From 28a75a4c35342c0a1b807b0036b330e07f619baa Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 5 Mar 2020 15:06:20 -0600
Subject: [PATCH] lastz: declare ch as type int (#15350)
---
.../packages/lastz/cast_signed_char.patch | 70 -----
.../repos/builtin/packages/lastz/package.py | 5 +-
.../builtin/packages/lastz/sequences.c.patch | 244 ++++++++++++++++++
3 files changed, 247 insertions(+), 72 deletions(-)
delete mode 100644 var/spack/repos/builtin/packages/lastz/cast_signed_char.patch
create mode 100644 var/spack/repos/builtin/packages/lastz/sequences.c.patch
diff --git a/var/spack/repos/builtin/packages/lastz/cast_signed_char.patch b/var/spack/repos/builtin/packages/lastz/cast_signed_char.patch
deleted file mode 100644
index 34fda31941..0000000000
--- a/var/spack/repos/builtin/packages/lastz/cast_signed_char.patch
+++ /dev/null
@@ -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;
-
diff --git a/var/spack/repos/builtin/packages/lastz/package.py b/var/spack/repos/builtin/packages/lastz/package.py
index d01068df51..4b0431b2e9 100644
--- a/var/spack/repos/builtin/packages/lastz/package.py
+++ b/var/spack/repos/builtin/packages/lastz/package.py
@@ -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):
diff --git a/var/spack/repos/builtin/packages/lastz/sequences.c.patch b/var/spack/repos/builtin/packages/lastz/sequences.c.patch
new file mode 100644
index 0000000000..b5c34108aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lastz/sequences.c.patch
@@ -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)
--
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