[R-pkg-devel] submitting package update failed, since old version out of date (?)

Am 17.08.2021 um 15:42 schrieb G?bor Cs?rdi <csardi.gabor at 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 at hsu-hh.de <mailto:aisouda.hoshiyar at 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 These are out of date problems of version 0.3-1, which are not relevant any more in version 1.0.0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 at manchester.ac.uk <mailto:georgi.boshnakov at 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 at r-project.org <mailto:r-package-devel-bounces at r-project.org>> on behalf of Aisouda Hoshiyar <aisouda.hoshiyar at hsu-hh.de <mailto:aisouda.hoshiyar at hsu-hh.de>>
Sent: Tuesday, August 17, 2021 12:59:13 PM
To: r-package-devel at r-project.org <mailto:r-package-devel at r-project.org> <r-package-devel at r-project.org <mailto:r-package-devel at 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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