I have actual data in one of them.
A little bit of testing show replacing 
gap_cmd=“gap -r”
by
gap_cmd=“gap”
in interface/gap.py has no side effects on doctesting apart from letting
the doctest in question pass when ~/.gap is not empty.
I’ll open a ticket later.

François

> On 27/05/2019, at 3:05 PM, Steven Trogdon <[email protected]> wrote:
> 
> Yes, the two important folders on vanilla sage are
> 
> ls -al local/share/gap/pkg/atlasrep/data*
> 
> local/share/gap/pkg/atlasrep/datagens:
> total 12
> drwxr-xr-x 2 strogdon math 4096 Mar 30 20:09 .
> drwxr-xr-x 9 strogdon math 4096 Mar 30 20:09 ..
> -rw-r--r-- 1 strogdon math   70 Mar 30 20:05 dummy
> 
> local/share/gap/pkg/atlasrep/dataword:
> total 12
> drwxr-xr-x 2 strogdon math 4096 Mar 30 20:09 .
> drwxr-xr-x 9 strogdon math 4096 Mar 30 20:09 ..
> -rw-r--r-- 1 strogdon math   70 Mar 30 20:05 dummy
> 
> And the contents of dummy, in both folders, is:
> 
> This file is only for causing that the directory is created by `zoo'.
> 
> On Sunday, May 26, 2019 at 5:59:52 PM UTC-5, François Bissey wrote:
> Actually this is a little bit more complicated than what I thought. This test 
> is likely to fail
> on sage-on-gentoo and probably other distro.
> atlasrep is a very naughty gap package that download data from the internet 
> and
> wants to put it in its installation directory. Which is a problem for a 
> system wide install
> where it belongs to root.
> So I adopted some patches from debian to have the data downloaded and stored 
> in
> ~/.gap. So what we see here in ~/.gap is not a package install but the result 
> of
> using atlasrep at any point. It is likely ~/.gap/pkg/AtlasRep will re-appear 
> all by
> itself during doctesting.
> 
> So we really need to improve on this situation.
> 1) does gap need to be run with "-r"
> 2) if it does what do we do about the fact that ~/.gap is skipped when using 
> the pexpect interface.
> 
> Francois
> 
> On Saturday, May 25, 2019 at 1:21:58 PM UTC+12, François Bissey wrote:
> We’ll want some kind of follow up. The test will fail if you have something 
> in ~/.gap. 
> Not just on sage-on-gentoo. 
> The question is whether the pexpect interface should continue starting `gap` 
> with the 
> “-r” option or not. 
> 
> François 
> 
> > On 25/05/2019, at 12:17 PM, Steven Trogdon <[email protected]> wrote: 
> > 
> > Found this also first on s-o-g. So should ~/.gap be empty or is a follow-up 
> > to https://trac.sagemath.org/ticket/27681 necessary? 
> > On Friday, May 24, 2019 at 7:04:53 PM UTC-5, François Bissey wrote: 
> > You have something in ~/.gap. See 
> > https://trac.sagemath.org/ticket/27681#comment:30 
> > 
> > > On 25/05/2019, at 12:02 PM, Steven Trogdon <[email protected]> wrote: 
> > > 
> > > As far as I know this failure started with this beta. 
> > > 
> > > sage -t --long src/sage/tests/gap_packages.py 
> > > ********************************************************************** 
> > > File "src/sage/tests/gap_packages.py", line 137, in 
> > > sage.tests.gap_packages.all_installed_packages 
> > > Failed example: 
> > >     all_installed_packages() == all_installed_packages(gap=gap) 
> > > Expected: 
> > >     True 
> > > Got: 
> > >     False 
> > > ********************************************************************** 
> > > 1 item had failures: 
> > >    1 of   4 in sage.tests.gap_packages.all_installed_packages 
> > >     [10 tests, 1 failure, 1.04 s] 
> > > 
> > > 
> > > For info: 
> > > 
> > > sage: from sage.tests.gap_packages import all_installed_packages 
> > > sage: all_installed_packages() 
> > > ('AtlasRep', 
> > >  'FactInt', 
> > >  'GAPDoc', 
> > >  'SmallGrp', 
> > >  'alnuth', 
> > >  'atlasrep', 
> > >  'autpgrp', 
> > >  'crisp', 
> > >  'ctbllib', 
> > >  'fga', 
> > >  'irredsol', 
> > >  'laguna', 
> > >  'polenta', 
> > >  'polycyclic', 
> > >  'primgrp', 
> > >  'resclasses', 
> > >  'sophus', 
> > >  'tomlib', 
> > >  'transgrp') 
> > > sage: all_installed_packages(gap=gap) 
> > > ('FactInt', 
> > >  'GAPDoc', 
> > >  'SmallGrp', 
> > >  'alnuth', 
> > >  'atlasrep', 
> > >  'autpgrp', 
> > >  'crisp', 
> > >  'ctbllib', 
> > >  'fga', 
> > >  'irredsol', 
> > >  'laguna', 
> > >  'polenta', 
> > >  'polycyclic', 
> > >  'primgrp', 
> > >  'resclasses', 
> > >  'sophus', 
> > >  'tomlib', 
> > >  'transgrp') 
> > > 
> > > ls ~/.gap/pkg/ 
> > > AtlasRep 
> > > 
> > > 
> > > 
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