[R-pkg-devel] submitting package update failed, since old version out of date (?)

Wed Aug 18 17:25:22 CEST 2021

But the example timing...:
Please reduce each example to less than 5 sec.

Best,
Uwe Ligges

On 17.08.2021 15:53, Aisouda Hoshiyar wrote:
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: ‘Aisouda Hoshiyar <aisouda.hoshiyar using hsu-hh.de>’
> 
> is just a change of the maintainer and already declared in my cran-comments.md file.
> 
> Best
> Aisouda
> 
> 
> 
>> Am 17.08.2021 um 15:42 schrieb Gábor Csárdi <csardi.gabor using gmail.com>:
>>
>> I think they are this:
>>
>> * checking CRAN incoming feasibility ... NOTE
>> ...
>>
>> and this:
>>
>> * checking examples ... [76s/77s] NOTE
>> Examples with CPU (user + system) or elapsed time > 5s
>>                   user system elapsed
>> ordPens-package 54.112  0.044  54.158
>> ordPCA          18.377  0.004  18.382
>>
>> G.
>>
>> On Tue, Aug 17, 2021 at 3:38 PM Aisouda Hoshiyar
>> <aisouda.hoshiyar using hsu-hh.de <mailto:aisouda.hoshiyar using hsu-hh.de>> wrote:
>>>
>>> The CRAN (pretest) email states:
>>>
>>> package ordPens_1.0.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
>>> Debian: <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/00check.log <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/00check.log> <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/00check.log <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/00check.log>>>
>>> Status: 2 NOTEs
>>>
>>> Last released version's CRAN status: NOTE: 13
>>> See: <https://CRAN.R-project.org/web/checks/check_results_ordPens.html <https://cran.r-project.org/web/checks/check_results_ordPens.html> <https://cran.r-project.org/web/checks/check_results_ordPens.html <https://cran.r-project.org/web/checks/check_results_ordPens.html>>>
>>>
>>> Please fix all problems and resubmit a fixed version via the webform.
>>> If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.
>>>
>>> I really don’t understand how else to fix (and what to fix). These are out of date problems of version 0.3-1, which are not relevant any more in version 1.0.0
>>> Version 1.0.0 exactly was a fix to those.
>>>
>>> Do you think I can reply-all & explain that this must be a false-positive?
>>>
>>> Best
>>> Aisouda
>>>
>>>
>>>
>>>> Am 17.08.2021 um 15:22 schrieb Georgi Boshnakov <georgi.boshnakov using manchester.ac.uk <mailto:georgi.boshnakov using manchester.ac.uk>>:
>>>>
>>>> When the previous version has problems, you get an email listing them, followed with something like 'Did you fix them? Please Reply-All...'
>>>>
>>>> Maybe you missed the last phrase?
>>>>
>>>> Georgi Boshnakov
>>>>
>>>>
>>>>
>>>> Get Outlook for Android <https://aka.ms/AAb9ysg <https://aka.ms/AAb9ysg>>
>>>> From: R-package-devel <r-package-devel-bounces using r-project.org <mailto:r-package-devel-bounces using r-project.org>> on behalf of Aisouda Hoshiyar <aisouda.hoshiyar using hsu-hh.de <mailto:aisouda.hoshiyar using hsu-hh.de>>
>>>> Sent: Tuesday, August 17, 2021 12:59:13 PM
>>>> To: r-package-devel using r-project.org <mailto:r-package-devel using r-project.org> <r-package-devel using r-project.org <mailto:r-package-devel using r-project.org>>
>>>> Subject: [R-pkg-devel] submitting package update failed, since old version out of date (?)
>>>>
>>>> Hi,
>>>>
>>>> submitting an update of our package ordPens failed (update version is 1.0.0), reporting the following:
>>>> Version: 1.0.0
>>>> ok
>>>> Version: 0.3-1
>>>> Check: R code for possible problems, Result: NOTE
>>>>   genRidge: no visible global function definition for 'plogis'
>>>>   ordGene: no visible global function definition for 'anova'
>>>>   ordGene: no visible global function definition for 'lm'
>>>>   ordSelect: no visible binding for global variable 'sd'
>>>>   ordSmooth: no visible binding for global variable 'sd'
>>>>   plot.ordPen: no visible global function definition for 'grey'
>>>>   plot.ordPen: no visible global function definition for 'devAskNewPage'
>>>>   plot.ordPen: no visible global function definition for 'lines'
>>>>   predict.ordPen: no visible global function definition for 'plogis'
>>>>   Undefined global functions or variables:
>>>>     anova devAskNewPage grey lines lm plogis sd
>>>>   Consider adding
>>>>     importFrom("grDevices", "devAskNewPage", "grey")
>>>>     importFrom("graphics", "lines")
>>>>     importFrom("stats", "anova", "lm", "plogis", "sd")
>>>>   to your NAMESPACE file.
>>>> Version: 0.3-1
>>>> Check: package dependencies, Result: NOTE
>>>>   Package suggested but not available for checking: ‘IsoGene’
>>>> https://cran.r-project.org/web/checks/check_results_ordPens.html <https://cran.r-project.org/web/checks/check_results_ordPens.html> <https://cran.r-project.org/web/checks/check_results_ordPens.html <https://cran.r-project.org/web/checks/check_results_ordPens.html>> <https://cran.r-project.org/web/checks/check_results_ordPens.html <https://cran.r-project.org/web/checks/check_results_ordPens.html> <https://cran.r-project.org/web/checks/check_results_ordPens.html <https://cran.r-project.org/web/checks/check_results_ordPens.html>>>
>>>>
>>>> https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/ <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/><https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/ <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/>> <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/ <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/><https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/ <https://win-builder.r-project.org/incoming_pretest/ordPens_1.0.0_20210817_114846/Debian/>>>
>>>>
>>>> But these are exactly the new changes that we already took care of in the updated version 1.0.0
>>>> The previous version 0.3-1 is from 2015 and due to R updates, the old package won’t work any more.
>>>> That is exactly the reason for update version 1.0.0, were everything is fixed now.
>>>>
>>>> Also,
>>>> - there is a NOTE about change in maintainer, which is already stated in the cran-comments.md, and the previous maintainer sent an e-main to CRAN as well
>>>> - there is a NOTE saying 'Examples with CPU (user + system) or elapsed time > 10s‘
>>>> which is also stated in the cran-comments.md explaining that cross-validation examples are important for illustrating the package usage.
>>>>
>>>>
>>>> So is this a false positive?
>>>>
>>>> Best
>>>> Aisouda
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
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>>>
>>>
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