[Bioc-devel] avoiding call to ".find.package"
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:
debug(.path.package)
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. Dan
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
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