[Bioc-devel] avoiding call to ".find.package"

Dan Tenenbaum dtenenba at fhcrc.org
Thu Mar 7 18:48:47 CET 2013

On Thu, Mar 7, 2013 at 8:24 AM, Thomas Sandmann
<sandmann.thomas at gene.com> wrote:
> My gCMAP package also throws this warning. I have been trying to find the
> guilty .path.package() through several layers of CRAN dependencies already,
> but am still looking.

One thing you could try would be to run R CMD check on the package
which will produce a gCMAP.Rcheck/gCMAP-Ex.R file contaning all your
example code (since the warning seems to come from one or more man
page examples).
Then start R:
source("gCMAP-Ex.R", echo=TRUE, max=Inf)

That may trigger it in which case R will say something like:
"debugging in .path.package('foo')" where foo is likely to be the
guilty party
However, I was not able to do this because a recent change to gCMAP
seems to cause an error--it fails build in today's build report.

> In case I cannot find / convince the author of the package containing the
> .path.package() call to correct the function call: Is there anything else I
> can do to deal with this warning other than removing the dependency ?

It's ok to let the warning happen in this case, once you've done all
you can. There are ways to suppress warnings but sometimes it's better
to know they are happening; you don't want to suppress an unexpected
warning by mistake.


> Thanks,
> Thomas
> On Tue, Mar 5, 2013 at 2:03 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> On Tue, Mar 5, 2013 at 1:29 PM, Elana Fertig <ejfertig at jhmi.edu> wrote:
>> > I'm having a similar problem with my package, CoGAPS, which Is giving a
>> > warning for .path.package that does not appear to be anywhere in my code,
>> > nor does it depend on Biobase.  Any suggestions would be greatly
>> > appreciated!
>> This means a package that you depend on, or some upstream dependency,
>> stil calls .path.package(). In your case it's the gdata package frm
>> CRAN.
>> Dan
>> >
>> > Elana
>> >
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> --
> Thomas Sandmann
> Computational biologist
> Genentech, Inc.
> 1 DNA Way
> South San Francisco, CA 94080
> Phone: +1 650 225 6273
> Fax: +1 650 225 5389
> Email: sandmann.thomas at gene.com

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