[R-pkg-team] Bug#945244: r-cran-sf: upstream regression, unaligned access on armhf

[Edzer Pebesma]

Thanks, this has probably been solved in

https://github.com/r-spatial/sf/pull/1154

and will be in the next release.

On 11/21/19 9:38 PM, Andreas Tille wrote:
> Control: tags -1 upstream
> Control: forwarded -1 Edzer Pebesma <edzer.pebesma at uni-muenster.de>
> 
> 
> Hi Edzer,
> 
> as you can read below there is a test suite regression in Ubuntu for
> the armhf architecture.  Do you have any idea how this can be fixed?
> 
> Kind regards
> 
>        Andreas.
> 
> 
> On Thu, Nov 21, 2019 at 11:08:59AM -0800, Steve Langasek wrote:
>> Source: r-cran-sf
>> Version: 0.8-0+dfsg-1
>> Severity: serious
>> User: ubuntu-devel at lists.ubuntu.com
>> 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 at entry=0xfffe7ddc, n_dims=n_dims at entry=2, 
>>     swap=swap at entry=false, cls=..., empty=empty at entry=0x0) at wkb.cpp:201
>> #2  0xf47434b0 in read_matrix_list (wkb=wkb at entry=0xfffe7ddc, 
>>     n_dims=n_dims at entry=2, swap=swap at entry=false, cls=..., 
>>     empty=empty at entry=0xfffe7d27) at /usr/include/c++/9/ext/new_allocator.h:89
>> #3  0xf474430c in read_data (wkb=wkb at entry=0xfffe7ddc, EWKB=EWKB at entry=true, 
>>     spatialite=spatialite at entry=false, endian=endian at entry=1, 
>>     addclass=addclass at entry=true, type=type at entry=0xfffe7dd4, 
>>     srid=srid at 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 at entry=true, 
>>     spatialite=spatialite at 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 at entry=0x2154c48, 
>>     geom=std::vector of length 1, capacity 1 = {...}, dim=<optimized out>, 
>>     free=free at 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)
>>
>> -- 
>> 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
> 
> 
> 
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> 
> 

-- 
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081
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