Bug#945244: r-cran-sf: upstream regression, unaligned access on armhf
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
> >
> >
> > 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-de...@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 (wkb=, wkb=)
> >> at wkb.cpp:201
> >> 201double d = wkb_read(wkb);
> >> (gdb) bt
> >> #0 0xf47431cc in wkb_read (wkb=, wkb= >> 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::allocator >> (GEOSGeom_t*)> > > >&, int, bool) (
> >> hGEOSCtxt=hGEOSCtxt@entry=0x2154c48,
> >> geom=std::vector of length 1, capacity 1 = {...}, dim=,
> >> 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=)
> >> 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/
> >> slanga...@ubuntu.com vor...@debian.org
> >
> >
> >
> >> ___
> >> R-pkg-team mailing list
> >> r-pkg-t...@alioth-lists.debian.net
> >> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team
> >
> >
>
> --
> Edzer Pebesma
> Institute for Geoinformatics
> Heisenbergstrasse 2, 48151 Muenster, Germany
> Phone: +49 251 8333081
pub RSA 3072/EC55D64D 2018-08-28 Edzer Pebesma
> sub RSA 3072/3953CA4C 2018-08-28
>
--
http://fam-tille.de
Bug#945244: r-cran-sf: upstream regression, unaligned access on armhf
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
>
>
> 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-de...@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 (wkb=, wkb=)
>> at wkb.cpp:201
>> 201 double d = wkb_read(wkb);
>> (gdb) bt
>> #0 0xf47431cc in wkb_read (wkb=, wkb=)
>> 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::allocator
>> > > >&, int, bool) (
>> hGEOSCtxt=hGEOSCtxt@entry=0x2154c48,
>> geom=std::vector of length 1, capacity 1 = {...}, dim=,
>> 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=)
>> 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/
>> slanga...@ubuntu.com vor...@debian.org
>
>
>
>> ___
>> R-pkg-team mailing list
>> r-pkg-t...@alioth-lists.debian.net
>> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team
>
>
--
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081
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Description: application/pgp-keys
Bug#945244: r-cran-sf: upstream regression, unaligned access on armhf
Control: tags -1 upstream
Control: forwarded -1 Edzer Pebesma
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-de...@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 (wkb=, wkb=)
> at wkb.cpp:201
> 201 double d = wkb_read(wkb);
> (gdb) bt
> #0 0xf47431cc in wkb_read (wkb=, wkb=)
> 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::allocator
> > > >&, int, bool) (
> hGEOSCtxt=hGEOSCtxt@entry=0x2154c48,
> geom=std::vector of length 1, capacity 1 = {...}, dim=,
> 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=)
> 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/
> slanga...@ubuntu.com vor...@debian.org
> ___
> R-pkg-team mailing list
> r-pkg-t...@alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team
--
http://fam-tille.de
Bug#945244: r-cran-sf: upstream regression, unaligned access on armhf
Source: r-cran-sf
Version: 0.8-0+dfsg-1
Severity: serious
User: ubuntu-de...@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 (wkb=, wkb=)
at wkb.cpp:201
201 double d = wkb_read(wkb);
(gdb) bt
#0 0xf47431cc in wkb_read (wkb=, wkb=)
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::allocator >
> >&, int, bool) (
hGEOSCtxt=hGEOSCtxt@entry=0x2154c48,
geom=std::vector of length 1, capacity 1 = {...}, dim=,
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=)
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/
slanga...@ubuntu.com vor...@debian.org
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