[Debian-med-packaging] Bug#953675: clearcut fails on armhf with glibc 2.31 and linux 4.15 (bad errno handling)

[Steve Langasek]

Package: clearcut
Version: 1.0.9-4
Severity: important
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu focal ubuntu-patch

Dear maintainers,

When introducing glibc 2.31 in Ubuntu, the clearcut autopkgtest showed a
regression on armhf:

[...]
autopkgtest [03:03:16]: test run-unit-test: [-----------------------
Clearcut: Distance value out-of-range.
Clearcut: Syntax error in distance matrix at offset 23.
autopkgtest [03:03:18]: test run-unit-test: -----------------------]
autopkgtest [03:03:20]: test run-unit-test:  - - - - - - - - - - results - - - -
 - - - - - -
run-unit-test        FAIL non-zero exit status 253
[...]

  (https://objectstorage.prodstack4-5.canonical.com/v1/AUTH_77e2ada1e7a84929a74ba3b87153c0ac/autopkgtest-focal/focal/armhf/c/clearcut/20200312_030404_e5698@/log.gz)

I've isolated this to a bug in clearcut itself, which is not handling errno
properly when using it to check for errors from atof() (which is not
standard anyway).  Since glibc 2.31 is opportunistically using a newer
syscall on armhf that's not present in Linux 4.15, errno winds up set to
ENOSYS due to an earlier function call, and clearcut fails to correctly
clear this prior to calling atof(), which has zero guarantee of resetting it
on success.

The attached patch fixes clearcut so that it will work more correctly in any
situation where this occurs, including on armhf with glibc 2.31 and Linux
4.15.

Thanks for considering,
-- 
Steve Langasek                   Give me a lever long enough and a Free OS
Debian Developer                   to set it on, and I can move the world.
Ubuntu Developer                                   https://www.debian.org/
slangasek at ubuntu.com                                     vorlon at debian.org
-------------- next part --------------
diff -Nru clearcut-1.0.9/debian/patches/clear-errno-before-checking.patch clearcut-1.0.9/debian/patches/clear-errno-before-checking.patch
--- clearcut-1.0.9/debian/patches/clear-errno-before-checking.patch	1969-12-31 16:00:00.000000000 -0800
+++ clearcut-1.0.9/debian/patches/clear-errno-before-checking.patch	2020-03-11 23:25:04.000000000 -0700
@@ -0,0 +1,26 @@
+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
+
+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");
diff -Nru clearcut-1.0.9/debian/patches/series clearcut-1.0.9/debian/patches/series
--- clearcut-1.0.9/debian/patches/series	2019-03-28 22:16:52.000000000 -0700
+++ clearcut-1.0.9/debian/patches/series	2020-03-11 23:21:27.000000000 -0700
@@ -1,2 +1,3 @@
 mothur_trivial_patch
 hardening.patch
+clear-errno-before-checking.patch