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

[Andreas Tille]

Thanks a lot - that was super quick!

On Thu, Nov 21, 2019 at 09:50:16PM +0100, Edzer Pebesma wrote:
> 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

pub   RSA 3072/EC55D64D 2018-08-28 Edzer Pebesma <edzer.pebesma at uni-muenster.de>
> sub   RSA 3072/3953CA4C 2018-08-28
> 

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