[Rd] Spurious warning in as.data.frame.factor()

2024-03-12 Thread Hervé Pagès 
Hi,

The acrobatics that as.data.frame.factor() is going thru in order to 
recognize a direct call don't play nice if as.data.frame() is an S4 
generic:

     df <- as.data.frame(factor(11:12))

     suppressPackageStartupMessages(library(BiocGenerics))
     isGeneric("as.data.frame")
     # [1] TRUE

     df <- as.data.frame(factor(11:12))
     # Warning message:
     # In as.data.frame.factor(factor(11:12)) :
     #   Direct call of 'as.data.frame.factor()' is deprecated. Use 
'as.data.frame.vector()' or 'as.data.frame()' instead

This spurious warning showed up on the recent Bioconductor daily build 
reports after we've updated the build machines to the latest R devel. 
It's causing some confusion and breaks at least one unit test.

Thanks,

H.

 > sessionInfo()
R Under development (unstable) (2024-03-06 r86056)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
  [3] LC_TIME=en_GB  LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
  [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

other attached packages:
[1] BiocGenerics_0.49.1

loaded via a namespace (and not attached):
[1] compiler_4.4.0

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [R-pkg-devel] Submission after archived version

2024-03-12 Thread Ivan Krylov via R-package-devel 
В Mon, 11 Mar 2024 23:45:13 +0100
Nils Mechtel  пишет:

> Debian:
> 
> Status: 3 NOTEs

>> * checking CRAN incoming feasibility ... [4s/6s] NOTE

>> Possibly misspelled words in DESCRIPTION:
>>  metabolomics (36:78)

This one can be explained in the submission comment. The rest of the
NOTE is to be expected.

>> * checking DESCRIPTION meta-information ... NOTE
>> Author field differs from that derived from Authors@R

Just remove the Author: field from your DESCRIPTION and let R CMD build
automatically generate it from Authors@R.

>> * checking for non-standard things in the check directory ... NOTE
>> Found the following files/directories:
>>  ‘metabolomics_data.csv’

Make sure that when your tests and examples create files, they do so in
the session temp directory and then remove the files afterwards. If a
user had a valuable file named metabolomics_data.csv in the current
directory, ran example(...) and had it overwritten as a result, they
would be very unhappy.

The NOTEs on Windows are similar.

Good luck!

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Submission after archived version

2024-03-12 Thread Duncan Murdoch 

On 11/03/2024 6:45 p.m., Nils Mechtel wrote:

Hi,

Our package was archived at the end of last year, and after some major rework 
we submitted a newer version yesterday. Despite R CMD check not giving any 
errors or warnings, the package doesn’t pass the pre-tests:

package MetAlyzer_1.0.0.tar.gz does not pass the incoming checks automatically, 
please see the following pre-tests:
Windows: 

Status: 2 NOTEs
Debian: 

Status: 3 NOTEs

Last released version's CRAN status: OK: 5, ERROR: 8
See: 


Do we miss something here?


The first note is mostly informational, though you might want to mention 
that metabolomics is spelled correctly in your submission message.


The second note should be fixed.  Apparently your package has both 
Authors and Authors@R fields.  Delete Authors and that should go away.


The third note only happened on one system, so it may be a false 
positive, but what it says is that your checks created a file called 
metabolomics_data.csv some place where it shouldn't have created it. 
You should only be writing in the temp directory, and you should clean 
up afterwards.


Duncan Murdoch

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[R-pkg-devel] Submission after archived version

2024-03-12 Thread Nils Mechtel 
Hi,

Our package was archived at the end of last year, and after some major rework 
we submitted a newer version yesterday. Despite R CMD check not giving any 
errors or warnings, the package doesn’t pass the pre-tests:

package MetAlyzer_1.0.0.tar.gz does not pass the incoming checks automatically, 
please see the following pre-tests:
Windows: 

Status: 2 NOTEs
Debian: 

Status: 3 NOTEs

Last released version's CRAN status: OK: 5, ERROR: 8
See: 


Do we miss something here?

Best,
Nils
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Re: [Bioc-devel] about deprecate package DNABarcode

2024-03-12 Thread Kern, Lori via Bioc-devel 
The package is deprecated in devel.  It will remain listed in the next Bioc 
3.19 release, but deprecated, and removed from anticipated 3.20.  The package 
will have up until the fall release (generally late Oct / early Nov) to 
reinstate before it will be removed.

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Sun Wenjie 

Sent: Tuesday, March 12, 2024 8:07 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] about deprecate package DNABarcode

Hi Bioconductor core team,

I saw the package of DNABarcode is listed as to be deprecated.

I am trying to reach the author. Do you know when will be the deadline?

Best,
Wenjie

--
Wenjie SUN
Postdoctoral researcher
UMR168, Curie Institute
E-mail: wenjie@curie.fr
Address: batiment Curie, RDC.13A
11 rue Pierre et Marie Curie, 75005 Paris
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Re: [R-pkg-devel] [EXTERN] Re: [EXTERN] Re: [EXTERN] Re: @doctype is deprecated. need help for r package documentation

2024-03-12 Thread Duncan Murdoch 

On 12/03/2024 6:58 a.m., Ivan Krylov via R-package-devel wrote:

В Mon, 11 Mar 2024 14:57:58 +
"Ruff, Sergej"  пишет:


I uploaded the old version of the package to my repo:
https://github.com/SergejRuff/boot


After installing this tarball, running RStudio and typing:

library(bootGSEA)
?bootGSEA

...I see the help page in RStudio's help tab, not in the browser. I
think this is the expected behaviour for RStudio.


You can tell R to use an external browser in RStudio by setting the 
"browser" option.  For example,


  options(browser="open")

causes help to open in the default browser on MacOS.  See ?browseURL for 
details of how to specify other browsers.


Duncan Murdoch

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Re: [Bioc-devel] Unable to install "spoon" package due to R version 4.4 dependence

2024-03-12 Thread Kern, Lori via Bioc-devel 
mac can get R-devel at this location
https://mac.r-project.org/


Cheers


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of James W. 
MacDonald 
Sent: Monday, March 11, 2024 2:55 PM
To: Kinnary Shah ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Unable to install "spoon" package due to R version 
4.4 dependence

It depends on your OS. If you are on a Linux derivative not named macOS, you 
can get the sources here: 
https://secure-web.cisco.com/1VKCo1TIgcVvB_RkbMNJOfTtQs5LtXoTcvqqbNlDQOQCCvqL1JIsYw5M2rB4WHdCCjRkjQgUfxG2oNGX4bIpaOAEcJ2Id_tXwOK8GbXblf2-RbzebBQwCqlU3yIG0pWu6ek7HBmaWIZLSO4kBVJM08iaGLzsvSW3u5pesul5JadBzOi-fLN8GJivzOPB4qVTi6GK_31gSj8ymQOJRX0qIeriaufkcJrMz8nkTyKyDG4veE11jyY5uFbVOJwrTTrtG5bpOHS9DLWanCVxdSPS5yek2CtytbYHfXKEoWjuJMxRN5NtyjGHSjHXwPOj7PKKK/https%3A%2F%2Fcran.r-project.org%2Fsrc%2Fbase-prerelease%2F
 You want R-devel with the latest date. If you are on Windows, you can get the 
installer here 
https://secure-web.cisco.com/12QgdaFs2d324PR9Ms_FzbMPQo2wMXcrsIVg019uHNHke8C_M-HKR1IWZuKkAMMS7Dj9ccPhGvWsle7M3R4yJq_JqUbWQlrw6Pbazoup6q9p3nJcxYyXm5rZjZ4juvoWI0SwQHjJIRj4C7wVz7wsr0nHU3Nysg15aa10sYErFR-1cNl2kS0i8M8Ml0nydpz1bahTb6rApr-OaVIQwf3MFpXqPjrgFGZidzUgynpi69-9l29HQ8eKBNtwURu3THEq1ppw6xz0vXT9Mm8p1-l1ZmZoKx99_qL0AUx0SOd0KviDOHppl_zXCo8L04d_WwLv-/https%3A%2F%2Fcran.r-project.org%2Fbin%2
 Fwindows%2Fbase%2Frdevel.html If you are on macOS, presumably you can get 
R-devel, but I don't use a Mac so cannot help with that.

Best,

Jim



-Original Message-
From: Bioc-devel  On Behalf Of Kinnary Shah
Sent: Monday, March 11, 2024 2:23 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Unable to install "spoon" package due to R version 4.4 
dependence

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Dear BioC developers,

My package, "spoon", was successfully built last week. I was told in the review 
process to update the dependence of R to version 4.4. When I try to install the 
devel version of Bioconductor to test my package installation, it also requires 
R version 4.4. Based on the cran website, it says the latest release is R 
version 4.3.3. Is there a way to I proceed if I need a newer version of R that 
is not released yet?

Thanks,
Kinnary

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Re: [Bioc-devel] Deprecate pwOmics package

2024-03-12 Thread Kern, Lori via Bioc-devel 
Thank you .  We will begin the deprecation process.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Torsten 
Schoeps 
Sent: Tuesday, March 12, 2024 6:45 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Deprecate pwOmics package

Hello,

I would like to deprecate the pwOmics-Package from Bioconductor.

The package wasn't written/developed by me and the original author
left our department long time ago.

Now building  the package for BioC 3.19 recently failed and
I have neither time nor knowledge to fix the package.

Regards,
Torsten Sch�ps

--
Dipl.-Inf.(FH)
Torsten Schoeps,
Network and System Administrator

Department of Medical Bioinformatics
University  Medical Center Goettingen
Goldschmidstr.1
37077 Goettingen

email: torsten.scho...@bioinf.med.uni-goettingen.de
phone: +49 551 3961785
fax:   +49 551 3961783

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[Bioc-devel] Deprecate pwOmics package

2024-03-12 Thread Torsten Schoeps 

Hello,

I would like to deprecate the pwOmics-Package from Bioconductor.

The package wasn't written/developed by me and the original author
left our department long time ago.

Now building  the package for BioC 3.19 recently failed and
I have neither time nor knowledge to fix the package.

Regards,
Torsten Schöps

--
Dipl.-Inf.(FH)
Torsten Schoeps,
Network and System Administrator

Department of Medical Bioinformatics
University  Medical Center Goettingen
Goldschmidstr.1
37077 Goettingen

email: torsten.scho...@bioinf.med.uni-goettingen.de
phone: +49 551 3961785
fax:   +49 551 3961783

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Re: [Bioc-devel] un-deprecation gscreend

2024-03-12 Thread Katharina Imkeller 
Thank you Lori!
I also pushed the changes to RELEASE_3_18 branch now.
Best, Katharina

On 11.03.24 16:47, Kern, Lori wrote:
> Yes we will un-deprecate the package.  If possible it would be great 
> to also push the changes to RELEASE_3_18 branch as well if you have 
> not done so already
> https://bioconductor.org/checkResults/release/bioc-LATEST/gscreend/
>
> Cheers,
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> *From:* Bioc-devel  on behalf of 
> Katharina Imkeller 
> *Sent:* Monday, March 11, 2024 11:41 AM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] un-deprecation gscreend
> Dear Bioconductor core team,
>
> I would like to request un-deprecation for the package gscreend.
>
> https://secure-web.cisco.com/14JVyxHsWuD9xTgZjxG019I7-lVyiIBJCtHPAUHylTVCJYqx1qHZEumCmsbct4T5tfhP9vinl9A9K4pW0CPqab5BC3Tj9Dy9BvLwPCwFdQeeSdlFHGTYxSiwcvNxLAApqTZ9zqTqUy_BDO6isJqbEdDoWFO4-Izj0jfaJqxpxg2mYUFT0BRRnQHa6kR8NrU_TXGuD6U1WDS57tHHRfV5yamGpJIQtC_Ro6ixAFPkX_g6Fbf_Io0DJref5OxOgH-ZD6rxQskJsJGUlXHwcQ9z5_LmwQ5rT2hhlmuIInUnhbhxa0EgilShPO00vpCg_B_RM/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2Fgscreend.html
>
> I fixed the error related to BiocStyle in the DESCRIPTION file.
>
> Thank you, Katharina
>
> ___
> Bioc-devel@r-project.org mailing list
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>
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> or agent responsible for the delivery of this message to the intended 
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> received this message in error, please notify the sender immediately 
> by e-mail and delete this email message from your computer. Thank you. 


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Re: [R-pkg-devel] [EXTERN] Re: [EXTERN] Re: [EXTERN] Re: @doctype is deprecated. need help for r package documentation

2024-03-12 Thread Ivan Krylov via R-package-devel 
В Mon, 11 Mar 2024 14:57:58 +
"Ruff, Sergej"  пишет:

> I uploaded the old version of the package to my repo:
> https://github.com/SergejRuff/boot

After installing this tarball, running RStudio and typing:

library(bootGSEA)
?bootGSEA

...I see the help page in RStudio's help tab, not in the browser. I
think this is the expected behaviour for RStudio.

-- 
Best regards,
Ivan

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