Bug 675490

Summary:	sci-chemistry/gromacs-2018.3 - sandbox violation in mkostemp /usr/share/fonts/util/.uuid.TMP-XXXXXX
Product:	Gentoo Linux	Reporter:	Vytautas <vytautas1987>
Component:	Current packages	Assignee:	Alexey Shvetsov <alexxy>
Status:	RESOLVED WORKSFORME
Severity:	normal	CC:	bkohler, sci-chemistry
Priority:	Normal
Version:	unspecified
Hardware:	AMD64
OS:	Linux
See Also:	https://bugs.gentoo.org/show_bug.cgi?id=679858
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	emerge --info

Description Vytautas 2019-01-15 13:36:14 UTC

Failed to emerge sci-chemistry/gromacs-2018.3

Comment 1 Vytautas 2019-01-15 13:38:28 UTC

Created attachment 561196 [details]
emerge --info

Comment 2 Vytautas 2019-01-15 13:40:27 UTC

Build log is whooping 1.6 Mb

Message like this repeated a lot:
 F: mkostemp
S: deny
P: /usr/share/fonts/util/.uuid.TMP-XXXXXX
A: /usr/share/fonts/util/.uuid.TMP-XXXXXX
R: /usr/share/fonts/util/.uuid.TMP-XXXXXX
C: /usr/bin/gs -P- -dSAFER -dCompatibilityLevel=1.4 -dEPSCrop -q -P- -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sstdout=%stderr -sOutputFile=/var/tmp/portage/sci-chemistry/gromacs-2018.3/work/gromacs-2018.3_float/docs/manual/plots/pulldirrel.pdf -P-  * --------------------------------------------------------------------------------

Comment 3 Ben Kohler gentoo-dev

2019-01-15 13:52:11 UTC

Try running "fc-cache -r" as root, then see if the gromacs emerge succeeds.

Comment 4 Vytautas 2019-01-21 09:13:37 UTC

I tried:
  fc-cache -r
  emerge gromacs
and it works.

Comment 5 Alexey Shvetsov archtester

2019-06-03 07:04:57 UTC

This version is no longer in portage. Latest one is 2019.2 or 2018.7 in previos branch