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-rw-r--r--var/spack/repos/builtin/packages/genometools/package.py2
-rw-r--r--var/spack/repos/builtin/packages/genometools/signed.patch231
2 files changed, 233 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/genometools/package.py b/var/spack/repos/builtin/packages/genometools/package.py
index ca42145a3e..91ddd7a9ea 100644
--- a/var/spack/repos/builtin/packages/genometools/package.py
+++ b/var/spack/repos/builtin/packages/genometools/package.py
@@ -23,6 +23,8 @@ class Genometools(MakefilePackage):
# build fails with gcc 7"
conflicts('%gcc@7.1.0:', when='@:1.5.9')
+ patch('signed.patch', when='%fj')
+
def install(self, spec, prefix):
make('install', 'prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/genometools/signed.patch b/var/spack/repos/builtin/packages/genometools/signed.patch
new file mode 100644
index 0000000000..57c09b7447
--- /dev/null
+++ b/var/spack/repos/builtin/packages/genometools/signed.patch
@@ -0,0 +1,231 @@
+diff -u -r -N a/src/core/io.c b/src/core/io.c
+--- a/src/core/io.c 2020-08-17 15:23:43.000000000 +0900
++++ b/src/core/io.c 2020-08-24 11:45:55.000000000 +0900
+@@ -87,21 +87,29 @@
+ return rval ? false : true;
+ }
+
+-signed char gt_io_peek(GtIO *io)
++int gt_io_peek(GtIO *io)
+ {
+ char c;
+ gt_assert(io);
+- gt_io_get_char(io, &c);
++ int e = gt_io_get_char(io, &c);
+ gt_io_unget_char(io, c);
+- return c;
++ if (e == -1) {
++ return EOF;
++ } else{
++ return c;
++ }
+ }
+
+-signed char gt_io_next(GtIO *io)
++int gt_io_next(GtIO *io)
+ {
+ char c;
+ gt_assert(io);
+- gt_io_get_char(io, &c);
+- return c;
++ int e = gt_io_get_char(io, &c);
++ if (e == -1) {
++ return EOF;
++ } else{
++ return c;
++ }
+ }
+
+ GtUword gt_io_get_line_number(const GtIO *io)
+@@ -122,9 +130,9 @@
+ return io->path;
+ }
+
+-int gt_io_expect(GtIO *io, char expected_char, GtError *err)
++int gt_io_expect(GtIO *io, int expected_char, GtError *err)
+ {
+- char cc;
++ int cc;
+ gt_error_check(err);
+ cc = gt_io_next(io);
+ if (cc != expected_char) {
+diff -u -r -N a/src/core/io.h b/src/core/io.h
+--- a/src/core/io.h 2020-08-17 15:23:43.000000000 +0900
++++ b/src/core/io.h 2020-08-24 11:46:21.000000000 +0900
+@@ -37,12 +37,12 @@
+ void gt_io_unget_char(GtIO*, char);
+ bool gt_io_line_start(const GtIO*);
+ bool gt_io_has_char(GtIO*);
+-signed char gt_io_peek(GtIO*);
+-signed char gt_io_next(GtIO*);
++int gt_io_peek(GtIO*);
++int gt_io_next(GtIO*);
+ GtUword gt_io_get_line_number(const GtIO*);
+ const char* gt_io_get_filename(const GtIO*);
+ GtStr* gt_io_get_filename_str(const GtIO*);
+
+-int gt_io_expect(GtIO*, char expected_char, GtError*);
++int gt_io_expect(GtIO*, int expected_char, GtError*);
+
+ #endif
+diff -u -r -N a/src/core/seq_iterator_fastq.c b/src/core/seq_iterator_fastq.c
+--- a/src/core/seq_iterator_fastq.c 2020-08-17 15:57:33.000000000 +0900
++++ b/src/core/seq_iterator_fastq.c 2020-08-20 17:28:23.000000000 +0900
+@@ -92,10 +92,10 @@
+
+ static inline int parse_fastq_seqname(GtSeqIteratorFastQ *seqit,
+ GtStr *buffer,
+- char startchar,
++ int startchar,
+ GtError *err)
+ {
+- char currentchar;
++ int currentchar;
+ bool firstsymbol = true;
+ gt_error_check(err);
+ gt_assert(seqit && buffer);
+@@ -127,7 +127,7 @@
+ GtError *err)
+ {
+ int had_err = 0;
+- char currentchar;
++ int currentchar;
+ GtStr *tmp_str = gt_str_new();
+
+ gt_error_check(err);
+@@ -207,7 +207,7 @@
+ static inline int parse_fastq_qualities(GtSeqIteratorFastQ *seqit,
+ GT_UNUSED GtError *err)
+ {
+- char currentchar;
++ int currentchar;
+ GtUword i = 0;
+ gt_assert(gt_str_length(seqit->sequencebuffer) > 0);
+ if ((currentchar = fastq_buf_getchar(seqit)) == EOF)
+diff -u -r -N a/src/extended/bed_parser.c b/src/extended/bed_parser.c
+--- a/src/extended/bed_parser.c 2020-08-17 16:16:25.000000000 +0900
++++ b/src/extended/bed_parser.c 2020-08-24 11:47:38.000000000 +0900
+@@ -84,7 +84,7 @@
+ gt_error_check(err);
+ had_err = gt_io_expect(bed_file, BLANK_CHAR, err);
+ while (!had_err) {
+- char cc = gt_io_peek(bed_file);
++ int cc = gt_io_peek(bed_file);
+ if (cc == GT_CARRIAGE_RETURN) {
+ gt_io_next(bed_file);
+ if (gt_io_peek(bed_file) == GT_END_OF_LINE)
+@@ -189,7 +189,7 @@
+
+ static bool bed_separator(GtIO *bed_file)
+ {
+- char cc = gt_io_peek(bed_file);
++ int cc = gt_io_peek(bed_file);
+ if (cc == BLANK_CHAR || cc == TABULATOR_CHAR)
+ return true;
+ return false;
+@@ -212,7 +212,7 @@
+
+ static int track_rest(GtBEDParser *bed_parser, GtIO *bed_file, GtError *err)
+ {
+- char cc;
++ int cc;
+ int had_err = 0;
+ gt_error_check(err);
+ bed_parser->offset = 0; /* reset offset for new track line */
+diff -u -r -N a/src/extended/match_iterator_blast.c b/src/extended/match_iterator_blast.c
+--- a/src/extended/match_iterator_blast.c 2020-08-17 16:28:49.000000000 +0900
++++ b/src/extended/match_iterator_blast.c 2020-08-20 17:46:58.000000000 +0900
+@@ -104,12 +104,15 @@
+ had_err = -1;
+ }
+ } else {
++ int intbuf;
+ while (true) {
+- while ((buffer[i] = gt_file_xfgetc(mib->pvt->gtmatchfilep)) != '\n') {
+- if (buffer[i] == EOF)
++ while ((intbuf = gt_file_xfgetc(mib->pvt->gtmatchfilep)) != '\n') {
++ if (intbuf == EOF)
+ return GT_MATCHER_STATUS_END;
++ buffer[i] = intbuf;
+ i++;
+ }
++ buffer[i] = '\n';
+ buffer[i+1] = '\0';
+ if (buffer[0] == '#') {
+ mib->pvt->curpos++;
+diff -u -r -N a/src/extended/match_iterator_open.c b/src/extended/match_iterator_open.c
+--- a/src/extended/match_iterator_open.c 2020-08-17 16:28:49.000000000 +0900
++++ b/src/extended/match_iterator_open.c 2020-08-20 17:46:40.000000000 +0900
+@@ -95,12 +95,15 @@
+ had_err = -1;
+ }
+ } else {
++ int intbuf;
+ while (true) {
+- while ((buffer[i] = gt_file_xfgetc(mpi->pvt->gtmatchfilep)) != '\n') {
+- if (buffer[i] == EOF)
++ while ((intbuf = gt_file_xfgetc(mpi->pvt->gtmatchfilep)) != '\n') {
++ if (intbuf == EOF)
+ return GT_MATCHER_STATUS_END;
++ buffer[i] = intbuf;
+ i++;
+ }
++ buffer[i] = '\n';
+ buffer[i+1] = '\0';
+ if (buffer[0] == '#') {
+ mpi->pvt->curpos++;
+diff -u -r -N a/src/extended/obo_parse_tree.c b/src/extended/obo_parse_tree.c
+--- a/src/extended/obo_parse_tree.c 2020-08-17 17:06:46.000000000 +0900
++++ b/src/extended/obo_parse_tree.c 2020-08-24 11:48:09.000000000 +0900
+@@ -181,7 +181,7 @@
+
+ static bool ignored_char(GtIO *obo_file)
+ {
+- char cc = gt_io_peek(obo_file);
++ int cc = gt_io_peek(obo_file);
+ if ((cc == OBO_BLANK_CHAR) || (cc == OBO_COMMENT_CHAR) ||
+ (cc == GT_CARRIAGE_RETURN) || (cc == GT_END_OF_LINE))
+ return true;
+@@ -218,7 +218,7 @@
+ gt_error_check(err);
+ had_err = gt_io_expect(obo_file, OBO_BLANK_CHAR, err);
+ while (!had_err) {
+- char cc = gt_io_peek(obo_file);
++ int cc = gt_io_peek(obo_file);
+ if (cc == OBO_COMMENT_CHAR)
+ return comment_line(obo_file, err);
+ else if (cc == GT_CARRIAGE_RETURN) {
+diff -u -r -N a/src/extended/xrf_abbr_parse_tree.c b/src/extended/xrf_abbr_parse_tree.c
+--- a/src/extended/xrf_abbr_parse_tree.c 2020-08-17 17:17:38.000000000 +0900
++++ b/src/extended/xrf_abbr_parse_tree.c 2020-08-24 11:48:48.000000000 +0900
+@@ -163,7 +163,7 @@
+
+ static bool gt_xrf_abbr_parse_tree_ignored_char(GtIO *xrf_abbr_file)
+ {
+- char cc = gt_io_peek(xrf_abbr_file);
++ int cc = gt_io_peek(xrf_abbr_file);
+ if ((cc == XRF_BLANK_CHAR) || (cc == XRF_COMMENT_CHAR) ||
+ (cc == GT_CARRIAGE_RETURN) || (cc == GT_END_OF_LINE))
+ return true;
+@@ -203,7 +203,7 @@
+ gt_log_log("blank");
+ had_err = gt_io_expect(xrf_abbr_file, XRF_BLANK_CHAR, err);
+ while (!had_err) {
+- char cc = gt_io_peek(xrf_abbr_file);
++ int cc = gt_io_peek(xrf_abbr_file);
+ if (cc == XRF_COMMENT_CHAR)
+ return gt_xrf_abbr_parse_tree_comment_line(xrf_abbr_file, err);
+ else if (cc == GT_CARRIAGE_RETURN) {
+diff -u -r -N a/src/ltr/pdom_model_set.c b/src/ltr/pdom_model_set.c
+--- a/src/ltr/pdom_model_set.c 2020-08-17 17:31:47.000000000 +0900
++++ b/src/ltr/pdom_model_set.c 2020-08-20 17:28:23.000000000 +0900
+@@ -65,7 +65,8 @@
+ {
+ GtStr *concat_dbnames, *cmdline, *indexfilename = NULL;
+ GtUword i;
+- char *md5_hash, ch;
++ char *md5_hash;
++ int ch;
+ const char *tmpdir;
+ int had_err = 0, rval;
+ FILE *dest;
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-11-06 07:53:25 +0000