R devel - May 2015 - example fails during R CMD CHECK but works interactively?

Make the example print out Sys.getenv() and then manually inspect?

Otherwise, you'll need to debug the code by adding print statements.
Something clearly is not as you expect, so you need carefully
empirically verify your assumptions about the inputs to and
environment of the function.

Hadley

On Fri, May 15, 2015 at 7:05 AM, Charles Determan <cdetermanjr at
gmail.com> wrote:
> Does anyone else have any thoughts about troubleshooting the R CMD check
> environment?
>
> Charles
>
> On Wed, May 13, 2015 at 1:57 PM, Charles Determan <cdetermanjr at
gmail.com>
> wrote:
>
>> Thank you Dan but it isn't my tests that are failing (all of them
pass
>> without problem) but one of the examples from the inst/examples
directory.
>> I did try, however, to start R with the environmental variables as you
>> suggest but it had no effect on my tests.
>>
>> Charles
>>
>> On Wed, May 13, 2015 at 1:51 PM, Dan Tenenbaum <dtenenba at
fredhutch.org>
>> wrote:
>>
>>>
>>>
>>> ----- Original Message -----
>>> > From: "Charles Determan" <cdetermanjr at
gmail.com>
>>> > To: r-devel at r-project.org
>>> > Sent: Wednesday, May 13, 2015 11:31:36 AM
>>> > Subject: [Rd] example fails during R CMD CHECK but works
interactively?
>>> >
>>> > Greetings,
>>> >
>>> > I am collaborating with developing the bigmemory package and
have run
>>> > in to
>>> > a strange problem when we run R CMD CHECK.  For some reason
that
>>> > isn't
>>> > clear to us one of the examples crashes stating:
>>> >
>>> > Error:  memory could not be allocated for instance of type
big.matrix
>>> >
>>> > You can see the output on the Travis CI page at
>>> > https://travis-ci.org/kaneplusplus/bigmemory where the error
starts
>>> > at line
>>> > 1035.  This is completely reproducible when running
>>> > devtools::check(args='--as-cran') locally.  The part
that is
>>> > confusing is
>>> > that the calls work perfectly when called interactively.
>>> >
>>> > Hadley comments on the 'check' page of his R packages
website (
>>> > http://r-pkgs.had.co.nz/check.html) regarding test failing
following
>>> > R CMD
>>> > check:
>>> >
>>> > Occasionally you may have a problem where the tests pass when
run
>>> > interactively with devtools::test(), but fail when in R CMD
check.
>>> > This
>>> > usually indicates that you?ve made a faulty assumption about
the
>>> > testing
>>> > environment, and it?s often hard to figure it out.
>>> >
>>> > Any thoughts on how to troubleshoot this problem?  I have no
idea
>>> > what
>>> > assumption we could have made.
>>>
>>> Note that R CMD check runs R with environment variables set as
follows
>>> (at least on my system; you can check $R_HOME/bin/check to see what
it does
>>> on yours):
>>>
>>>  R_DEFAULT_PACKAGES= LC_COLLATE=C
>>>
>>> So try staring R like this:
>>>
>>>  R_DEFAULT_PACKAGES= LC_COLLATE=C  R
>>>
>>> And see if that reproduces the test failure. The locale setting
could
>>> affect tests of sort order, and the default package setting could
>>> potentially affect other things.
>>>
>>> Dan
>>>
>>>
>>>
>>> >
>>> > Regards,
>>> > Charles
>>> >
>>> >       [[alternative HTML version deleted]]
>>> >
>>> > ______________________________________________
>>> > R-devel at r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/r-devel
>>> >
>>>
>>
>>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


-- 
http://had.co.nz/

On 15 May 2015 at 07:13, Hadley Wickham wrote:
| Make the example print out Sys.getenv() and then manually inspect?

On the systems I use    system("env")     is more efficient as it gets
you
all at once. 
 
| Otherwise, you'll need to debug the code by adding print statements.
| Something clearly is not as you expect, so you need carefully
| empirically verify your assumptions about the inputs to and
| environment of the function.

Exactly. No magic here, just plainstaken debugging.

As an old ~/.signature of mine said: "In theory, theory and practice are
the
same. In practie, they are not."  Assumptions are good.  We all get a good
laugh out of them after the fact.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

On 15 May 2015 at 07:47, Dirk Eddelbuettel wrote:
| 
| On 15 May 2015 at 07:13, Hadley Wickham wrote:
| | Make the example print out Sys.getenv() and then manually inspect?
| 
| On the systems I use    system("env")     is more efficient as it
gets you
| all at once. 

Ahh, yes, and I have since been told (thanks, Hadley) that Sys.getenv() does
just that -- and I remain a big fan of how R generally abstracts the OS away.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org