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

[Kevin R. Coombes]

Oh, I forgot to mention explicitly that checking (with --as-cran) on the 
development version of R on Windows also produces no errors or warnings.

On 11/11/2020 1:39 PM, Kevin R. Coombes wrote:
> 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]]
>>>>>
>>>>> ______________________________________________
>>>>> R-package-devel using r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>
>>>>
>>>
>>
>