bugGNU Octave - Bugs: bug #43948, Installing the geometry package...

 
 

bug #43948: Installing the geometry package fails or causes a crash

Submitted by:  Colin Foster <cfoster>
Submitted on:  Wed 07 Jan 2015 12:56:35 AM UTC  
 
Category:  Octave Forge Package Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Installation Failure
Status:  Works For Me Assigned to:  None
Originator Name:  Colin Foster Open/Closed:  Closed
Release:  3.8.1 Operating System:  GNU/Linux

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Tue 24 Mar 2015 05:27:56 PM UTC, comment #3: 

Is this bug report still valid? I cannot reproduce it with Octave-4.0.0-rc1 and geometry-1.7.0

Philip Nienhuis <philipnienhuis>
Project Member
Wed 07 Jan 2015 01:05:59 AM UTC, comment #2: 

Well, that didn't take too long:

I didn't follow the scientific method and changed two things at once. I ran octave as root and added the -global flag.

Here is the list of all of the packages I had installed, in case there were some dependencies that I might have missed for some reason or another.

Package Name        | Version | Installation directory
--------------------+---------+-----------------------
    communications *|   1.2.0 | /usr/share/octave/packages/communications-1.2.0
           control *|   2.6.6 | /home/colin/octave/control-2.6.6
           general *|   1.3.4 | /usr/share/octave/packages/general-1.3.4
          geometry *|   1.7.0 | /usr/share/octave/packages/geometry-1.7.0
             image  |   2.2.2 | /home/colin/octave/image-2.2.2
instrument-control  |   0.2.0 | /home/colin/octave/instrument-control-0.2.0
    linear-algebra *|   2.2.0 | /usr/share/octave/packages/linear-algebra-2.2.0
            signal *|   1.3.0 | /usr/share/octave/packages/signal-1.3.0
          symbolic *|   1.1.0 | /usr/share/octave/packages/symbolic-1.1.0

Colin Foster <cfoster>
Wed 07 Jan 2015 01:01:42 AM UTC, comment #1: 

More info:

The seg fault happens whether I run the forge or the local version for a second time, so it doesn't seem to have anything to do with downloading it on the fly

Colin Foster <cfoster>
Wed 07 Jan 2015 12:56:35 AM UTC, original submission:  

I apologize for the "or" in the title, but I see two different results when I try to install the geometry package from forge vs locally.

The first:

GNU Octave, version 3.8.1
Copyright (C) 2014 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type 'warranty'.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/get-involved.html

Read http://www.octave.org/bugs.html to learn how to submit bug reports.
For information about changes from previous versions, type 'news'.

octave:1> pkg install -forge -verbose geometry
mkdir (/tmp/oct-ck6rHb)
untar (/home/colin/octave/geometry-1.7.0.tar.gz, /tmp/oct-ck6rHb)
make: Entering directory '/tmp/oct-ck6rHb/geometry/src'
# -i - ignore errors
make[1]: Entering directory '/tmp/oct-ck6rHb/geometry/src/octclip'
/usr/bin/mkoctfile -Wall -Wextra -I. -c calctopo.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c compilador.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c dpeucker.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c errores.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c eucli.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c fgeneral.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c geocnan.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c geocomp.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c greiner.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c polig.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c polil.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c ptopol.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c recpolil.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c segmento.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c ventorno.c
/usr/bin/mkoctfile _oc_polybool.cc calctopo.o compilador.o dpeucker.o errores.o eucli.o fgeneral.o geocnan.o geocomp.o greiner.o polig.o polil.o ptopol.o recpolil.o segmento.o ventorno.o -Wall -Wextra -v  -I.
g++ -c -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-3.8.1/octave/.. -I/usr/include/octave-3.8.1/octave -I/usr/include/mpi  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -pthread -fopenmp  -Wall -Wextra  -I.  _oc_polybool.cc -o _oc_polybool.o
g++ -shared -Wl,-Bsymbolic  -Wall -Wextra -o _oc_polybool.oct  calctopo.o compilador.o dpeucker.o errores.o eucli.o fgeneral.o geocnan.o geocomp.o greiner.o polig.o polil.o ptopol.o recpolil.o segmento.o ventorno.o _oc_polybool.o   -L/usr/lib/x86_64-linux-gnu/octave/3.8.1 -L/usr/lib/x86_64-linux-gnu -loctinterp -loctave -Wl,-Bsymbolic-functions -Wl,-z,relro 
cp _oc_polybool.oct ..
rm fgeneral.o eucli.o polig.o geocomp.o polil.o compilador.o greiner.o geocnan.o dpeucker.o segmento.o errores.o calctopo.o recpolil.o ventorno.o ptopol.o
make[1]: Leaving directory '/tmp/oct-ck6rHb/geometry/src/octclip'
make: Leaving directory '/tmp/oct-ck6rHb/geometry/src'
copyfile /tmp/oct-ck6rHb/geometry/src/_oc_polybool.oct /tmp/oct-ck6rHb/geometry/inst/x86_64-pc-linux-gnu-api-v49+
warning: addpath: //home/colin/octave/geom2d: No such file or directory
warning: addpath: //home/colin/octave/io: No such file or directory
warning: addpath: //home/colin/octave/polygons2d: No such file or directory
warning: addpath: //home/colin/octave/shape2d: No such file or directory
warning: addpath: //home/colin/octave/octclip: No such file or directory
warning: addpath: //home/colin/octave/graphs: No such file or directory
warning: addpath: //home/colin/octave/geom3d: No such file or directory
warning: addpath: //home/colin/octave/meshes3d: No such file or directory
warning: addpath: //home/colin/octave/polynomialCurves2d: No such file or directory
warning: addpath: //home/colin/octave/geom2d: No such file or directory
warning: addpath: //home/colin/octave/io: No such file or directory
warning: addpath: //home/colin/octave/polygons2d: No such file or directory
warning: addpath: //home/colin/octave/shape2d: No such file or directory
warning: addpath: //home/colin/octave/octclip: No such file or directory
warning: addpath: //home/colin/octave/graphs: No such file or directory
warning: addpath: //home/colin/octave/geom3d: No such file or directory
warning: addpath: //home/colin/octave/meshes3d: No such file or directory
warning: addpath: //home/colin/octave/polynomialCurves2d: No such file or directory
/home/colin/octave/geometry-1.7.0/x86_64-pc-linux-gnu-api-v49+/_oc_polybool.oct: failed to load: /home/colin/octave/geometry-1.7.0/x86_64-pc-linux-gnu-api-v49+/_oc_polybool.oct: undefined symbol: GOMP_critical_start
error: called from 'doc_cache_create>create_cache' in file /usr/share/octave/3.8.1/m/help/doc_cache_create.m near line 101, column 18
error: called from:
error:   /usr/share/octave/3.8.1/m/pkg/private/install.m at line 248, column 5
error:   /usr/share/octave/3.8.1/m/pkg/pkg.m at line 394, column 9

Or, when I tried to manually download the package, worse things happened:

octave:4> pkg install -verbose /home/colin/Downloads/geometry-1.7.0.tar.gz
warning: load_path: /home/colin/octave/geometry-1.7.0/x86_64-pc-linux-gnu-api-v49+: No such file or directory
mkdir (/tmp/oct-efzNmJ)
untar (/home/colin/Downloads/geometry-1.7.0.tar.gz, /tmp/oct-efzNmJ)
warning: load_path: /home/colin/octave/geometry-1.7.0/x86_64-pc-linux-gnu-api-v49+: No such file or directory
warning: load_path: /home/colin/octave/geometry-1.7.0/x86_64-pc-linux-gnu-api-v49+: No such file or directory
warning: load_path: /home/colin/octave/geometry-1.7.0/x86_64-pc-linux-gnu-api-v49+: No such file or directory
warning: load_path: /home/colin/octave/geometry-1.7.0/x86_64-pc-linux-gnu-api-v49+: No such file or directory
make: Entering directory '/tmp/oct-efzNmJ/geometry/src'
# -i - ignore errors
make[1]: Entering directory '/tmp/oct-efzNmJ/geometry/src/octclip'
/usr/bin/mkoctfile -Wall -Wextra -I. -c calctopo.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c compilador.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c dpeucker.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c errores.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c eucli.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c fgeneral.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c geocnan.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c geocomp.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c greiner.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c polig.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c polil.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c ptopol.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c recpolil.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c segmento.c
/usr/bin/mkoctfile -Wall -Wextra -I. -c ventorno.c
/usr/bin/mkoctfile _oc_polybool.cc calctopo.o compilador.o dpeucker.o errores.o eucli.o fgeneral.o geocnan.o geocomp.o greiner.o polig.o polil.o ptopol.o recpolil.o segmento.o ventorno.o -Wall -Wextra -v  -I.
g++ -c -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-3.8.1/octave/.. -I/usr/include/octave-3.8.1/octave -I/usr/include/mpi  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -pthread -fopenmp  -Wall -Wextra  -I.  _oc_polybool.cc -o _oc_polybool.o
g++ -shared -Wl,-Bsymbolic  -Wall -Wextra -o _oc_polybool.oct  calctopo.o compilador.o dpeucker.o errores.o eucli.o fgeneral.o geocnan.o geocomp.o greiner.o polig.o polil.o ptopol.o recpolil.o segmento.o ventorno.o _oc_polybool.o   -L/usr/lib/x86_64-linux-gnu/octave/3.8.1 -L/usr/lib/x86_64-linux-gnu -loctinterp -loctave -Wl,-Bsymbolic-functions -Wl,-z,relro 
cp _oc_polybool.oct ..
rm fgeneral.o eucli.o polig.o geocomp.o polil.o compilador.o greiner.o geocnan.o dpeucker.o segmento.o errores.o calctopo.o recpolil.o ventorno.o ptopol.o
make[1]: Leaving directory '/tmp/oct-efzNmJ/geometry/src/octclip'
make: Leaving directory '/tmp/oct-efzNmJ/geometry/src'
warning: load_path: /home/colin/octave/geometry-1.7.0/x86_64-pc-linux-gnu-api-v49+: No such file or directory
copyfile /tmp/oct-efzNmJ/geometry/src/_oc_polybool.oct /tmp/oct-efzNmJ/geometry/inst/x86_64-pc-linux-gnu-api-v49+
panic: Segmentation fault -- stopping myself...
Segmentation fault (core dumped)

I'm running Ubuntu 14.10

Colin Foster <cfoster>

 

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    Follow 3 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2016-02-22 mtmiller StatusNeed Info => Works For Me
        Open/ClosedOpen => Closed
    2015-03-24 philipnienhuis StatusNone => Need Info

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