[med-svn] [Git][med-team/readseq][master] 4 commits: fix-gets.patch: new: replace gets by fgets.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / readseq


Commits:
2d13ad1b by Étienne Mollier at 2024-03-14T22:01:04+01:00
fix-gets.patch: new: replace gets by fgets.

Closes: #1066478

- - - - -
3dbd9be9 by Étienne Mollier at 2024-03-14T21:07:33+00:00
Remove unnecessary get-orig-source-target.

Changes-By: lintian-brush
Fixes: lintian: debian-rules-contains-unnecessary-get-orig-source-target
See-also: https://lintian.debian.org/tags/debian-rules-contains-unnecessary-get-orig-source-target.html

- - - - -
6db151e4 by Étienne Mollier at 2024-03-14T21:07:33+00:00
Update standards version to 4.6.2, no changes needed.

Changes-By: lintian-brush
Fixes: lintian: out-of-date-standards-version
See-also: https://lintian.debian.org/tags/out-of-date-standards-version.html

- - - - -
a90817c6 by Étienne Mollier at 2024-03-14T22:09:39+01:00
ready to upload to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/fix-gets.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+readseq (1-15) unstable; urgency=medium
+
+  * Team upload.
+  * fix-gets.patch: new: replace gets by fgets. (Closes: #1066478)
+  * Remove unnecessary get-orig-source-target.
+  * Update standards version to 4.6.2, no changes needed.
+
+ -- Étienne Mollier <emollier at debian.org>  Thu, 14 Mar 2024 22:07:41 +0100
+
 readseq (1-14) unstable; urgency=medium
 
   * Standards-Version: 4.5.0 (routine-update)


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                ncbi-tools-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/readseq
 Vcs-Git: https://salsa.debian.org/med-team/readseq.git
 Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/


=====================================
debian/patches/fix-gets.patch
=====================================
@@ -0,0 +1,41 @@
+Description: fix gets invocations.
+ gets(3) manual page explicitly mentions to not make use of this function
+ anymore.  This patch replaces their invocations to fgets instead, with a
+ hardcoded size allocation.  This is not pretty perhaps, but way better than
+ the unbound gets invocations.
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1066478
+Forwarded: no
+Last-Update: 2024-03-14
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- readseq.orig/readseq.c
++++ readseq/readseq.c
+@@ -798,7 +798,7 @@
+   if (askout && !closeout && !quietly) {
+     askout = false;
+     fprintf(stderr,"\nName of output file (?=help, defaults to display): \n");
+-    gets(oname= onamestore);
++    fgets(oname= onamestore, 127, stdin);
+     skipwhitespace(oname);
+     if (*oname == '?') { usage(); exit_main(0); }
+     else if (*oname != 0) {
+@@ -862,7 +862,7 @@
+       fprintf(stderr,"\nName an input sequence or -option: \n");
+       inputfile= inputfilestore;
+ 
+-      gets(stemp= stempstore);
++      fgets(stemp= stempstore, 127, stdin);
+       if (*stemp==0) goto fini;  /* !! need this to finish work during interactive use */
+       stemp= strtok(stempstore, " \n\r\t");
+       while (stemp) {
+@@ -908,7 +908,7 @@
+       else if (whichSeq > nseq || !quietly) {
+         dumpSeqList(seqlist, format);
+         fprintf(stderr,"\nChoose a sequence (# or All): \n");
+-        gets(stemp= stempstore);
++        fgets(stemp= stempstore, 127, stdin);
+         skipwhitespace(stemp);
+         if (to_lower(*stemp) == 'a') {
+           chooseall= true;


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ enable_tests.patch
 hardening.patch
 buffer_overflow.patch
 fix_tests.patch
+fix-gets.patch


=====================================
debian/rules
=====================================
@@ -10,6 +10,3 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 override_dh_clean:
 	dh_clean
 	rm -f readseq
-
-get-orig-source:
-	. debian/get-orig-source



View it on GitLab: https://salsa.debian.org/med-team/readseq/-/compare/ead6764ec373dd5c05557e6a2ca8a75474fcf9f8...a90817c6038aa23167be9708823602d024e2ca62

-- 
View it on GitLab: https://salsa.debian.org/med-team/readseq/-/compare/ead6764ec373dd5c05557e6a2ca8a75474fcf9f8...a90817c6038aa23167be9708823602d024e2ca62
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240314/b303f261/attachment-0001.htm>