606770 – sci-libs/shogun-4.1.0 Cannot build. 5 variations of SandBox violations from R support.

Bug 606770 - sci-libs/shogun-4.1.0 Cannot build. 5 variations of SandBox violations from R support.

Summary: sci-libs/shogun-4.1.0 Cannot build. 5 variations of SandBox violations from R...

Status:	RESOLVED FIXED

Alias:	None

Product:	Gentoo Linux
Classification:	Unclassified
Component:	Current packages (show other bugs)
Hardware:	AMD64 Linux

Importance:	Normal normal (vote)
Assignee:	Gentoo Science Related Packages

URL:
Whiteboard:
Keywords:

Depends on:
Blocks:

Reported:	2017-01-22 05:38 UTC by deference
Modified:	2017-02-04 21:09 UTC (History)
CC List:	1 user (show)

See Also:
Package list:
Runtime testing required:	---

Attachments
build (build-shogun-4.1.0-0.log.gz,54.36 KB, text/plain) 2017-01-22 05:44 UTC, deference	Details
build2 (build-shogun-4.1.0-1.log.gz,76.17 KB, text/plain) 2017-01-22 05:44 UTC, deference	Details
build3 (build-shogun-4.1.0-2.log.gz,67.47 KB, text/plain) 2017-01-22 05:44 UTC, deference	Details
build4 (build-shogun-4.1.0-3.log.gz,61.73 KB, text/plain) 2017-01-22 05:45 UTC, deference	Details
build5 (build-shogun-4.1.0-4.log.gz,61.73 KB, text/plain) 2017-01-22 05:45 UTC, deference	Details
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Description deference 2017-01-22 05:38:35 UTC

0
[ebuild   R   ] sci-libs/shogun-4.1.0  USE="R doc* -examples -lua -mono -octave -python -ruby -static-libs {-test}" PYTHON_SINGLE_TARGET="python3_4 -python2_7 -python3_5" PYTHON_TARGETS="python2_7 python3_4 -python3_5" 
1
[ebuild   R   ] sci-libs/shogun-4.1.0  USE="R examples* -doc -lua -mono -octave -python -ruby -static-libs {-test}" PYTHON_SINGLE_TARGET="python3_4 -python2_7 -python3_5" PYTHON_TARGETS="python2_7 python3_4 -python3_5" 
2
[ebuild   R   ] sci-libs/shogun-4.1.0  USE="R lua* -doc -examples -mono -octave -python -ruby -static-libs {-test}" PYTHON_SINGLE_TARGET="python3_4 -python2_7 -python3_5" PYTHON_TARGETS="python2_7 python3_4 -python3_5" 
3
[ebuild   R   ] sci-libs/shogun-4.1.0  USE="R mono* -doc -examples -lua -octave -python -ruby -static-libs {-test}" PYTHON_SINGLE_TARGET="python3_4 -python2_7 -python3_5" PYTHON_TARGETS="python2_7 python3_4 -python3_5" 
4
[ebuild     UD] sci-mathematics/octave-3.6.4 [3.8.2-r1] USE="X curl doc fftw glpk gnuplot hdf5 imagemagick opengl postscript qhull qrupdate readline sparse static-libs zlib -graphicsmagick (-gui%*) (-java%*)" 
[ebuild   R   ] sci-libs/shogun-4.1.0  USE="R octave* -doc -examples -lua -mono -python -ruby -static-libs {-test}" PYTHON_SINGLE_TARGET="python3_4 -python2_7 -python3_5" PYTHON_TARGETS="python2_7 python3_4 -python3_5" 

This may be simmilar to 587324.

* --------------------------- ACCESS VIOLATION SUMMARY ---------------------------
 * LOG FILE: "/var/log/sandbox/sandbox-6689.log"
  *
  VERSION 1.0
  FORMAT: F - Function called
  FORMAT: S - Access Status
  FORMAT: P - Path as passed to function
  FORMAT: A - Absolute Path (not canonical)
  FORMAT: R - Canonical Path
  FORMAT: C - Command Line
  
  F: open_wr
  S: deny
  P: /usr/lib64/R/library/sg/DESCRIPTION
  A: /usr/lib64/R/library/sg/DESCRIPTION
  R: /usr/lib64/R/library/sg/DESCRIPTION
  C: bash /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0/src/.r-install.sh /usr/lib64/R/library sg so saveRDS
  
  F: fopen_wr
  S: deny
  P: /usr/lib64/R/library/sg/Meta/package.rds
  A: /usr/lib64/R/library/sg/Meta/package.rds
  R: /usr/lib64/R/library/sg/Meta/package.rds
  C: /usr/lib64/R/bin/exec/R --no-save
  
  F: open_wr
  S: deny
  P: /usr/lib64/R/library/sg/NAMESPACE
  A: /usr/lib64/R/library/sg/NAMESPACE
  R: /usr/lib64/R/library/sg/NAMESPACE
  C: bash /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0/src/.r-install.sh /usr/lib64/R/library sg so saveRDS
  
  F: open_wr
  S: deny
  P: /usr/lib64/R/library/sg/R/sg
  A: /usr/lib64/R/library/sg/R/sg
  R: /usr/lib64/R/library/sg/R/sg
  C: bash /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0/src/.r-install.sh /usr/lib64/R/library sg so saveRDS
   * --------------------------------------------------------------------------------

Comment 1 deference 2017-01-22 05:44:25 UTC

Created attachment 460880 [details]
build

Comment 2 deference 2017-01-22 05:44:40 UTC

Created attachment 460882 [details]
build2

Comment 3 deference 2017-01-22 05:44:53 UTC

Created attachment 460884 [details]
build3

Comment 4 deference 2017-01-22 05:45:05 UTC

Created attachment 460886 [details]
build4

Comment 5 deference 2017-01-22 05:45:48 UTC

Created attachment 460888 [details]
build5

Comment 6 David Seifert gentoo-dev

2017-02-04 21:09:48 UTC

Fixed for me in 5.0.0, reopen if issue persists with latest version.

commit 8d85f22fd38976093c4b3d3a9f5d30954e689c14
Author: David Seifert <soap@gentoo.org>
Date:   Sat Feb 4 22:02:10 2017 +0100

    sci-libs/shogun: Version bump to 5.0.0
    
    Gentoo-bug: 550134, 570014, 587324, 593310,
                602534, 604670, 606770, 607122