[R-pkg-devel] Package Rejection Error Help

[Duncan Murdoch]

On 07/04/2021 10:50 a.m., Andrew Dhawan wrote:
> Thank you again Uwe,
> 
> So, to clarify - is the error occurring because RankProd is not found in
> BioC 3.13 (current release is 3.12)?  If so, I'm not sure how I can fix
> this...

I suspect the only thing you could do in the short term is to remove 
that dependency (or move it to Suggests, and check for it before using). 
  If that's not feasible, then you just need to wait for it to become 
available.  Based on its status page, it shouldn't be long.  Try 
submitting again tomorrow?

Duncan Murdoch


> 
> Thanks
> Andrew
> 
> 
> On Wed, Apr 7, 2021 at 5:45 AM Uwe Ligges <ligges using statistik.tu-dortmund.de>
> wrote:
> 
>>
>>
>> On 06.04.2021 19:26, Robert M. Flight wrote:
>>> Andrew,
>>>
>>> I think if you want to include a Bioconductor dependency, then I think
>> you
>>> add the "biocViews:" line to your description file to enable bioconductor
>>
>> Not needed for CRAN.
>>
>> You simply need to declare the dependency, but BioC 3.13 is what we
>> should use to check with R-devel and that was recetnly still pretty
>> iunstable.
>>
>> Best,
>> Uwe Ligges
>>
>>> package installation.
>>>
>>> See this answer on Bioinformatics stackexchange:
>>> https://bioinformatics.stackexchange.com/a/3375/51
>>>
>>> Hope that helps!
>>>
>>> -Robert
>>>
>>> On Tue, Apr 6, 2021 at 1:14 PM Andrew Dhawan <adhawan using qmed.ca> wrote:
>>>
>>>> Thank you both very kindly - I have addressed both notes. I am still
>>>> wondering though about the RankProd dependency error - any insight into
>>>> this?
>>>>
>>>> Thanks!
>>>> Andrew
>>>>
>>>> On Tue, Apr 6, 2021 at 11:58 AM Uwe Ligges <
>>>> ligges using statistik.tu-dortmund.de>
>>>> wrote:
>>>>
>>>>>
>>>>>
>>>>> On 06.04.2021 17:39, Patrick Giraudoux wrote:
>>>>>> I had a similar problem with intepreting "notes" in pgirmess checks.
>>>>>> Some are lethal and lead to rejection and some not (just informative
>>>>>> comments). Fortunately Uwe has been kind enough to tell me what I
>>>> missed
>>>>>> (I thought that all notes were just "informative").
>>>>>> Would it be possible to call lethal notes "errors" to keep us aware
>>>> that
>>>>>> we must really do something with them and fix what is actually a
>>>> problem?
>>>>>
>>>>> These are Notes as it may not be a serious issue or may be a false
>>>>> positive, nevertheless, we like to get clean packages to CRAN.
>>>>>
>>>>> WARNINGs and ERRORs will never be accepted.
>>>>>
>>>>> The policies clearly say that significant Notes have to be addressed.
>>>>> The only Note that is always acceptable is the CRAN maintainer Note
>>>>> about the package maintainer's address. All other Notes should be fixed
>>>>> generally or need manual attention in case of the really very few
>>>>> exceptions.
>>>>>
>>>>> Best,
>>>>> Uwe Ligges
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Best,
>>>>>> Patrick
>>>>>>
>>>>>>
>>>>>> Le 06/04/2021 à 17:33, Uwe Ligges a écrit :
>>>>>>> Two Notes:
>>>>>>>
>>>>>>>
>>>>>>> Found the following (possibly) invalid URLs:
>>>>>>>    URL: http://imagemagick.org/script/download.php (moved to
>>>>>>> https://imagemagick.org/script/download.php)
>>>>>>>      From: inst/doc/vignette.html
>>>>>>>      Status: 200
>>>>>>>      Message: OK
>>>>>>>
>>>>>>>
>>>>>>> Please change http --> https, add trailing slashes, or follow moved
>>>>>>> content as appropriate.
>>>>>>>
>>>>>>> * checking LazyData ... NOTE
>>>>>>>    'LazyData' is specified without a 'data' directory
>>>>>>>
>>>>>>> Simply omit the field if you have no data.
>>>>>>>
>>>>>>> Best,
>>>>>>> Uwe Ligges
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 06.04.2021 16:27, Andrew Dhawan wrote:
>>>>>>>> Dear all,
>>>>>>>>
>>>>>>>> I am a bit puzzled by this error for the sigQC package being
>> uploaded
>>>>> to
>>>>>>>> CRAN. Checks on my end pass without issue. There is one error
>>>>>>>> regarding the
>>>>>>>> bioConductor dependency RankProd that comes up only on the Debian OS
>>>>>>>> when
>>>>>>>> checking. See here for further details:
>>>>>>>>
>>>>>
>>>>
>> https://win-builder.r-project.org/incoming_pretest/sigQC_0.1.22_20210406_110708/
>>>>>>>>
>>>>>>>>
>>>>>>>> I am not sure how to resolve this - it seems to me that the
>>>> dependency
>>>>>>>> *should* be available across platforms, and short of removing the
>>>>>>>> dependency (which we rely on a fair bit), I'm not sure what  we can
>>>> do.
>>>>>>>>
>>>>>>>> Any thoughts or suggestions would be massively appreciated.
>>>>>>>>
>>>>>>>> Thank you so kindly!
>>>>>>>> Andrew
>>>>>>>>
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>>>>>>>>
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>>>>>>
>>>>>>
>>>>>
>>>>
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