[med-svn] [Git][med-team/clearcut][master] 7 commits: clear errno before using it to check failure from atof()
Andreas Tille
gitlab at salsa.debian.org
Thu Mar 12 10:08:32 GMT 2020
Andreas Tille pushed to branch master at Debian Med / clearcut
Commits:
72550355 by Andreas Tille at 2020-03-12T09:40:20+01:00
clear errno before using it to check failure from atof()
- - - - -
0ab28bbf by Andreas Tille at 2020-03-12T09:40:49+01:00
routine-update: Standards-Version: 4.5.0
- - - - -
57008fec by Andreas Tille at 2020-03-12T09:40:50+01:00
routine-update: debhelper-compat 12
- - - - -
03bb9665 by Andreas Tille at 2020-03-12T09:40:54+01:00
R-U: Trailing whitespace in debian/copyright
- - - - -
70721f02 by Andreas Tille at 2020-03-12T09:40:54+01:00
routine-update: Add salsa-ci file
- - - - -
08c20cda by Andreas Tille at 2020-03-12T11:05:59+01:00
Propagate CFLAGS to upstream Makefile
- - - - -
6a365aed by Andreas Tille at 2020-03-12T11:07:36+01:00
Upload to unstable
- - - - -
8 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/clear-errno-before-checking.patch
- debian/patches/hardening.patch
- debian/patches/series
- + debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+clearcut (1.0.9-5) unstable; urgency=medium
+
+ [ Steve Langasek ]
+ * clear errno before using it to check failure from atof()
+ Closes: #953675
+
+ [ Andreas Tille ]
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 12 (routine-update)
+ * Remove trailing whitespace in debian/copyright (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Propagate CFLAGS to upstream Makefile
+
+ -- Andreas Tille <tille at debian.org> Thu, 12 Mar 2020 11:06:18 +0100
+
clearcut (1.0.9-4) unstable; urgency=medium
* Team upload.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,8 +4,8 @@ Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.2.1
+Build-Depends: debhelper-compat (= 12)
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/clearcut
Vcs-Git: https://salsa.debian.org/med-team/clearcut.git
Homepage: http://bioinformatics.hungry.com/clearcut/
=====================================
debian/copyright
=====================================
@@ -32,7 +32,7 @@ License: getopt
Files: prng.*
Copyright: (C) 1997-2002, Makoto Matsumoto <m-mat at math.sci.hiroshima-u.ac.jp>
- and Takuji Nishimura, All rights reserved.
+ and Takuji Nishimura, All rights reserved.
License: BSDlike
License: BSDlike
@@ -47,8 +47,8 @@ License: BSDlike
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
.
- 3. The names of its contributors may not be used to endorse or promote
- products derived from this software without specific prior written
+ 3. The names of its contributors may not be used to endorse or promote
+ products derived from this software without specific prior written
permission.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
=====================================
debian/patches/clear-errno-before-checking.patch
=====================================
@@ -0,0 +1,27 @@
+Description: clear errno before using it to check failure from atof()
+ The atof() function is not guaranteed to clear errno on success, so if
+ any earlier errors have been set prior to calling atof(), these will
+ result in a spurious failure. On armhf, glibc 2.31 now opportunistically
+ calls a new syscall that may not be supported on older kernels (Linux 4.15),
+ resulting in errno == ENOSYS:
+ .
+ syscall_0x193(0x5, 0xffb2b650, 0xf77b7000, 0, 0x5, 0xffb2b650) = -1 ENOSYS (Function not implemented)
+ .
+ Therefore we should clear errno before calling atof() to make sure any
+ errors actually originate from this function.
+Author: Steve Langasek <steve.langasek at ubuntu.com>
+Last-Update: 2020-03-11
+Bug-Debian: https://bugs.debian.org/953675
+
+Index: clearcut-1.0.9/dmat.c
+===================================================================
+--- clearcut-1.0.9.orig/dmat.c
++++ clearcut-1.0.9/dmat.c
+@@ -570,6 +570,7 @@
+ goto XIT_BAD;
+ }
+
++ errno = 0;
+ val = atof(token->buf);
+ if(errno) {
+ fprintf(stderr, "Clearcut: Distance value out-of-range.\n");
=====================================
debian/patches/hardening.patch
=====================================
@@ -4,6 +4,15 @@ Description: Propagate hardening options
--- a/Makefile
+++ b/Makefile
+@@ -73,7 +73,7 @@ CC = gcc
+ ######################## ALL ARCHITECTURES ##################################
+
+ # DEFAULT GCC OPTIMIZATION CONFIGURATION (ALL ARCHITECTURES)
+-CFLAGS = -O3 -Wall -funroll-loops -fomit-frame-pointer
++CFLAGS += -O3 -Wall -funroll-loops -fomit-frame-pointer
+
+ # BASIC OPTIMIZATION
+ #CFLAGS = -O3
@@ -124,7 +124,7 @@ clean:
$(CC) -c $(INCDIRS) $(CFLAGS) $(OPTFLAG) $(DEFS) $<
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
mothur_trivial_patch
hardening.patch
+clear-errno-before-checking.patch
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
View it on GitLab: https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45
--
View it on GitLab: https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45
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