[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
>>>>
>>>>      [[alternative HTML version deleted]]
>>>>
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>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>
>>>
>>
>