[R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Alberto Garre]

Dear community,

I feel dismay for having to write this email, but the issue must be brought
up. On the 20th of October, I received an email from CRAN warning me of an
issue with one of the packages I maintain (bioOED). The package depended on
MEIGOR, a package that was no longer available in Bioconductor. I was given
until 2023-11-03 to fix the issue.

I contacted the MEIGOR maintainers and they told me they were migrating to
CRAN. Yesterday, they contacted me again, telling me they needed more time
for the migration. Hence, I responded to the email I received from CRAN,
asking for an extension of the previous deadline (2023-11-03).

To my surprise, it is not just that the extension was not granted, but the
package has been removed from CRAN today (2023-11-01). Two days before the
deadline (2023-11-03): https://cran.r-project.org/package=bioOED

Then, I checked my inbox and I saw an email from one of the CRAN
maintainers, showing that the package was removed because he had felt
offended by my email. I copy-paste the email below.

I understand that maintaining CRAN must be a huge work. I also work in
academia, so I am totally aware of all the extra work that is required from
us. But it is unreasonable that a package can be removed just because a
maintainer throws a tantrum

Again, I am really sorry I had to write this email, but CRAN cannot work if
we allow this type of situation.

Kind regards,
Alberto Garre

## Mail from rip...@stats.ox.ac.uk on 2023-11-01 8:28

On 31/10/2023 17:21, Alberto Garre wrote:
> Dear Brian,

Do be respectful whoever you are (you lack the manners to use a
signature block but send HTML when you agreed not to!).  What exactly
have you done for me that would allow you treat me as if I were your peer?

Your ingratitude (for CRAN and R) is deafening.

> I have talked to the MEIGOR developers and they need a bit more time to
> update their package. Would it be possible to get a 4 weeks extension for
> the update of bioOED?

No one can even install it in current R, so it has been removed.

"The time of the volunteers is CRAN’s most precious resource"

Professor Ripley

>
> Thank you very much,
> Alberto
>
>
> El vie, 20 oct 2023 a las 9:24, Alberto Garre ()
> escribió:
>
>> Thank you very much, Brian.
>>
>> I have just contacted the developers of MEIGOR because I think they were
>> planning a migration to CRAN. I will update the package asap.
>>
>> Best,
>> Alberto
>>
>>
>> El vie, 20 oct 2023 a las 9:22, Prof Brian Ripley ()
>> escribió:
>>
>>> On 20/10/2023 08:17, Prof Brian Ripley wrote:
>>>> Dear maintainer,
>>>>
>>>> Please see the problems shown on
>>>> <https://cran.r-project.org/web/checks/check_results_bioOED.html>.
>>>>
>>>> Please correct before 2023-11-03 to safely retain your package on CRAN.
>>>>
>>>> The CRAN Team
>>>>
>>> This requires package MEIGOR which is not part of BioC 3.18 and has been
>>> deprecated so it very unlikely to be part of the final release next
week.
>>>
>>>
>>> --
>>> Brian D. Ripley,  rip...@stats.ox.ac.uk
>>> Emeritus Professor of Applied Statistics, University of Oxford
>>>
>>>

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Re: [R-pkg-devel] How to communicate WARNINGS fixed from *last* CRAN version of a package

[Alberto Garre]

Yes, the submission contains a cran-comments.md, which mentions these
changes.


El mar, 22 jun 2021 a las 14:36, Spencer Graves (<
spencer.gra...@effectivedefense.org>) escribió:

> Have you followed the advice in chapter 20 of Wickham and Bryan, R
> Packages:
>
>
> https://r-pkgs.org/release.html
>
>
>   In particular, does your package include a file
> "cran-comments.md",
> as described therein?
>
>
>   I believe that's where the CRAN maintainers look for info like
> that.
>
>
>   Also, those instructions suggest you check reverse
> dependencies.  The
> last time I tried to follow those instructed, it didn't work.  Instead I
> needed:
>
>
> https://github.com/r-lib/revdepcheck
>
>
> devtools::install_github("r-lib/revdepcheck")
>
>
> library(revdepcheck)
>
>
> revdep_check()
>
>
>   Hope this helps.
>   Spencer Graves
>
>
> On 6/22/21 6:53 AM, Alberto Garre wrote:
> > Thanks. I just "replied-to-all" again. Gmail then sends the email to
> > cran-submissi...@r-project.org. Is this the correct address?
> >
> > El mar, 22 jun 2021 a las 12:38, Georgi Boshnakov (<
> > georgi.boshna...@manchester.ac.uk>) escribió:
> >
> >>> ... Hence please reply-all and explain: Have these been fixed?
> >>
> >> Maybe 'reply-all' to CRAN team's  email?
> >>
> >> Georgi Boshnakov
> >>
> >> -Original Message-
> >> From: R-package-devel  On Behalf
> >> Of Alberto Garre
> >> Sent: 22 June 2021 09:11
> >> To: R-package-devel@r-project.org
> >> Subject: [R-pkg-devel] How to communicate WARNINGS fixed from *last*
> CRAN
> >> version of a package
> >>
> >> Hi,
> >>
> >> I submitted yesterday a new version of the biogrowth package (
> >> https://cran.r-project.org/package=biogrowth). In the automatic
> response,
> >> I got the following message:
> >>
> >> The auto-check found additional issues for the *last* version released
> on
> >> CRAN:
> >>donttest <https://www.stats.ox.ac.uk/pub/bdr/donttest/biogrowth.out>
> >>M1mac <https://www.stats.ox.ac.uk/pub/bdr/M1mac/biogrowth.out>
> >> CRAN incoming checks do not test for these additional issues.
> >> Hence please reply-all and explain: Have these been fixed?
> >>
> >> I resubmitted mentioning in cran-comments.md that these problems had
> been
> >> resolved, but I got again the same automatic response. Then, I answered
> >> directly to the automatic email with no effect.
> >>
> >> How should I communicate these issues have been fixed? Is there any
> >> additional issue I am not seeing?
> >>
> >> Thank you,
> >> Alberto
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> __
> >> R-package-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>

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Re: [R-pkg-devel] How to communicate WARNINGS fixed from *last* CRAN version of a package

[Alberto Garre]

Thanks. I just "replied-to-all" again. Gmail then sends the email to
cran-submissi...@r-project.org. Is this the correct address?

El mar, 22 jun 2021 a las 12:38, Georgi Boshnakov (<
georgi.boshna...@manchester.ac.uk>) escribió:

> >... Hence please reply-all and explain: Have these been fixed?
>
> Maybe 'reply-all' to CRAN team's  email?
>
> Georgi Boshnakov
>
> -Original Message-
> From: R-package-devel  On Behalf
> Of Alberto Garre
> Sent: 22 June 2021 09:11
> To: R-package-devel@r-project.org
> Subject: [R-pkg-devel] How to communicate WARNINGS fixed from *last* CRAN
> version of a package
>
> Hi,
>
> I submitted yesterday a new version of the biogrowth package (
> https://cran.r-project.org/package=biogrowth). In the automatic response,
> I got the following message:
>
> The auto-check found additional issues for the *last* version released on
> CRAN:
>   donttest <https://www.stats.ox.ac.uk/pub/bdr/donttest/biogrowth.out>
>   M1mac <https://www.stats.ox.ac.uk/pub/bdr/M1mac/biogrowth.out>
> CRAN incoming checks do not test for these additional issues.
> Hence please reply-all and explain: Have these been fixed?
>
> I resubmitted mentioning in cran-comments.md that these problems had been
> resolved, but I got again the same automatic response. Then, I answered
> directly to the automatic email with no effect.
>
> How should I communicate these issues have been fixed? Is there any
> additional issue I am not seeing?
>
> Thank you,
> Alberto
>
> [[alternative HTML version deleted]]
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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Re: [R-pkg-devel] How to communicate WARNINGS fixed from *last* CRAN version of a package

[Alberto Garre]

Yes, I answered on 21 jun at 18:56

El mar, 22 jun 2021 a las 11:26, Martin Maechler (<
maech...@stat.math.ethz.ch>) escribió:

> >>>>> Alberto Garre
> >>>>> on Tue, 22 Jun 2021 10:52:26 +0200 writes:
>
> > Thanks! It is the first time I got this message, so I was a bit
> puzzled
> > about what to do. I will be patient, then :)
>
> > Alberto
>
> well, as Sebastian said
>
> >> The auto-check e-mail said "Hence please reply-all and explain". If
> you
> >> followed these instructions, you will just need some more patience.
>
> so, did you "reply-all" to that automated e-mail and explain
> that you fixed them?
>
> You need to do this even when you had it in the "submitter's comments".
>
> Martin
>
>
>
> > El mar, 22 jun 2021 a las 10:50, Sebastian Meyer ( >)
> > escribió:
>
> >> Am 22.06.21 um 10:11 schrieb Alberto Garre:
> >> > Hi,
> >> >
> >> > I submitted yesterday a new version of the biogrowth package (
> >> > https://cran.r-project.org/package=biogrowth). In the automatic
> >> response, I
> >> > got the following message:
> >> >
> >> > The auto-check found additional issues for the *last* version
> released on
> >> > CRAN:
> >> >   donttest <
> https://www.stats.ox.ac.uk/pub/bdr/donttest/biogrowth.out>
> >> >   M1mac <https://www.stats.ox.ac.uk/pub/bdr/M1mac/biogrowth.out>
> >> > CRAN incoming checks do not test for these additional issues.
> >> > Hence please reply-all and explain: Have these been fixed?
> >> >
> >> > I resubmitted mentioning in cran-comments.md that these problems
> had been
> >> > resolved, but I got again the same automatic response. Then, I
> answered
> >> > directly to the automatic email with no effect.
> >> >
> >> > How should I communicate these issues have been fixed? Is there
> any
> >> > additional issue I am not seeing?
> >>
> >> The auto-check e-mail said "Hence please reply-all and explain". If
> you
> >> followed these instructions, you will just need some more patience.
> You
> >> submitted only yesterday evening and these checks require manual
> >> inspection by the CRAN team. I can see your submission in the
> "inspect"
> >> folder of the incoming queue (https://CRAN.R-project.org/incoming/
> ).
> >>
> >> Best regards,
> >>
> >> Sebastian Meyer
> >>
> >> >
> >> > Thank you,
> >> > Alberto
> >> >
> >> >   [[alternative HTML version deleted]]
> >> >
> >> > __
> >> > R-package-devel@r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> >
> >>
>
> > [[alternative HTML version deleted]]
>
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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Re: [R-pkg-devel] How to communicate WARNINGS fixed from *last* CRAN version of a package

[Alberto Garre]

Thanks! It is the first time I got this message, so I was a bit puzzled
about what to do. I will be patient, then :)

Alberto


El mar, 22 jun 2021 a las 10:50, Sebastian Meyer ()
escribió:

> Am 22.06.21 um 10:11 schrieb Alberto Garre:
> > Hi,
> >
> > I submitted yesterday a new version of the biogrowth package (
> > https://cran.r-project.org/package=biogrowth). In the automatic
> response, I
> > got the following message:
> >
> > The auto-check found additional issues for the *last* version released on
> > CRAN:
> >   donttest <https://www.stats.ox.ac.uk/pub/bdr/donttest/biogrowth.out>
> >   M1mac <https://www.stats.ox.ac.uk/pub/bdr/M1mac/biogrowth.out>
> > CRAN incoming checks do not test for these additional issues.
> > Hence please reply-all and explain: Have these been fixed?
> >
> > I resubmitted mentioning in cran-comments.md that these problems had been
> > resolved, but I got again the same automatic response. Then, I answered
> > directly to the automatic email with no effect.
> >
> > How should I communicate these issues have been fixed? Is there any
> > additional issue I am not seeing?
>
> The auto-check e-mail said "Hence please reply-all and explain". If you
> followed these instructions, you will just need some more patience. You
> submitted only yesterday evening and these checks require manual
> inspection by the CRAN team. I can see your submission in the "inspect"
> folder of the incoming queue (https://CRAN.R-project.org/incoming/).
>
> Best regards,
>
> Sebastian Meyer
>
> >
> > Thank you,
> > Alberto
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>

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[R-pkg-devel] How to communicate WARNINGS fixed from *last* CRAN version of a package

[Alberto Garre]

Hi,

I submitted yesterday a new version of the biogrowth package (
https://cran.r-project.org/package=biogrowth). In the automatic response, I
got the following message:

The auto-check found additional issues for the *last* version released on
CRAN:
  donttest 
  M1mac 
CRAN incoming checks do not test for these additional issues.
Hence please reply-all and explain: Have these been fixed?

I resubmitted mentioning in cran-comments.md that these problems had been
resolved, but I got again the same automatic response. Then, I answered
directly to the automatic email with no effect.

How should I communicate these issues have been fixed? Is there any
additional issue I am not seeing?

Thank you,
Alberto

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[R-pkg-devel] check_win_release cannot find tidyr and other common packages?

[Alberto Garre]

Hi!

I am preparing an R package to be uploaded to CRAN. I have already checked
using rhub and every check passed. I have also checked using winbuilder for
the release version of R (devtools:check_win_release) and there were no
ERRORs or WARNINGs. However, for the devel version
(devtools:check_win_devel) I got the following error:

checking package dependencies ... ERROR
Packages required but not available:
  'tidyr', 'googlesheets', 'stringr', 'readtext'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

I would really appreciate some help to figure out what's going on. This is
the relevant part of my DESCRIPTION file:

Imports:
XML (>= 3.98),
purrr (>= 0.2.4),
dplyr (>= 0.7.8),
tibble (>= 2.0.0),
tidyr (>= 0.7.2),
rlang (>= 0.3.0.1),
googlesheets (>= 0.3.0),
stringr (>= 1.4.0),
readxl (>= 1.3.1),
readtext (>= 0.7.1),
zip (>= 2.0.4),
xml2 (>= 1.2.0),
rjson (>= 0.2.20),
shiny (>= 1.3.2),
tools (>= 3.5.3),
utils (>= 3.5.3),
R.utils (>= 2.9.0)
Suggests:
knitr (>= 1.9),
rmarkdown (>= 1.12),
testthat
VignetteBuilder: knitr


Report from win_builder:
https://win-builder.r-project.org/EYkQRkLpS8oa/00check.log

Thanks!
Alberto

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