Your message dated Fri, 29 Nov 2019 08:43:50 +0000
with message-id <[email protected]>
and subject line Bug#945244: fixed in r-cran-sf 0.8-0+dfsg-3
has caused the Debian Bug report #945244,
regarding r-cran-sf: upstream regression, unaligned access on armhf
to be marked as done.
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Bug report if necessary, and/or fix the problem forthwith.
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945244: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=945244
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: r-cran-sf
Version: 0.8-0+dfsg-1
Severity: serious
User: [email protected]
Usertags: origin-ubuntu focal
Hi Andreas,
With the upload of r-cran-sf 0.8-0+dfsg-1, the autopkgtests are failing in
Ubuntu only on armhf due to a regression in alignment handling:
[...]
Attribute-geometry relationship: 0 constant, 1 aggregate, 1 identity
geometry type: MULTIPOLYGON
dimension: XY
bbox: xmin: 0 ymin: 0 xmax: 1 ymax: 1
epsg (SRID): NA
proj4string: NA
Group.1 a geometry
1 1 1.5 MULTIPOLYGON (((0 0, 1 0, 1...
> (a = aggregate(s, list(c(1,1)), mean, do_union = TRUE))
Bus error (core dumped)
autopkgtest [11:32:17]: test run-unit-test: -----------------------]
[...]
(https://objectstorage.prodstack4-5.canonical.com/v1/AUTH_77e2ada1e7a84929a74ba3b87153c0ac/autopkgtest-focal/focal/armhf/r/r-cran-sf/20191109_113707_4303b@/log.gz)
Since Debian only runs autopkgtests on amd64, this did not block migration
of the new version of the package to Debian testing; nevertheless this is a
serious failure of the package on armhf. I have grabbed a backtrace which
points to a problem in r-cran-sf itself, not in any of its dependencies:
Program received signal SIGBUS, Bus error.
0xf47431cc in wkb_read<double> (wkb=<optimized out>, wkb=<optimized out>)
at wkb.cpp:201
201 double d = wkb_read<double>(wkb);
(gdb) bt
#0 0xf47431cc in wkb_read<double> (wkb=<optimized out>, wkb=<optimized out>)
at wkb.cpp:201
#1 read_numeric_matrix (wkb=wkb@entry=0xfffe7ddc, n_dims=n_dims@entry=2,
swap=swap@entry=false, cls=..., empty=empty@entry=0x0) at wkb.cpp:201
#2 0xf47434b0 in read_matrix_list (wkb=wkb@entry=0xfffe7ddc,
n_dims=n_dims@entry=2, swap=swap@entry=false, cls=...,
empty=empty@entry=0xfffe7d27) at /usr/include/c++/9/ext/new_allocator.h:89
#3 0xf474430c in read_data (wkb=wkb@entry=0xfffe7ddc, EWKB=EWKB@entry=true,
spatialite=spatialite@entry=false, endian=endian@entry=1,
addclass=addclass@entry=true, type=type@entry=0xfffe7dd4,
srid=srid@entry=0xfffe7dd8)
at /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/generic_proxy.h:37
#4 0xf474590a in CPL_read_wkb (wkb_list=..., EWKB=EWKB@entry=true,
spatialite=spatialite@entry=false)
at /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/generic_proxy.h:37
#5 0xf472d5da in sfc_from_geometry(GEOSContextHandle_HS*,
std::vector<std::unique_ptr<GEOSGeom_t, std::function<void (GEOSGeom_t*)> >,
std::allocator<std::unique_ptr<GEOSGeom_t, std::function<void (GEOSGeom_t*)> >
> >&, int, bool) (
hGEOSCtxt=hGEOSCtxt@entry=0x2154c48,
geom=std::vector of length 1, capacity 1 = {...}, dim=<optimized out>,
free=free@entry=true)
at /usr/lib/R/site-library/Rcpp/include/Rcpp/vector/traits.h:65
#6 0xf472f542 in CPL_geos_union (sfc=..., by_feature=<optimized out>)
at geos.cpp:600
#7 0xf47100d8 in _sf_CPL_geos_union (sfcSEXP=0x1f0d988,
by_featureSEXP=0x419568)
at /usr/lib/R/site-library/Rcpp/include/Rcpp/as.h:151
#8 0xf7ce238c in ?? () from /usr/lib/R/lib/libR.so
Backtrace stopped: previous frame identical to this frame (corrupt stack?)
(gdb)
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--- End Message ---
--- Begin Message ---
Source: r-cran-sf
Source-Version: 0.8-0+dfsg-3
We believe that the bug you reported is fixed in the latest version of
r-cran-sf, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated r-cran-sf package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 29 Nov 2019 08:53:08 +0100
Source: r-cran-sf
Binary: r-cran-sf
Architecture: source
Version: 0.8-0+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
r-cran-sf - Simple Features for R
Closes: 945244
Changes:
r-cran-sf (0.8-0+dfsg-3) unstable; urgency=medium
.
* Resolve UBSAN error in wkb_read
Closes: #945244
* Standards-Version: 4.4.1
* Set upstream metadata fields: Bug-Submit.
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