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 <[email protected]> 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 <[email protected]>, Andreas Tille <[email protected]> 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 <[email protected]> - 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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