start of next sequence)
- { seq_ungetc (ch, _seq); break; }
+ { seq_ungetc ((char)ch, _seq); break; }
chType = char_to_csfasta_type[(u8)ch];
switch (chType)
@@ -3324,7 +3324,7 @@
// {
// if ((prevCh == '\n')
// && ((ch == '#') || (ch == '>'))) // (start of next sequence)
-// { seq_ungetc (ch, _seq); break; }
+// { seq_ungetc ((char)ch, _seq); break; }
//
// switch (char_to_csfasta_type[(u8)ch])
// {
@@ -4701,10 +4701,10 @@
else if (magic == oldQdnaMagicBig) { oldFormat = bigEndian = true; }
else
{
- seq_ungetc ((magic >> 24) & 0xFF, _seq);
- seq_ungetc ((magic >> 16) & 0xFF, _seq);
- seq_ungetc ((magic >> 8) & 0xFF, _seq);
- seq_ungetc ( magic & 0xFF, _seq);
+ seq_ungetc ((char) ((magic >> 24) & 0xFF), _seq);
+ seq_ungetc ((char) ((magic >> 16) & 0xFF), _seq);
+ seq_ungetc ((char) ((magic >> 8) & 0xFF), _seq);
+ seq_ungetc ((char) ( magic & 0xFF), _seq);
oldFormat = true;
}
@@ -5050,7 +5050,7 @@
_seq->filename);
if (ch == EOF) return false; // we're at end of file now
- seq_ungetc (ch, _seq); // save what we peeked at
+ seq_ungetc ((char)ch, _seq); // save what we peeked at
return true; // we have characters to process
}
@@ -5074,7 +5074,8 @@
int headerLen;
int mustBeHeader;
int leadingWhite;
- char ch, *s;
+ int ch;
+ char* s;
int ix;
debugNamesFile_12;
@@ -5118,7 +5119,7 @@
ch = seq_getc (_seq);
if (ch == EOF) goto failure;
- while ((ch != '\n') && (isspace (ch)))
+ while ((ch != '\n') && (isspace (ch))) // nota bene: isspace's arg type is an int
{
leadingWhite++;
ch = seq_getc (_seq);
@@ -5186,7 +5187,7 @@
// unget the header
- seq_ungetc (ch, _seq); // (ch terminated the header)
+ seq_ungetc ((char)ch, _seq); // (ch terminated the header)
for (ix=strlen(buffer) ; ix>0 ; )
seq_ungetc (buffer[--ix], _seq);
@@ -5218,7 +5219,8 @@
char buffer[maxSequenceHeader+1];
char* header;
int headerLen;
- char ch, *s;
+ int ch;
+ char* s;
int ix;
int ok;
@@ -5257,7 +5259,7 @@
if (ch == '\r') // handle possible DOS CR-LF line ending
{
ch = seq_getc (_seq);
- if (ch != '\n') seq_ungetc (ch, _seq);
+ if (ch != '\n') seq_ungetc ((char)ch, _seq);
}
// if we have a name trigger, locate the sequence's name
@@ -5310,7 +5312,7 @@
// unget the header
- seq_ungetc (ch, _seq); // (ch terminated the header)
+ seq_ungetc ((char)ch, _seq); // (ch terminated the header)
for (ix=strlen(buffer) ; ix>0 ; )
seq_ungetc (buffer[--ix], _seq);
@@ -9067,10 +9069,10 @@
// put those four bytes back in the file (in reverse of the read order)
- seq_ungetc (magic >> 24, _seq);
- seq_ungetc (magic >> 16, _seq);
- seq_ungetc (magic >> 8, _seq);
- seq_ungetc (magic , _seq);
+ seq_ungetc ((char) (magic >> 24), _seq);
+ seq_ungetc ((char) (magic >> 16), _seq);
+ seq_ungetc ((char) (magic >> 8), _seq);
+ seq_ungetc ((char) magic , _seq);
if (type != seq_type_unknown)
return type;
@@ -9080,7 +9082,7 @@
//////////
ch = seq_getc (_seq);
- seq_ungetc (ch, _seq);
+ seq_ungetc ((char)ch, _seq);
if (ch == '@')
return seq_type_fastq;
@@ -9095,12 +9097,12 @@
ch = seq_getc (_seq);
if (ch == '#')
{
- seq_ungetc (ch, _seq);
+ seq_ungetc ((char)ch, _seq);
return seq_type_csfasta;
}
if (ch != '>')
- seq_ungetc (ch, _seq);
+ seq_ungetc ((char)ch, _seq);
else
{
// read header
@@ -9122,12 +9124,12 @@
intCh = seq_getc (_seq);
if (intCh == EOF) goto unknown;
- buffer[bufferLen++] = intCh;
+ buffer[bufferLen++] = (char) intCh;
if (ustrchr ("ACGTacgtNn", intCh) != NULL)
{
intCh = seq_getc (_seq);
if (intCh == EOF) goto unknown;
- buffer[bufferLen++] = intCh;
+ buffer[bufferLen++] = (char) intCh;
if (ustrchr ("ACGTacgtNn", intCh) != NULL)
type = seq_type_fasta;
else if (ustrchr ("0123", intCh) != NULL)