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

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]]

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]]

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 05/15/2015 05:05 AM, Charles Determan wrote:
> Does anyone else have any thoughts about troubleshooting the R CMD check
> environment?
In the pkg.Rcheck directory there is a file pkg-Ex.R.

LANGUAGE=en _R_CHECK_INTERNALS2_=1 $(R_HOME)/bin/R --vanilla pkge-Ex.R

followed by the usual strategy of bisecting the file into smaller chunks that 
still reproduce the example.

(this is based on my parsing of the complicated source, most relevant at

   https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L2467

and

   https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L36

)

Martin
>
> 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
>

-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

The error can be reproduced by running the bigmemory-Ex.R script which
you can find in the bigmemory.Rcheck directory, either in batch mode or
via source() in an interactive session.

It seems that you have underlying memory allocation problems. I can get
the script to running by adding gc() calls when necessary (i.e. when a
failure is reported, add gc() just before this point in the script and
rerun).

Martyn

On Fri, 2015-05-15 at 07:05 -0500, Charles Determan
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