Re: [R-pkg-devel] Strange error from CRAN on package submission

[Kevin R. Coombes]

Hi Duncan,

I just sent a longer version of this message, but it looks to me like 
the underlying issue is the fact that flexmix and Mercator both define 
and export "show" methods for their S4 classes.  What confuses me is why 
the NAMESPACE of a package that is merely Suggest'ed by something 
several layers down the hierarchy should get attached and cause an issue 
like this one. (The attached NAMESPACE happens in current versions of R.)

Thanks,
  Kevin

On 11/11/2020 1:07 PM, Duncan Murdoch wrote:
Okay, I've tried testing on my Mac with R 4.0.3 and R-devel for the 
new one, 4.0.3 for the CRAN version.

I'm not seeing any check error with the CRAN version.  I get an error 
trying to check 0.11.4 from R-forge because I don't have flexmix 
installed.  If I take flexmix out of the Suggests list, it checks with 
no error on 4.0.3, but I get the error you saw on R-devel when checked 
with --as-cran.

I tried debugging this, and narrowed it down a bit.  It happens when 
your package is installed, in particular in the do_install_source() 
function in src/library/tools/R/install.R. But that function runs a 
new R instance, and I didn't get to debugging that.  I'll try again 
later today if nobody else figures it out.

Duncan Murdoch




On 11/11/2020 12:03 p.m., Kevin R. Coombes wrote:
Hi Duncan,

Oops; I didn't realize I had forgotten to push updates to the OOMPA web
site.

The code for Mercator is contained as part of the Thresher project in
the subversion repository on R-Forge.
(https://r-forge.r-project.org/projects/thresher/) It's under
pkg/Mercator below that URL

Thanks,
    Kevin

On 11/11/2020 11:30 AM, Duncan Murdoch wrote:
Uwe suggested you suggest flexmix, but I see below you already tried
that.

I'd like to take a look, but I can't find your package.  The existing
version on CRAN gives the URL as http://oompa.r-forge.r-project.org/,
but I can't see it mentioned there.

Duncan Murdoch

On 11/11/2020 8:44 a.m., Kevin R. Coombes wrote:
Hi,

I am trying to figure out how to fix warnings from two of the CRAN
machines on the submission of an update to a package. The only 
change to
my package was to add a "show" method to one of the S4 classes, which
was requested by a reviewer of the paper we submitted. The 
inability to
get this updated package into CRAN  is the only thing holding up the
revision (and probable acceptance) of the manuscript.

The same "warnings"s were found in the previous version. The 
package is
called Mercator, and the CRAN check results from the  last version
are here:
https://cran.r-project.org/web/checks/check_results_Mercator.html

I get warnings from the two fedora machine instances (clang and gcc).
They both report

Check: whether package can be installed.
Result: WARN
       Found the following significant  warnings:
       Warning: namespace ‘flexmix’ is  not available and has been
replaced
   >
   > Check: data for non-ASCII characters
Result: WARN
        Warning: namespace 'flexmix'  is not available and has been
replaced
        by .GlobalEnv when processing  object '<unknown>'

The relationships in the DESCRIPTION files are:

1. Mercator depends on Thresher
2. Thresher imports moVMF
3. moMVF suggests flexmix

On my Windows machine, the package builds and installs with no 
errors or
warnings even if flexmix is not available (which I believe to be the
correct behavior). On R-Forge, both the Windows and LINUX versions 
build
and install with no errors or warnings. On R-Hub, tested on multiple
LINUX versions, the package builds and installs with no errors or
warnings.

And flexmix is still clearly available from CRAN:
https://cran.r-project.org/web/packages/flexmix/index.html

In the latest attempt to get things to work, I added
     Suggests: flexmix
into the DESCRIPTION file for Mercator, but this didn't help fix the
problem on CRAN.

Is there anything I can do to fix this problem (other than moan 
here on
this list and hope that CRAN can just install flexmix on those
machines)?

Thanks in advance for your help,
     Kevin

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