[R-pkg-devel] How to fix Archived Package Rpdb?
Dear Members, I would like to reanimate the archived package Rpdb: https://cran.r-project.org/web/packages/Rpdb/index.html 1.) I have tried to contact the original author by email, but got no response. 2.) New Repository on GitHub I have copied the existing code to a new repository on GitHub: https://github.com/discoleo/Rpdb - fixed the use of deprecated functions (rgl); - fixed some bug with Roxygen2; - I hope that all errors are now fixed; 2.b.) Description file - I left the original author as the author (with the provided e-mail address): should I delete this email? - I have added myself as maintainer; - I have increased the last digit of the version number; - I have added links to this new GitHub repository: I did not find any other links in the previous version (except to the pdb-format); - updated the licence to GPL v3: the original does not specify any version number; Is there anything else that needs to be done? I may wait another 1 or 2 days and will try to submit the new version of the package. Many thanks, Leonard __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] How to fix Archived Package Rpdb?
Thank you very much for this help.
1.) I am a little bit unsure about the LICENSE file - see below (in-text).
2.) There is a new error in the meantime:
- the check works on Windows, but fails everywhere else with:
Warning: Found the following significant warnings:
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
Googling the web was not very informative either: it mentions something
about quartz device - but I am uncertain what to do.
On 9/8/2023 6:59 PM, Hadley Wickham wrote:
> On Fri, Sep 8, 2023 at 6:02 AM Leonard Mada via R-package-devel
> wrote:
>> Dear Members,
>>
>> I would like to reanimate the archived package Rpdb:
>> https://cran.r-project.org/web/packages/Rpdb/index.html
>>
>> [...]
>> 2.b.) Description file
>> - I left the original author as the author (with the provided e-mail
>> address): should I delete this email?
> It probably doesn't matter than much either way, but since the author
> doesn't appear to respond to emails to that address, I personally
> would lean towards deleting it.
>
>> - I have added myself as maintainer; [...]
>> - updated the licence to GPL v3: the original does not specify any
>> version number;
>>
>>
>> Is there anything else that needs to be done?
> There are at least three 3 R CMD check failures you need to address:
>
> * [...]
>
> * You need to add LICENSE to .Rbuildignore, or and IMO better, delete
> that file and use usethis::use_gpl3_license() to the license in
> markdown form, and correctly ignored for CRAN submission
If I understand correctly:
- delete the "LICENSE" file and use usethis::use_gpl3_license(), which
adds the "LICENSE.md" file;
- should I also add some code to the DESCRIPTION file?
>
> * Many examples use `\%in\%` instead of `%in%.
Hopefully, this is fixed now. But it was quit a hassle to find out which
files were affected. [I could have used gawk, but the error-reporting
could be improved as well!]
Sincerely,
Leonard
>
> To make these sorts of problems easier to spot in the future I'd
> suggest setting up a GitHub action to automatically run R CMD check
> every time you push to GitHub. One easy way to do that is to run
> usethis::use_github_action("check-standard").
>
> Hadley
>
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Re: [R-pkg-devel] How to fix Archived Package Rpdb?
Thank you very much for your response.
I actually tried yesterday to publish the package to CRAN.
Unfortunately, my computer seems to behave funny; and I did not receive
a confirmatory e-mail either.
Messages & Errors:
✔ Package submission successful
ℹ Check your email for confirmation link.
! Don't forget to tag this release once accepted by CRAN
Error in (function (..., row.names = NULL, check.rows = FALSE,
check.names = TRUE, :
arguments imply differing number of rows: 1, 0
In addition: Warning messages:
1: In system2("git", c("rev-parse", "--abbrev-ref", "HEAD"), stdout =
TRUE) :
running command '"git" rev-parse --abbrev-ref HEAD' had status 127
2: In system2("git", c("status", "--porcelain=v1"), stdout = TRUE) :
running command '"git" status --porcelain=v1' had status 127
3: In system2("git", c("rev-parse", "HEAD"), stdout = TRUE) :
running command '"git" rev-parse HEAD' had status 127
✔ Setting active project to 'C:/.../Rpdb'
1.) I do not understand if this means, that the submission actually failed?
2.) Should I try to resubmit?
If yes: should I increase the version number to 2.3.2 (from 2.3.1)?
3.) Old questions
The remaining questions should be sorted out now:
- the issue was if to delete the e-mail from the original author;
- I left the e-mail for now; I will phase out the e-mail address, once I
start to work on my own on the package (maybe I'll have some time next
month);
Sincerely,
Leonard
On 9/12/2023 4:02 PM, Uwe Ligges wrote:
On 09.09.2023 20:15, Leonard Mada via R-package-devel wrote:
Thank you very much for this help.
1.) I am a little bit unsure about the LICENSE file - see below (in-text).
2.) There is a new error in the meantime:
- the check works on Windows, but fails everywhere else with:
Warning: Found the following significant warnings:
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
On non Windows systems, You cannot use rgl if you do not have any X11
available.
Support for Unix alikes is optional, so in packages X11() should be used
conditionally after checking capabilities("X11").
Googling the web was not very informative either: it mentions something
about quartz device - but I am uncertain what to do.
>
On 9/8/2023 6:59 PM, Hadley Wickham wrote:
On Fri, Sep 8, 2023 at 6:02 AM Leonard Mada via R-package-devel
wrote:
Dear Members,
I would like to reanimate the archived package Rpdb:
https://cran.r-project.org/web/packages/Rpdb/index.html
[...]
2.b.) Description file
- I left the original author as the author (with the provided e-mail
address): should I delete this email?
It probably doesn't matter than much either way, but since the author
doesn't appear to respond to emails to that address, I personally
would lean towards deleting it.
Do *not* delete any authours/copyright holders.
- I have added myself as maintainer; [...]
- updated the licence to GPL v3: the original does not specify any
version number;
Is there anything else that needs to be done?
There are at least three 3 R CMD check failures you need to address:
* [...]
* You need to add LICENSE to .Rbuildignore, or and IMO better, delete
that file and use usethis::use_gpl3_license() to the license in
markdown form, and correctly ignored for CRAN submission
If I understand correctly:
- delete the "LICENSE" file and use usethis::use_gpl3_license(), which
adds the "LICENSE.md" file;
- should I also add some code to the DESCRIPTION file?
LICENSE: GPL-3
in the DESCRIPTION should be fine, and no license file unless you want
to add additional restrictions that are permitted by GPL-3 such as
attribution requirements.
No idea what usethis::use_gpl3_license() does.
Best,
Uwe Ligges
* Many examples use `\%in\%` instead of `%in%.
Hopefully, this is fixed now. But it was quit a hassle to find out which
files were affected. [I could have used gawk, but the error-reporting
could be improved as well!]
Sincerely,
Leonard
To make these sorts of problems easier to spot in the future I'd
suggest setting up a GitHub action to automatically run R CMD check
every time you push to GitHub. One easy way to do that is to run
usethis::use_github_action("check-standard").
Hadley
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[R-pkg-devel] Spelling of PDB in Package Description
Dear List Members, After resubmitting the updated version of the Rpdb package (2.3.1), the following Notes were generated: 1.) Spelling PDB https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Windows/00check.log https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Debian/00check.log The PDB stands for Protein Data Bank: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html It should be the correct spelling (and was the same in the previous versions of the package). 2.) Small Sample PDB Files * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘Rpdb.pdb’ There is a directory with 3 very small sample pdb-files. The directory was also present in the previous version. How should I proceed? Or did I miss something? Sincerely, Leonard __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Spelling of PDB in Package Description
Dear Uwe,
I found out what is going on. There is an example:
## Write the pdb object in file "Rpdb.pdb" into the current directory
write.pdb(pdb, file = "Rpdb.pdb")
The example was present in the previous version as well. So I did not
thought about it. I do not know how to handle this: although the example
should probably remain.
Sincerely,
Leonard
On 9/15/2023 12:27 AM, Uwe Ligges wrote:
The spellng is fine and not a problem.
For
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘Rpdb.pdb’
You need to move this to ./inst or a subdirectory or, if data,
consider ./extdata See Writing R Extensions.
Best,
Uwe Ligges
On 14.09.2023 22:06, Avraham Adler wrote:
Regarding PDB, in Rd format it’s best to wrap that in an \acronym{}
tag. See section 2.3 of
https://cran.r-project.org/doc/manuals/R-exts.html#Marking-text
Avi
Sent from my iPhone
On Sep 14, 2023, at 3:40 PM, Leonard Mada via R-package-devel
wrote:
Dear List Members,
After resubmitting the updated version of the Rpdb package (2.3.1),
the following Notes were generated:
1.) Spelling PDB
https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Windows/00check.log
https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Debian/00check.log
The PDB stands for Protein Data Bank:
http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
It should be the correct spelling (and was the same in the previous
versions of the package).
2.) Small Sample PDB Files
* checking for non-standard things in the check directory ...
NOTE Found the following files/directories: ‘Rpdb.pdb’
There is a directory with 3 very small sample pdb-files. The
directory was also present in the previous version.
How should I proceed? Or did I miss something?
Sincerely,
Leonard
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[R-pkg-devel] Discrepancy between R CMD check results and usethis::use_cran_comments
Dear List-Members, There are no errors/warnings/notes when I run the check: ── R CMD check results Rpdb 2.3.3 Duration: 2m 50.1s 0 errors ✔ | 0 warnings ✔ | 0 notes ✔ However, there is a discrepancy when I run: usethis::use_cran_comments(open = rlang::is_interactive()) => 0 errors ✔ | 0 warnings ✔ | 1 note For some reason, the file is saved with 1 note. The discrepancy remains even if I restart R, delete the old cran-comments.md file, and re-run the check. By the way: what is the purpose of this cran-comments.md file? It does not seem to be included in the package archive? Sincerely, Leonard __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] 2 Return values for 2 Functions
Dear Members,
How should the return values be documented, when the help page covers 2
related functions:
1.) Variant 1: fails the checks
\value{
\code{cryst1} returns a list of class \sQuote{cryst1} with the
following components:
\describe{
\item{abc}{a numeric vector of length 3 containing the norms of the lattice
vectors a, b and c there are more items}
}
\item{}{}
\code{is.cryst1} returns TRUE if \code{x} is an object of class
\sQuote{cryst1}
and FALSE otherwise.
}
2.) Variant 2: fails in Latex
\value{
\code{cryst1} returns a list of class \sQuote{cryst1} with the
following components:
\describe{
\item{abc}{a numeric vector of length 3 containing the norms of the lattice
vectors a, b and c there are more items}
}
\cr\cr
\code{is.cryst1} returns TRUE if \code{x} is an object of class
\sQuote{cryst1}
and FALSE otherwise.
}
3.) 2 separate Value-Sections
Did not generate actually 2 sections: only the 1st one.
Sincerely,
Leonard
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[R-pkg-devel] CMD check: Examples vs DEPENDS pkg
Dear List members, Package Rpdf depends on package rgl. Multiple examples will call internally the rgl package to visualize the pdb molecule. When performing the CMD check: 1) Is the rgl package loaded each time anew for any of those examples? 2) If this is the case: Is it possible to load it only once per CMD check? Sincerely, Leonard __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
