[med-svn] [Git][med-team/staden-io-lib][master] 4 commits: Work around missing declaration of encode_names in libhtscodecs2 version 1.3.0

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / staden-io-lib


Commits:
fc2a8e11 by Andreas Tille at 2022-10-28T07:16:28+02:00
Work around missing declaration of encode_names in libhtscodecs2 version 1.3.0

- - - - -
c3f481ed by Andreas Tille at 2022-10-28T07:19:40+02:00
routine-update: Standards-Version: 4.6.1

- - - - -
c702dda3 by Andreas Tille at 2022-10-28T07:19:53+02:00
Set upstream metadata fields: Archive.

Changes-By: lintian-brush

- - - - -
6aab4d95 by Andreas Tille at 2022-10-28T07:24:32+02:00
routine-update: Ready to upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/tok3_decode_names.patch
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+staden-io-lib (1.14.14+dfsg-2) unstable; urgency=medium
+
+  * Work around missing declaration of encode_names in libhtscodecs2
+    version 1.3.0
+    Closes: #1022282
+  * Standards-Version: 4.6.1 (routine-update)
+  * Set upstream metadata fields: Archive.
+
+ -- Andreas Tille <tille at debian.org>  Fri, 28 Oct 2022 07:19:58 +0200
+
 staden-io-lib (1.14.14+dfsg-1) unstable; urgency=medium
 
   * Fix watchfile to detect new versions on github


=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
                d-shlibs,
                libbz2-dev,
                liblzma-dev
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/staden-io-lib
 Vcs-Git: https://salsa.debian.org/med-team/staden-io-lib.git
 Homepage: https://github.com/jkbonfield/io_lib


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@
 pathmax.patch
 fix_fseeko.patch
 usedebianhtscodecs.patch
+tok3_decode_names.patch


=====================================
debian/patches/tok3_decode_names.patch
=====================================
@@ -0,0 +1,42 @@
+Author: Bernhard Übelacker <bernhardu at mailbox.org>
+Last-Update: Thu, 27 Oct 2022 16:21:53 +0200
+Origin: https://bugs.debian.org/1022282#12
+Bug-Debian: https://bugs.debian.org/1022282
+Description: short term solution for missing declaration of encode_names in libhtscodecs2 version 1.3.0
+ libhtscodecs2 version 1.3.0 renamed e.g. function encode_names
+ to tok3_encode_names.  It added a compatibility function
+ encode_names, but does not declare it in the header file.
+ Therefore in the build of staden-io-lib the function encode_names
+ is implicitly declared - therefore seems to default to
+ a return type of int - and therefore the returned pointer
+ gets truncated to the lower 4 bytes.
+ This get through unnoticed until the pointer is freed and
+ produces a segfault there.
+ .
+ Probably the right thing would be to have the short function name
+ in the header file of htscodecs, therefore solve this issue for
+ other packages using htscodecs.
+ .
+ This patch implements a short term solution which makes
+ the build and tests succeed without "implicit declarations".
+
+--- a/io_lib/cram_io.c
++++ b/io_lib/cram_io.c
+@@ -2162,7 +2162,7 @@ int cram_uncompress_block(cram_block *b)
+ 
+     case NAME_TOK3: {
+ 	uint32_t out_len;
+-	uint8_t *cp = decode_names(b->data, b->comp_size, &out_len);
++	uint8_t *cp = tok3_decode_names(b->data, b->comp_size, &out_len);
+ 	b->orig_method = NAME_TOK3;
+ 	b->method = RAW;
+ 	free(b->data);
+@@ -2417,7 +2417,7 @@ static char *cram_compress_by_method(cra
+ 	int lev = level;
+ 	if (method == NAME_TOK3 && lev > 3)
+ 	    lev = 3;
+-	uint8_t *cp = encode_names(in, in_size, lev, strat, &out_len, NULL);
++	uint8_t *cp = tok3_encode_names(in, in_size, lev, strat, &out_len, NULL);
+ 	*out_size = out_len;
+ 	return (char *)cp;
+     }


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Archive: SourceForge
 Repository: https://github.com/jkbonfield/io_lib.git
 Repository-Browse: https://github.com/jkbonfield/io_lib
 Bug-Database: https://github.com/jkbonfield/io_lib/issues



View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/f1180dbbb7f531fe0488fc29524bf060e3565e91...6aab4d9567e9e6ed048f4c19e6de30767a3aa4ef

-- 
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/f1180dbbb7f531fe0488fc29524bf060e3565e91...6aab4d9567e9e6ed048f4c19e6de30767a3aa4ef
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