From 27de7a2726da78d3f1c692fadbd9d00258f003fb Mon Sep 17 00:00:00 2001
From: noguchi-k <55966120+noguchi-k@users.noreply.github.com>
Date: Mon, 2 Mar 2020 10:58:27 +0900
Subject: [PATCH] lastz: cast from char to signed char (#15263)
---
.../packages/lastz/cast_signed_char.patch | 70 +++++++++++++++++++
.../repos/builtin/packages/lastz/package.py | 3 +
2 files changed, 73 insertions(+)
create mode 100644 var/spack/repos/builtin/packages/lastz/cast_signed_char.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
new file mode 100644
index 0000000000..34fda31941
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lastz/cast_signed_char.patch
@@ -0,0 +1,70 @@
+--- 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 cbe4ee4e14..e590aec533 100644
--- a/var/spack/repos/builtin/packages/lastz/package.py
+++ b/var/spack/repos/builtin/packages/lastz/package.py
@@ -14,5 +14,8 @@ class Lastz(MakefilePackage):
version('1.04.00', sha256='a4c2c7a77430387e96dbc9f5bdc75874334c672be90f5720956c0f211abf9f5a')
+ # cast from char to signed char
+ patch('cast_signed_char.patch')
+
def install(self, spec, prefix):
make('install', 'LASTZ_INSTALL={0}'.format(prefix.bin))
--
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