Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

[Michael Dewey]

Dear Zeinab

Perhaps the insights in https://github.com/tidymodels/infer/issues/455 
will help you especially if you are using roxygen2


Michael

On 16/05/2024 17:01, Zeinab Mashreghi wrote:

Hi,

Thank you very much for your helpful suggestion! Following your advice, I 
revisited the package and made necessary adjustments to the description file. 
However, it appears that there are now some issues with HTML validation in the 
.Rd files. Here's the relevant excerpt, and I've attached the log for further 
reference.

checking HTML version of manual ... NOTE
Found the following HTML validation problems:
All.data.html:4:1 (All.data.Rd:10): Warning:  inserting "type" attribute
All.data.html:12:1 (All.data.Rd:10): Warning: 

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

[Michael Dewey]

Dear Zeinab

It would help if you gave us more information. What exactly was the NOTE 
which it gave you?


Michael

On 16/05/2024 04:22, Zeinab Mashreghi wrote:

Hi,

I hope this message finds you well.

I recently submitted my R package to CRAN, and I received this note from the CRAN teams: 
"checking CRAN incoming feasibility ... NOTE."

When I run R CMD check on my device, I do not encounter any issues, and I am 
unsure of the specific steps I need to take to resolve this note.

Could you please provide guidance on how to address this note and ensure my 
package meets CRAN's requirements for submission? Any insights or 
recommendations you can offer would be greatly appreciated.

Thank you in advance for your assistance.

Best regards,
Zeinab

---

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Associate Professor
Department of Mathematics and Statistics

P 204.786.9366


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Re: [R-pkg-devel] Inquiry Regarding Package Organization in CRAN

[Michael Dewey]

Dear Andriy

I would second the advice that David and Ivan have already given.

I woouls also add that I suspect that most users search for packages by 
functionality so you might want to study techniques for search engine 
optimisation and then advise authors how to increase the visibility of 
their packages.


If the goal is just to record all package from your university then why 
not establish a page on your university website which links to all of 
them? The main problem there will be updating it after you have 
graduated and moved institutions.


Michael

On 19/01/2024 14:34, Protsak Andriy via R-package-devel wrote:

Hi all!



My name is Andriy, and I�m a student at University of Alcal�, currently working 
on my final year project.



I�m tasked with organizing the R packages developed by our university that are 
currently available on CRAN. The goal is to enhance their discoverability, to 
achieve this the initial focus is on exploring the possibility of renaming the 
packages so that they share a common prefix, making it easier for uses to 
locate them in the package list.

If you believe there are alternative strategies to achieve a similar result, 
please feel free to share your perspective.



Additionally, I�m looking into the prospect of merging two packages that 
contain similar functionalities. The aim is to create a more comprehensive 
package by incorporation additional features and ensuring seamless 
compatibility.



Your assistance is key to the successful completion of my final year project, 
and I would be immensely grateful for any insights you can provide. Thank you 
for your time and consideration.



Best regards,



Andriy

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Re: [R-pkg-devel] winbuilder

[Michael Dewey]

Dear Roy

When I just checked using the winbuilder_queue function from the foghorn 
package it seemed to respond and had one package in the queue. Not sure 
that is definitive evicence.


Michael

On 18/10/2023 16:16, Roy Mendelssohn - NOAA Federal via R-package-devel 
wrote:

I am not sure who is the appropriate person to contact,  but thought I would 
try here since WInbuilder is a big help in package testing.  Winbuilder appears 
to be down at the moment.

Thanks,

-Roy

**
"The contents of this message do not reflect any position of the U.S. Government or 
NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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Re: [R-pkg-devel] CRAN Submission to update archived packages (mdsdt)

[Michael Dewey]

Dear Joe

Comments in-line.

On 14/10/2023 21:47, Joe Houpt via R-package-devel wrote:

Hello,
I am having some trouble submitting a package to CRAN that had previously been 
archived.  I went through all of the notes and all that is left is pasted 
below.  Anything I am missing or that I need to get updated?
Regards,
Joe

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Joe Houpt '


That is normal. No action needed.



New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
   Ashby (12:36)
   invariance (14:36)


It usually flags proper nouns, not sure why it disikes invariance, but 
those are presumably fase positives which you could mention in the 
covering note.


CRAN repository db overrides:
   X-CRAN-Comment: Archived on 2023-08-18 as email to the maintainer is
 undeliverable.



Not sure about that one. Were you the original maintainer? If not did 
CRAN know you were taking over?


Michael



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Department of Computer Science
University of Texas at San Antonio

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Re: [R-pkg-devel] Problem persists, was Re: Problem compressing vignettes for CRAN

[Michael Dewey]

Dear Ivan (and list)

Using Ivan's advice I traced the problem to a difference of opinio 
between Microsoft and R about paht names. I had mistakenly enclosed 
parts of the names in "" which was fine for MS but not R. Sys.which() 
was my saviour here.


Many thanks to Ivan for broadening my knowledge of useful functions like 
Sys.which().


Michael

On 09/10/2023 08:51, Ivan Krylov wrote:

On Sun, 8 Oct 2023 16:47:41 +0100
Michael Dewey  wrote:


Following on from Ivan's advice I have now installed qpdf and
Ghostview. I have checked that they are both on my path by typing
their name at the command line and verifying they open.



I then built the package with the --compress-vignettes=both and then
checked it with --as-cran I still get a complaint that it needs qpdf
to check compression.


While running R, does Sys.which('qpdf') return the path to qpdf.exe?
Does Sys.getenv('PATH') match your expectations?


I notice that in the Writing R Extensions manual in section 1.6.1 it
states "The full path to the qpdf command can be supplied as
environment variable R_QPDF ..."

Is that a typo for "must be supplied"?


Well, R tries to resolve the path to qpdf.exe using Sys.which(), so it
must work if it's on the %PATH%, but if all else fails, setting this
environment variable should help.


If it is where can I find the answers to questions about how R
accepts Windows paths? Do I need to enclose parts of names containing
spaces in "" signs?


It always depends on how the final command line is built by a
particular function, but it should work by taking plain file paths
without any escaping and quotation. The directory separators shouldn't
matter either.

(tools::compactPDF uses system2(), so it quotes the path to the
executable by itself.)


Does it mean the path up to, in this case, bin or must I include
qpdf.exe after it?


It must be the full path to the executable, including the final
qpdf.exe.


I assume I do not need to do anything special to get it to find
Ghostscript?


tools::compactPDF() expects gswin64c.exe or gswin32c.exe on the PATH.
If it's not there, R_GSCMD must be set to the full path to the
executable. Judging by the NOTE you've received, it's Ghostscript that
performed most of the compaction in your case.



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[R-pkg-devel] Problem persists, was Re: Problem compressing vignettes for CRAN

[Michael Dewey]

Following on from Ivan's advice I have now installed qpdf and Ghostview. 
I have checked that they are both on my path by typing their name at the 
command line and verifying they open. I then built the package with the 
--compress-vignettes=both and then checked it with --as-cran I still get 
a complaint that it needs qpdf to check compression.


I notice that in the Writing R Extensions manual in section 1.6.1 it states
"The full path to the qpdf command can be supplied as environment 
variable R_QPDF ..."


Is that a typo for "must be supplied"? If it is where can I find the 
answers to questions about how R accepts Windows paths? Do I need to 
enclose parts of names containing spaces in "" signs? Does it mean the 
path up to, in this case, bin or must I include qpdf.exe after it?


I assume I do not need to do anything special to get it to find Ghostscript?

Michael

On 06/10/2023 16:30, Michael Dewey wrote:

Dear Ivan

You must have psychic powers. After some digging I find that the copy 
installed by TexLive is hidden from other software so I need to install 
it again. I suppose while I am at it I should try installing qpdf.


Michael

On 06/10/2023 15:48, Ivan Krylov wrote:

В Fri, 6 Oct 2023 15:36:45 +0100
Michael Dewey  пишет:


But I did use the option --compact-vignettes=both when I built the
tarball.



I do have gs installed but not qpdf. I built the package under
Windows if that is relevant.


Is the Ghostscript executable on the %PATH%? It might help to install a
newer version. It may also be informative to extract the vignette *.pdf
files from the source package tarball and run tools::compactPDF(pdfs,
gs_quality='ebook', verbose = TRUE) to see whether it breaks at any
point.





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Re: [R-pkg-devel] Problem compressing vignettes for CRAN

[Michael Dewey]

Dear Ivan

You must have psychic powers. After some digging I find that the copy 
installed by TexLive is hidden from other software so I need to install 
it again. I suppose while I am at it I should try installing qpdf.


Michael

On 06/10/2023 15:48, Ivan Krylov wrote:

В Fri, 6 Oct 2023 15:36:45 +0100
Michael Dewey  пишет:


But I did use the option --compact-vignettes=both when I built the
tarball.



I do have gs installed but not qpdf. I built the package under
Windows if that is relevant.


Is the Ghostscript executable on the %PATH%? It might help to install a
newer version. It may also be informative to extract the vignette *.pdf
files from the source package tarball and run tools::compactPDF(pdfs,
gs_quality='ebook', verbose = TRUE) to see whether it breaks at any
point.



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[R-pkg-devel] Problem compressing vignettes for CRAN

[Michael Dewey]

I am trying to update my CRAN package metap. When I ran a final check on 
winbuilder I got the warning


* checking sizes of PDF files under 'inst/doc' ... WARNING
  'gs+qpdf' made some significant size reductions:
 compacted 'compare.pdf' from 498Kb to 243Kb
 compacted 'plotmetap.pdf' from 349Kb to 91Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files,
  or build the source package with --compact-vignettes=both

But I did use the option --compact-vignettes=both when I built the tarball.

I do have gs installed but not qpdf. I built the package under Windows 
if that is relevant.


Any suggestions?

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Re: [R-pkg-devel] Unfortunate function name generic.something

[Michael Dewey]

Dear Ulrike

Even though it will undobtedly be a lot of work to rename levels.no I 
cannot help feeling that by fighting against the system you may be 
storing up trouble for yourself in future when some upgrade breaks your 
current solution and you have to make yet more changes.


Michael

On 09/05/2023 07:13, Ulrike Groemping wrote:

Am 09.05.2023 um 01:23 schrieb Duncan Murdoch:

On 08/05/2023 6:58 p.m., Simon Urbanek wrote:



On 8/05/2023, at 11:58 PM, Duncan Murdoch  
wrote:


There really isn't such a thing as "a function that looks like an S3 
method, but isn't".  If it looks like an S3 method, then in the 
proper circumstances, it will be called as one.





I disagree - that was the case in old versions, but not anymore. The 
whole point of introducing namespaces and method registration was to 
make it clear when a function is a method and when it is a function. 
If you export a function it won't be treated as a method:


In a package NAMESPACE:
export(foo.cls)
package R code: foo.cls <- function(x) "foo.cls"

in R:

cls=structure(1,class="cls")
foo=function(x) UseMethod("foo")
foo(cls)

Error in UseMethod("foo") :
   no applicable method for 'foo' applied to an object of class "cls"

foo.cls(cls)

[1] "foo.cls"

So R knows very well what is a method and what is a function. If you 
wanted it to be a method, you have to use S3method(foo, cls) and that 
**is** different from export(foo.cls) - quite deliberately so.


That is true for package users, but it's not true within the package. 
I just tested this code in a package:


  levels.no <- function(xx, ...) {
    stop("not a method")
  }

  f <- function() {
    x <- structure(1, class = "no")
    levels(x)
  }

Both levels.no and f were exported.  If I attach the package and call 
f(), I get the error


  > library(testpkg)
  > f()
  Error in levels.no(x) : not a method

because levels.no is being treated as a method when levels() is called 
in the package.


If I create an x like that outside of the package and call levels(x) 
there, I get NULL, because levels.no is not being treated as a method 
in that context.


As far as I know, there is no possible way to have a function in a 
package that is called "levels.no" and not being treated as a method 
within the package.  I don't think there's any way to declare "this is 
not a method", other than naming it differently.


Duncan


Before the current check notes, I did not think about that problem. I 
think that it is quite unlikely to hit a user of mine, because the 
package calls levels() in a few places on columns of designs only. I 
still think that it should remain possible to have an *internal* 
function that is named in whatever way I like it named (I would of 
course not choose that name now, but it's there, and it would break a 
lot of my own non-package code if I changed it in the package). My 
current "fix" made the problem worse.
Would it have been permissible to not register the function ? I could 
then revert to not registering it, but keeping the error message in 
place, just in case the unlikely event happens.


Ulrike





Cheers,
Simon


In your case the function name is levels.no, and it isn't exported. 
So if you happen to have an object with a class inheriting from 
"no", and you call levels() on it, levels.no might be called.


This will only affect users of your package indirectly.  If they 
have objects inheriting from "no" and call levels() on them, 
levels.no will not be called.  But if they pass such an object to 
one of your package functions, and that function calls levels() on 
it, they could end up calling levels.no(). It all depends on what 
other classes that object inherits from.


You can test this yourself.  Set debugging on any one of your 
functions, then call it in the normal way.  Then while still in the 
debugger set debugging on levels.no, and create an object using


  x <- structure(1, class = "no")

and call levels(x).  You should break to the code of levels.no.

That is why the WRE manual says "First, a caveat: a function named 
gen.cl will be invoked by the generic gen for class cl, so do not 
name functions in this style unless they are intended to be methods."


So probably the best solution (even if inconvenient) is to rename 
levels.no to something that doesn't look like an S3 method.


Duncan Murdoch

On 08/05/2023 5:50 a.m., Ulrike Groemping wrote:
Thank your for the solution attempt. However, using the keyword 
internal
does not solve the problem, the note is still there. Any other 
proposals
for properly documenting a function that looks like an S3 method, 
but isn't?

Best, Ulrike
Am 05.05.2023 um 12:56 schrieb Iris Simmons:

You can add

\keyword{internal}

to the Rd file. Your documentation won't show up the in the pdf
manual, it won't show up in the package index, but you'll still be
able to access the doc page with ?levels.no  or
help("levels.no ").

This is usually used in a package's deprecated and 

Re: [R-pkg-devel] correcting errors in an existing package

[Michael Dewey]

Comment in-line

On 02/04/2023 06:37, Ivan Krylov wrote:

On Fri, 31 Mar 2023 16:51:40 -0400
Dennis Boos  wrote:


Also, I keep getting the message in the Rstudio check

WARNING
'qpdf' is needed for checks on size reduction of PDFs


but I got the latest versions of R and Rstudio and was able to get
qpdf to install and loaded with library(qpdf), but Rstudio still gives
that message.


Almost there.

The 'qpdf' package interfaces to the same code that the 'qpdf' command
line tool uses to do its job. R CMD check uses the latter, not the
former. It looks like you're on Windows, so you need to install Rtools
in order to get a compatible version of 'qpdf':
https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html



I always get the warning about qpdf (on Windows) but it does not seem to 
be a problem on CRAN or winbuilder.


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Re: [R-pkg-devel] CRAN submission with warnings

[Michael Dewey]

Dear Kent

I think the canonical way to report these is in the space on the 
submission form, unless I have not correctly grasped what you did.


Michael

On 26/07/2021 16:02, Kent Johnson wrote:

Hi,

What is the usual process to submit a new package to CRAN which has 
false-positive warnings?

I submitted rtree_0.2.0 last week (7/21). This package compiles with warnings 
from Boost headers. The warnings are expected, unavoidable, and unimportant, 
which I documented in cran-comments.md. After submitting the package, I got an 
email that the package failed the pre-test due to the warnings. I replied-all, 
pointing to the explanation in cran-comments.md. I haven't heard anything 
since, and the package is still in the archive folder at 
ftp://cran.r-project.org/incoming.

I'm new to this process. Is there something else I should do, or should I just 
sit tight and wait for a response?

win-builder results are here: 
https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log
cran-comments.md here: 
https://github.com/akoyabio/rtree/blob/master/cran-comments.md

Thank you for any guidance,
Kent Johnson
Akoya Biosciences

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Re: [R-pkg-devel] Error concerning rtracklayer

[Michael Dewey]

Dear Danielle

If you search the most recent postings on this list
https://stat.ethz.ch/pipermail/r-package-devel/2021q2/subject.html
you will see that several of them have rtracklayer in their title. Does 
any of them help you?


Note that if they had used an uninformative title as you do it would be 
harder to find them so I have added that to your title.


Michael

On 06/05/2021 22:59, Danielle Maeser wrote:

Hello,

The R CMD check passed with 0 errors and warnings, so I proceeded to submit
to CRAN. However, CRAN reported 1 error (see below). If you have any
insight as to what this error means, please let me know.

I'm perplexed because *rtracklayer *is not a package dependency, and
I'm not sure where it came from. Perhaps this is a false positive?

** installing *source* package 'oncoPredict' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]]) :
   namespace 'rtracklayer' 1.48.0 is being loaded, but >= 1.51.5 is required
Calls:  ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'oncoPredict'
* removing 'd:/RCompile/CRANincoming/R-devel/lib/oncoPredict'
* restoring previous 'd:/RCompile/CRANincoming/R-devel/lib/oncoPredict'*

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Re: [R-pkg-devel] Package submission error

[Michael Dewey]

Coments in-line

On 15/01/2021 14:50, sare ameri wrote:

Hi Everyone,

I hope this email finds you well.

I get errors when submitting my package. I didn't get the error when I
submitted the first version of my package.

Here is the error:

Package name: "ftrCOOL".

Error message:

Flavor: r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
   Maintainer: 'Sare Amerifar '

   New submission



That is only a note


   Package was archived on CRAN

   Possibly mis-spelled words in DESCRIPTION:
 nucleotide (7:224)
 peptide (7:239)


You could mention that in the comments when you re-submit that these are 
correctly spelled.




   CRAN repository db overrides:
 X-CRAN-Comment: Archived on 2021-01-13 for policy violation.

 Writes to user library.


Are you knowingly writing to a user library? If so, do not. If not 
explain to CRAN in your submission why you believe this is a false 
epositive.






Flavor: r-devel-linux-x86_64-debian-gcc
Check: CRAN incoming feasibility, Result: NOTE
   Maintainer: 'Sare Amerifar '

   New submission

   Package was archived on CRAN

   CRAN repository db overrides:
 X-CRAN-Comment: Archived on 2021-01-13 for policy violation.

 Writes to user library.


Thanks for any suggestion.

Have a nice day and Best,
Sareh Ameri Far

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Re: [R-pkg-devel] Sweave vignette and bibtex

[Michael Dewey]

Dear Jarrod

It works for me with Sweave so perhaps we need some more details.

Michael

On 06/01/2021 11:20, Jarrod Hadfield wrote:

Hi,

I have a Sweave vignette in a package I have written. When building, the
citations are not put into the pdf - perhaps because two passes of the
tex file are required but only one is executed. Is there a way to force
two passes of the tex file?

Kind Regards,

Jarrod

The University of Edinburgh is a charitable body, registered in 
Scotland, with registration number SC005336.


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Re: [R-pkg-devel] ggplot2 axis title with various size fonts

[Michael Dewey]

I think you have found your way onto the wrong list as R-help seems more 
appropriate.


When you do re-post please set your mailer to work in plain text not HTML.

Michael

On 08/12/2020 09:24, neonira Arinoem wrote:

Is it possible to compose a string to be used as axis title in ggplot2,
with the main part being drawn using one given font and font size, and the
last part being drawn with another font and font size. See below for an
example

*my axis title **(units)*

Currently struggling to achieve this.
Thanks in advance for suggestions.

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Re: [R-pkg-devel] Warning on r-oldrel-macos-x86_64

[Michael Dewey]

Dear Helmut

I think the protocol is to always bump the version number for a 
re-submission even when the first one did not get onto CRAN.


Michael

On 25/10/2020 11:02, Helmut Schütz wrote:

Hi Hugh,

Hugh Parsonage wrote on 2020-10-25 11:45:

If you click on WARN in the table on your check results page (i.e. if
you go to 
 


) you will see in the first line:

* using R version 3.6.2 (2019-12-12)


Oh, dear!


Hope that helps.


I does. THX.
An opinions of the list-members about a re-submission?

Helmut




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Re: [R-pkg-devel] changing maintainer email address

[Michael Dewey]

Dear Josef

From the policy

Explain any change in the maintainer’s email address and if possible 
send confirmation from the previous address (by a separate email to 
cran-submissi...@r-project.org) or explain why it is not possible.


Burned into my cortex since I did it incorrectly a few years back.

Michael

On 27/08/2020 17:45, Tracy, Josef wrote:

Hi,

I submitted a package, "PhysActBedRest" to the CRAN a couple of years ago and 
am trying to update it.  In writing the update, I realized I forgot to update my email 
address when I changed institutions.  As a consequence, when I run CMD check on the 
updated package there is a NOTE that the maintainer has changed.  How to I get my update 
to pass the check and correct my email address?

Thanks,
Dustin

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Re: [R-pkg-devel] Error in winbuilder

[Michael Dewey]

Dear Nicholas

Do you in fact have many examples in the package? Perhaps for some 
mysterious reason they take longer there than when you check at home.


Michael

On 25/08/2020 14:54, Nicholas Tierney wrote:

Hi Everyone,

I have an error when submitting to Winbuilder for my R package, naniar
.

When using `devtools::check_win_devel()` or `devtools::check_win_release()`
on naniar, I get the following logfile from winbuilder:

```
* using log directory 'd:/RCompile/CRANguest/R-release/naniar.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'naniar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'naniar' version '0.5.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... ERROR
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

 End of example output (where/before crash/hang up occured ?)

```

(submission URL here: https://win-builder.r-project.org/77PYyM2kMri1/)

I had previously thought this was a problem to do with CRAN being closed
last week, but apparently this is not the case, and it should have been
working. I cannot find any details on CRAN for this, but it passes build on
R HUB for windows, and it passes build with no warnings, errors, or notes
for me on Mac OSX, as well as on github actions (windows, macOS, and
ubuntu).

Just wondering if anyone has thoughts on this? I have also cross
posted on Rstudio
community
<
https://community.rstudio.com/t/winbuilder-error-check-process-probably-crashed-or-hung-up-for-20-minutes-killed/77492

,

in case that is of interest.

Thanks for your time, and apologies if I have missed something obvious.

All the best,

Nick

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Re: [R-pkg-devel] References in DESCRIPTION file

[Michael Dewey]

Dear Alan

Without seeing your file it is hard to know but there are many examples 
on CRAN in the list of packages. It may be something simple like 
forgetting the full stop.


Michael

On 25/05/2020 15:38, Cantin, Alan (NRCan/RNCan) wrote:

Hi folks,

Upon manual inspection of my package by CRAN maintainers I have been asked to 
put my references in the description field of the DESCRIPTION file. I have 
formatted all of my references as requested and put them there but get a note 
when checking the package (Malformed Description field: should contain one or 
more complete sentences.).  Does anyone have advice on how to place these here 
so I can clear this final hurdle to get the package back up on CRAN?

Thanks,

Alan Cantin


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Re: [R-pkg-devel] Update my package

[Michael Dewey]

Dear Francisco

It is hard to answer this without more details. If you mean to update a 
package which you have on CRAN then the CRAN policy document has a short 
section on re-submission at the very end. If it is a private package not 
for distribution then you just update the version in the DESCRIPTION file.


Michael

On 13/04/2020 11:29, Francisco Palomares wrote:


Hi,

I want to update the version of my package

What is the procedure?

Best,
Francisco

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Re: [R-pkg-devel] Including in my vignette a figure drawn outside R

[Michael Dewey]

Thank you Dirk for the last point which has helped my grasp the 
implications of something in WRE which will help me go forward.


Michael

On 03/12/2019 16:17, Dirk Eddelbuettel wrote:


On 3 December 2019 at 15:36, Michael Dewey wrote:
| I am planning to include a flow-chart in the vignette of one of my
| packages (metap). I am planning to draw it using dot from Graphviz. I
| know that there is Rgraphviz which would do the whole thing in R but I
| do this sort of thing rarely and I suspect the overhead of learning how
| to do it in Rgraphviz would outweigh the benefit.
|
| So my question is: if I wish to be a good Open Source citizen should I
| just bundle the .pdf file resulting from dot with the vignette or should

That seems like it is the appropriate move.

| I provide the .gv file which generated it? I think from reading Writing
| R Extensions that in either case I just put them in the directory along
| with my .Rnw file but please disabuse me of that impression if false.

You can use subdirectories in the source repository such that the sources are
present in the .tar.gz but are not necessarily installed with the package.
  
Dirk




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[R-pkg-devel] Including in my vignette a figure drawn outside R

[Michael Dewey]

I am planning to include a flow-chart in the vignette of one of my 
packages (metap). I am planning to draw it using dot from Graphviz. I 
know that there is Rgraphviz which would do the whole thing in R but I 
do this sort of thing rarely and I suspect the overhead of learning how 
to do it in Rgraphviz would outweigh the benefit.


So my question is: if I wish to be a good Open Source citizen should I 
just bundle the .pdf file resulting from dot with the vignette or should 
I provide the .gv file which generated it? I think from reading Writing 
R Extensions that in either case I just put them in the directory along 
with my .Rnw file but please disabuse me of that impression if false.


The package will need to live on CRAN if that makes a difference.

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Re: [R-pkg-devel] Appropriate usage of 'Suggests' -- package installed conditional on other software not found

[Michael Dewey]

Dear Charles

If your package prints a message to the user suggesting how to get a 
Latex installation then I do not think you need to do anything else. 
After all they could install Latex some other way if they pleased or try 
to work out why the installation they thought they had is not working.


Michael

On 03/10/2019 11:10, Driver, Charles wrote:

I have a function that outputs / compiles some latex. To do this I use 
Sys.which('pdflatex') and if nothing is found, prompt the user whether to 
install tinytex package. So, normally I understand the use of 'Suggests' in the 
package description to be for when there are only certain functions / tests 
that require the package. In this case, the package requirement is also 
conditional on other software (ie a tex distribution) not being found, 
otherwise it is unnecessary. There are no tests or examples that depend on the 
package. Should tinytex be in the 'Suggests' list?


Cheers,

Charles

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Re: [R-pkg-devel] Problems installing dependences of my package

[Michael Dewey]

Dear Andrea

Comments in-line

On 09/09/2019 15:47, Andrea Vilar Alvarez wrote:



Hi,

I am writting because I am doing a package in R and I have some problems 
installing dependences which appear at DESCRIPTION file.

First of all, I am not sure about the difference between Depends and Imports, 
but I only use Depends.
My problem is that my package is going to be used at different computers and 
for different persons so I want that when other person use my package, it can 
be able to check  if the necesary packages are installed and if they are not 
installed, the package must be able to install  them.


If I understand you correctly that is what install.packages() does for 
your users.



I supposed that this problem was solved including the necesary packages and their 
versions at �Depends�. And now, I have another problem because the versions are usually 
indicated using �>=�, for example: forecast (>=8.7) but I need to use exactly the 
versi�n 8.7 because sometimes when packages are updated, they lost some functions. But 
if I use <= or == and the package is update to versi�n 8.8, my package installation 
fail.


As I read the manual. you can specify both and upper and lower bound. It 
is at the bottom of page 9 in the pdf I am reading.



How can I solve this? If I use R normaly (outside my package), I can install older 
versions of other packages using devtools::install_version() so why when I 
indicate  forecast (<=8.7) at Depends on the DESCRIPTION file, R is not able to 
install an older version if a new one is avaliable?

Thanks in advance for your attention.

Best regards,

Andrea.


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Please do not do that as it mangles your post. Please set your mailer o 
post in plain text not HTML






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Re: [R-pkg-devel] General considerations about vignettes

[Michael Dewey]

Comments in-line

On 30/08/2019 14:59, Iñaki Ucar wrote:

On Fri, 30 Aug 2019 at 15:26, J C Nash  wrote:


I'm seeking some general advice about including vignettes in my packages,
which are largely for nonlinear estimation and function minimization 
(optimization).
This means that my packages offer alternatives to many other tools, and the user
then has the chore of deciding which is appropriate. Bad choices can be very
costly in inappropriate results or computational efficiencies. Hence, I include
vignettes to offer comparisons and examples of use.

Unfortunately, as in a case this week, changes in the comparison packages break
my package(s), and I get an email from CRAN telling me to fix it before some
date not far in the future. This means a) work for me, possibly at an 
inopportune
time; b) risk of loss of capability, in the present case in the nlsr package 
which
offers some unique capabilities, and c) extra work for CRAN for what is, 
arguably,
updating of peripheral documentation. Updating optimization packages on CRAN 
can be,
I have discovered, a very time-consuming task. Package optimx took over 3 months
to get updated.

It should be noted in the present situation that just before I got the msg from
CRAN I got a msg from the maintainer of the package that has changed and breaks
the vignette with some suggestions on a fix. The issue is that his package has
changed function syntax -- a situation all of us know is fraught with troubles,
since improvements may cause breakage.

I am NOT saying that my vignettes should not be updated. However, I'm wondering
if I should set up a repository for my vignettes on Github/Gitlab or similar, 
and
simply link to them. This would separate the updating of vignettes from the 
central
packages. Their updating could be less strictly tied to CRAN activities, and 
could
also be a task undertaken by others who are not listed as maintainer.

I'd welcome some (hopefully constructive) comments. Would CRAN maintainers feel
this to be helpful, or does it lower the value of official R packages? Do
other maintainers experience the same requests, or do they just not include
vignettes (and many do not)?


My two cents:

For me, as a user, vignettes are the most valuable form of
documentation in a package. Of course, this is personal opinion.


Yes, but it is widely shared (in the sense that I think it too).

I think the issue here is whether the intention is to compare with a 
particular implementation of a technique in which case you probably do 
need to do what you are currently doing or to compare with the technique 
in general terms. If the latter then Iñaki's solution seems perfect to 
me since even if the package interface changes it still implemented the 
same technique (I assume).


Michael

 But

these days with so many good packages out there, I don't have time to
install all of them and dive into the manual and the examples just to
decide which one is better for my use case. A good written vignette
most of the time is my driving factor (sometimes, if it's a small
package with one particular functionality, a good README is enough,
but that's not the case here).

Thus, as a maintainer, I try to lead by example. It's time consuming,
but on the other hand, many times a help request by a user can be
resolved with "please, take a look at section x of vignette y".

One thing I do to make them as maintainable as possible is to try to
avoid dependencies on third-party packages as much as possible. In
your case, comparing yourself with other alternatives may be
important. I'd suggest to set eval=FALSE for chunks with expensive
demonstrations of other packages, and then show a static figure with
the comparison that you made once, but doesn't need to be recreated
each time the vignette is built. In this way, issues like the one you
described won't affect your package, at least immediately. Until some
user reaches you to say, hey, I've tried the code in this vignette for
package x and it doesn't work for me. Then it's time to revisit that
code and rebuild the figure.

You could have vignettes that you don't rebuild constantly in a
separate repo and link them from a main vignette on CRAN, but that's
no different from what I propose above, and it's one click away.

Hope it helps. Regards,



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Re: [R-pkg-devel] False Positive WARNING in devtools::check_built

[Michael Dewey]

Dear Jarrett

Not clear what is going on here but that seems to be an error in your 
source code not the documentation file as you hint.


Michael

On 03/05/2019 15:02, Jarrett Phillips wrote:

Hello,


I have run devtools::check_built() on my package tarball to ensure the
presence of no ERRORS/WARNINGS or NOTES. The below WARNING was found:


W  checking for unstated dependencies in examples ...

Warning: parse error in file 'HACSim-Ex.R':

197:17: unexpected symbol

196: # user prompted to select appropriate FASTA file of

197: aligned/trimmed DNA

 ^


My documentation doesn't run up to line 197. All documentation is below 100
lines in length.


Prior to a small fix (changing \dontrun to \donttest), my package had zero
WARNINGS, ERRORS and NOTES.


The WARNING seems to stem from the 'DNA' reference within the comment.


Is the above WARNING a false positive?


i recently updated to R 3.5.3, could this have caused this issue?



Thanks!



Cheers,


Jarrett

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Re: [R-pkg-devel] Best practice for releasing heavy internal data

[Michael Dewey]

Dear Paul

The advantage of a data-only supplementary package is that users who 
live in countries where they have either a very slow connection or where 
they have to pay per byte to download will be spared 5MB every time you 
update your main package. I do not think the fact that you never expect 
them to explicitly access the data is a worry.


Michael

On 22/02/2019 14:05, Paul Hibbing wrote:

Hi all,

I am revisiting this and wondering if it would be a case in which I should
submit as-is, and include justification for ignoring the NOTE about
excessive directory size.

Best,
Paul Hibbing

On Mon, Feb 18, 2019 at 3:20 PM Paul Hibbing  wrote:


Hi all,

I am preparing a package that makes use of several neural networks,
which are quite large. They aren't
intended for public use, so they're currently stored in sysdata.R, but
they make the R directory too heavy
(close to 5MB).

What is best practice in this case? I'm aware the general
recommendation is to set up a separate data
package that updates infrequently, but that seems undesirable since
these objects weren't going to be
exported in the first place.

Thanks for your help.
-Paul Hibbing



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Re: [R-pkg-devel] package docu

[Michael Dewey]

Well in the usage section it says Kw but elsewhere kw so you need to 
make them match. Probably some "helpful" part of your system is 
capitalising things without you noticing.


Michael

On 26/01/2019 14:04, Troels Ring wrote:

Thanks a lot - I tried with prompt(kw) and that warning disappeared but instead 
I got another

checking for code/documentation mismatches ... WARNING

   Data with usage in documentation object 'kw' but not in code:
 Kw

And the code is really full og kw -

I'm so sorry to bother
BW
Troels

-Oprindelig meddelelse-
Fra: Duncan Murdoch 
Sendt: 26. januar 2019 14:45
Til: Troels Ring ; 'Michael Dewey' ; 
'package-develop' 
Emne: Re: [R-pkg-devel] package docu

On 26/01/2019 8:31 a.m., Troels Ring wrote:

Dear Michael - fantastic: TOTAL is now acknowledged -- so I only need the 
constants kw, K3, and Kc from the utility_acid.r file - how for format their 
documentation - they are available as required inside and outside the package.


Within R, set your working directory to the man directory for your package, 
then run

prompt(kw)

and it will create kw.Rd in the right format.  You just need to edit it to fill in the 
details.  There will be comments in the file explaining what to do.  Don't put quotes on 
the name; prompt("kw") is wrong.

Duncan Murdoch




All best wishes
Troels

-Oprindelig meddelelse-
Fra: Michael Dewey 
Sendt: 26. januar 2019 13:17
Til: Troels Ring ; package-develop

Emne: Re: [R-pkg-devel] package docu

Dear Troels

What happens if you add \alias{TOTAL}

Michael

On 26/01/2019 08:15, Troels Ring wrote:

Dear friends - I'm struggling to get the documentation of my package
correct. The working package is now (with your help!) at

devtools::install_github("troelsring/ABCharge")

and in its proto version includes only a single dataset "brom.RData"
which has two components, a data.frame "brom" and a matrix TOTAL.
These are documented in the brom.RD file shown below.






\name{brom}

\alias{brom}

\docType{data}

\title{

bromic acid data from Glaser et al 2014

}

\description{

 Data to find optimal pK for bromic acid

}

\usage{data("brom")}

\format{

A workspace.

 \describe{

   \item{brom}{Dataframe of Table S4 in Glaser et al.}

   \item{TOTAL}{Matrix of buffer concentrations.}

 }

}

\source{

Glaser RE et al. Dynamical approach to multiequilibria problems for
mixtures of

acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016

}

\examples{

data(brom)

- a long example - works well




Now when running ctrl-shift-E, I get




checking for missing documentation entries ... WARNING


 Undocumented code objects:

   'K3' 'Kc' 'kw'

 Undocumented data sets:

   'TOTAL'

 All user-level objects in a package should have documentation entries.

 See chapter 'Writing R documentation files' in the 'Writing R

 Extensions' manual.




0 errors v | 1 warning x | 0 notes v

Fejl: R CMD check found WARNINGs

run stoppet




Exited with status 1.




I wonder why the specification of TOTAL in the RD file is ignored?




Also the three constants kw, Kc, and K3 are not properly documented.
They are declared and exported in the utility_acid.r file and I have
tried to document them as  @params in that file but it seems to be
ignored and cause other problems so I have them at present
undocumented since I don't know where to put the documentation.


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Re: [R-pkg-devel] package docu

[Michael Dewey]

Dear Troels

What happens if you add \alias{TOTAL}

Michael

On 26/01/2019 08:15, Troels Ring wrote:

Dear friends - I'm struggling to get the documentation of my package
correct. The working package is now (with your help!) at

devtools::install_github("troelsring/ABCharge")

and in its proto version includes only a single dataset "brom.RData" which
has two components, a data.frame "brom" and a matrix TOTAL. These are
documented in the brom.RD file shown below.

  

  


\name{brom}

\alias{brom}

\docType{data}

\title{

bromic acid data from Glaser et al 2014

}

\description{

   Data to find optimal pK for bromic acid

}

\usage{data("brom")}

\format{

A workspace.

   \describe{

 \item{brom}{Dataframe of Table S4 in Glaser et al.}

 \item{TOTAL}{Matrix of buffer concentrations.}

   }

}

\source{

Glaser RE et al. Dynamical approach to multiequilibria problems for mixtures
of

acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016

}

\examples{

data(brom)

- a long example - works well

  


Now when running ctrl-shift-E, I get

  


checking for missing documentation entries ... WARNING


   Undocumented code objects:

 'K3' 'Kc' 'kw'

   Undocumented data sets:

 'TOTAL'

   All user-level objects in a package should have documentation entries.

   See chapter 'Writing R documentation files' in the 'Writing R

   Extensions' manual.

  


0 errors v | 1 warning x | 0 notes v

Fejl: R CMD check found WARNINGs

run stoppet

  


Exited with status 1.

  


I wonder why the specification of TOTAL in the RD file is ignored?

  


Also the three constants kw, Kc, and K3 are not properly documented. They
are declared and exported in the utility_acid.r file and I have tried to
document them as  @params in that file but it seems to be ignored and cause
other problems so I have them at present undocumented since I don't know
where to put the documentation.


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[R-pkg-devel] Can I put my small data-sets into one .rda file in my CRAN package?

[Michael Dewey]

At the moment my package (metap) has a number of small data-sets each as
a separate .rda file. It works fine. I thought it would be neater to put
them all into one file which I called data.rda (original choice of name
there).

Now when I do R CMD build metap
it fails when trying to build the vignette when that executes
data(validity)
where validity is contained in data.rda.

I cannot find anything in writing R extensions which explicitly forbids
this but equally nothing which explicitly permits it. Am I missing
something? Obviously this is not an important problem and as the title
says the solution should work on CRAN too.

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Re: [R-pkg-devel] (no subject)

[Michael Dewey]

Your documentation files do not match the functions and you have some 
files R was not expecting. See inline below for more detail


On 19/11/2018 10:53, Oloyede Isiaq wrote:

  I am developing a package in R, but I encountered the below problems,
kindly assist.


Updating relrisks documentation
Loading relrisksWarning: The existing 'NAMESPACE' file was not
generated by roxygen2, and will not be overwritten.-- Building
- relrisks
--Setting env vars:
* CFLAGS: -Wall -pedantic -fdiagnostics-color=always
* CXXFLAGS  : -Wall -pedantic -fdiagnostics-color=always
* CXX11FLAGS: -Wall -pedantic
-fdiagnostics-color=always-v
  checking for file
'C:\Users\DrIOloyede\Documents\relrisks/DESCRIPTION' (1.6s)-
preparing 'relrisks': (3.1s)v  checking DESCRIPTION meta-information-
checking for LF line-endings in source and make files and shell
scripts (845ms)-  checking for empty or unneeded directories-
building 'relrisks_0.1.0.tar.gz'
-- Checking -
relrisks --Setting env vars:
* _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
* _R_CHECK_CRAN_INCOMING_   : FALSE
* _R_CHECK_FORCE_SUGGESTS_  : FALSE-- R CMD check
--
using log directory 'C:/Users/DrIOloyede/Documents/relrisks.Rcheck'
(2.3s)-  using R version 3.5.1 (2018-07-02)-  using platform:
x86_64-w64-mingw32 (64-bit)-  using session charset: ISO8859-1-  using
options '--no-manual --as-cran' (1.3s)v  checking for file
'relrisks/DESCRIPTION'-  checking extension type ... Package-  this is
package 'relrisks' version '0.1.0'-  package encoding: UTF-8v
checking package namespace information ...v  checking package
dependencies (3m 54.2s)v  checking if this is a source package ...v
checking if there is a namespacev  checking for executable files
(982ms)v  checking for hidden files and directoriesv  checking for
portable file names ...v  checking serialization versionsv  checking
whether package 'relrisks' can be installed (7.8s)v  checking
installed package size (533ms)v  checking package directoryv  checking
DESCRIPTION meta-information (1s)N  checking top-level files ...
Non-standard files/directories found at top level:
  'rrisks.Rmd' 'rrisks.html'v  checking for left-over filesv
checking index informationv  checking package subdirectories (517ms)v
checking R files for non-ASCII characters (482ms)v  checking R files
for syntax errors (460ms)v  checking whether the package can be loaded
(967ms)v  checking whether the package can be loaded with stated
dependencies (342ms)v  checking whether the package can be unloaded
cleanly (451ms)v  checking whether the namespace can be loaded with
stated dependencies (455ms)v  checking whether the namespace can be
unloaded cleanly (563ms)v  checking loading without being on the
library search path (705ms)v  checking dependencies in R code (352ms)v
  checking S3 generic/method consistency (1.2s)v  checking replacement
functions (335ms)v  checking foreign function calls (469ms)v  checking
R code for possible problems (8.9s)v  checking Rd files (582ms)v
checking Rd metadata (370ms)v  checking Rd line widths (359ms)v
checking Rd cross-references (2.2s)v  checking for missing
documentation entries (674ms)v  checking for code/documentation
mismatches (2.1s)W  checking Rd \usage sections (907ms)


So here, for example, you have not documented coefs, se and df


Undocumented arguments in documentation object 'rrci'
  'coefs' 'se' 'df'


But you have documented arguments which do not exist in the function in 
the code.



Documented arguments not in \usage in documentation object 'rrci':
  'coefficients'

Undocumented arguments in documentation object 'rrcip'
  'coefs' 'se' 'df'
Documented arguments not in \usage in documentation object 'rrcip':
  'coefficients'

Undocumented arguments in documentation object 'rrciqr'
  'coefs' 'se' 'iqr' 'df'
Documented arguments not in \usage in documentation object 'rrciqr':
  'coefficients'

Undocumented arguments in documentation object 'rrciqrp'
  'coefs' 'se' 'iqr' 'df'
Documented arguments not in \usage in documentation object 'rrciqrp':
  'coefficients'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.v  checking Rd contents (2.5s)v  checking for
unstated dependencies in examples (453ms)-  checking examples ... NONE
(841ms)

See
  'C:/Users/DrIOloyede/Documents/relrisks.Rcheck/00check.log'
for details.

-- R CMD check results -
relrisks 0.1.0 
Duration: 4m 36.5s

checking Rd \usage 

Re: [R-pkg-devel] How do I know if/when my package is fit for CRAN?

[Michael Dewey]

Comments in-line

On 07/06/2018 11:23, Voeten, C.C. wrote:

Dear list,

I have been working on an R package for the past two years. It started as a 
programming exercise for me to get acquainted with R, and because I had some 
issues with lmerTest::step (the aim of my package was to automate the protocol 
I use for performing model comparisons using LRT, also when one of the models 
does not converge or is not an lme4 model; these three things of LRT, 
nonconvergence, and non-lme4 models are not handled by lmerTest::step). Over 
the past two years, I have completely refactored the package multiple times as 
I realized there were better/cleaner ways to do things, and it has now grown 
into something that I use in my day-to-day statistical life.

Now, it occurs to me that my code may be of use to other people. However, at 
the same time, I also feel that the package is nowhere near 'done', in the 
sense of polished code that is free of my personal quirks; here I do not mean 
little things like coding style, but rather more generally my overall approach 
to things. (I also know of a few bugs that need fixing, but that is easy - just 
need to find the time to do it.)
My question is: how do I know (1) if my package belongs on CRAN (it did start 
out as a personal project, after all)


There are quite a few packages on CRAN which are collections of things 
which people personally found useful so I would have thought your 
package might well be of benefit.


; and (2) when the code is in good enough shape to be submitted without 
me wasting the time of the people reviewing the submissions?  The code 
is currently at [1], but my question is explicitly not for other people 
to review my code - instead, I am asking how I can do that myself!


If it passes the standard checks it should be accepted. There are 
packages which contain stylistic features which I would not write myself 
but that would not matter. If people start using it they will probably 
give you feedback anyway.


One thing which occurs to me though is whether the maintaner of lmerTest 
would accept it into the package? If it has a different philosophy 
probably not but perhaps worth asking?


Michael



Thank you for any advice,
Cesko

[1] https://github.com/cvoeten/buildmer

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Re: [R-pkg-devel] Package check help: Package required but not available

[Michael Dewey]

Dear David

I am afraid R does not know what your flag is doing so you should try 
wrapping the command as you suggested.


Michael

On 01/03/2018 16:05, David Stanley wrote:

Hi Everyone,

I’m new to this list but hopefully you can help me.

I’m working on updating my apaTables package (most recent code: 
https://github.com/dstanley4/apaTables)

However, I’m encountering problems passing the CRAN check because of a package 
I use (MBESS). MBESS is available on all platforms except r-patched-solaris-x86 
(see https://cran.r-project.org/web/checks/check_results_apaTables.html)

To work around this I did three things that have not worked.

1) I modified the DESCRIPTION file. I moved MBESS from Imports to Suggests

2) I manipulated a flag (show.confidence.interval) in my file apaDvalueTable.R show that 
it is always FALSE if the following is FALSE: requireNamespace("MBESS", quietly 
= TRUE) . That is, if the package is not there do no calculate the confidence intervals 
that require it. But I still fail the check. Is this perhaps because I didn’t wrap the 
MBESS command on line 97 with an “if” using requireNamespace? This command will never be 
executed without the package though because of the flag.

3) I also wrapped a command that uses MBESS in apaRegressionTable.R (line 276) 
that uses MBESS.

Any help much appreciated in resolving this "Package required but not 
available” problem.

(Detailed CRAN message below. Fixing the Notes issues are easy.)

Cheers,
David



David Stanley, PhD | Associate Professor
Department of Psychology | University of Guelph
4002 MacKinnon | 50 Stone Rd E | Guelph, ON | N1G 2W1
dstan...@uoguelph.ca  | 519-824-4120 Ext. 58590
uoguelph.ca/psychology/users/david-stanley
@dstanley4


Dear maintainer,

package apaTables_2.0.1.tar.gz does not pass the incoming checks automatically, 
please see the pre-test at:

Status: 2 NOTEs

Current CRAN status: ERROR: 1, OK: 11
See: 

Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the 
R-package-devel mailing list:

If you are fairly certain the rejection is a false positive, please reply-all 
to this message and explain.

More details are given in the directory:

The files will be removed after roughly 7 days.


Best regards,
CRAN teams' auto-check service


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Re: [R-pkg-devel] referring to a package data object by two names

[Michael Dewey]

Dear Greg

Do any of the suggestions in section 1.5.3 of Writing R Extensions "Load 
hooks" work?


Michael

On 08/10/2017 08:40, Gregory Jefferis wrote:

Dear R colleagues,

I have a set of versioned data objects in a package. Let's call them

landmarks.2016
landmarks.2017

I need to have access to both of these objects for different calculations both 
internal to the package and for end users. The objects are saved as rda files 
in the package's data folder.

I would also like to define an object – an alias if you will – that contains 
the *current* landmarks. This is useful so that some package functions and 
external scripts do not require editing when the default object changes.

For this, somewhere in the package, I would like to do something like:

# set the current default landmarks
landmarks <- landmarks.2017

I cannot figure out a place to do this in my package because check always 
complaints that landmarks.2017 does not exist – I guess lazy loading can only 
happen after all the R code is evaluated.

* Can anyone suggest a workaround that does not involve saving a third 
redundant rda object into the package's data folder?

I have placed a toy example package on GitHub:

   https://github.com/jefferis/testdataalias

With many thanks,

Greg Jefferis.

--
Gregory Jefferis, PhD
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://www.zoo.cam.ac.uk/departments/connectomics

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Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages

[Michael Dewey]

Your log says you have no examples but you do in your Rd file.
Your examples look the wrong way round x(function) rather than function(x)

Not sure whether those are relevant issues but perhaps they help.

On 10/08/2017 15:47, david.kaeth...@dlr.de wrote:

Thank you for the replies!

First of all, here is the test package:
https://github.com/c06n/helpers2

Session info and the log of R CMD check at the end. There is an error: "LaTeX errors when 
creating PDF version." However, it says "checking Rd files ... OK".

I have tried the install now on 4 different computers (via 
devtools::install_github), they all did not work.

Further points:
- Unfortunately, installation from a tarball did not work either. I build the tarball from the 
command line (Cygwin), then used R CMD, but tried it also from within RStudio ("Build Source 
Package", then "install.packages")
- I have managed to create another package WHICH WORKS. I have not been able to 
do it again though, I just don't know what I did differently.
- I played around with the documentation lines in the test package, to no avail.

I am sure that it is something very minor where I went wrong, and in all 
likelihood the problem is on my side. I just cannot figure out what it might be.

David

-

sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252

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

other attached packages:
[1] _0.1.0

loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1


* using log directory '/cygdrive/d/Home/projects/R_package_dev/helpers2.Rcheck'
* using R version 3.4.0 (2017-04-21)
* using platform: x86_64-unknown-cygwin (64-bit)
* using session charset: ISO8859-1
* checking for file 'helpers2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'helpers2' version '0.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'helpers2' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  testlicense
Standardizable: FALSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... NONE
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
Status: 1 ERROR, 2 WARNINGs












-Ursprüngliche Nachricht-
Von: Dirk Eddelbuettel [mailto:dirk.eddelbuet...@gmail.com] Im Auftrag von Dirk 
Eddelbuettel
Gesendet: Donnerstag, 10. August 2017 14:32
An: Duncan Murdoch
Cc: Käthner, David; r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages


On 9 August 2017 at 08:38, Duncan Murdoch wrote:
| Nothing that you've written is reproducible by others.  See if you can
| put together a short self-contained series of instructions that
| display the problems (or just one of them).  It might involve
| installing from Github, or making a package tarball available somewhere.

I am fairly certain I have observed this myself, and I *think* it simply stems 
from running R 

Re: [R-pkg-devel] Errors during R package development

[Michael Dewey]

Dear Ranjit

Do you in fact have fracdiff.rdb and if so where is it in your file 
structure?


On 12/07/2017 12:00, Ranjit Paul wrote:

I am trying to develop one package but getting the following errors and
notes. Please suggest for the possible solutions.


* checking R code for possible problems ... NOTE
StructuralBrekwithLongmemory: Error while checking: cannot open file
  'd:/temp/RtmpeMJ2np/RLIBS_2fe0425c94fc3/fracdiff/R/fracdiff.rdb': No
  such file or directory

** running examples for arch 'i386' ... ERROR
Running examples in 'TSF-Ex.R' failed
The error most likely occurred in:

base::assign(".ptime", proc.time(), pos = "CheckExEnv")

StructuralBrekwithLongmemory(Xt,bandwidth)
Error in StructuralBrekwithLongmemory(Xt, bandwidth) :
  cannot open file
'd:/temp/RtmpeMJ2np/RLIBS_2fe0425c94fc3/fracdiff/R/fracdiff.rdb':
No such file or directory
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'TSF-Ex.R' failed
The error most likely occurred in:

base::assign(".ptime", proc.time(), pos = "CheckExEnv")



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Re: [R-pkg-devel] Changing a package's name

[Michael Dewey]

Dear David

It is your package and you can choose the name you prefer. If you feel 
uncomfortable with the current one then change it. I do not think anyone 
else's opinion is relevant unless a package author picks a name that all 
right thinking people would find offensive.


On 11/06/2017 14:51, David Hugh-Jones wrote:

Hello all,

A short while ago I released the "huxtable" package for writing HTML and
LaTeX tables:
https://www.github.com/hughjonesd/huxtable

The name seemed cute to me, but I later found out that to Americans it has
special associations. The Huxtables were the family in the Cosby show. That
would be fine, except that Bill Cosby is now on trial for one case of rape,
and there are accusations of many other cases.

So, two questions:

* Do you think I should change the name?

Comments welcome from Americans and others on this difficult cultural issue.

* If I do, what's the best and least disruptive way to do it? Bear in mind
that I have a couple of thousand users.

My first thought would be to release an update which gives a warning about
the future change when the package is loaded; then release a package with
the new name and continue development on this branch.

David

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Re: [R-pkg-devel] UseR! Session: Navigating the jungle of R packages.

[Michael Dewey]

Dear all

That seems an interesting session. I am the maintainer of one of the 
CRAN Task Views (MetaAnalysis) and will attend unless I am successful in 
the draw for Wimbledon tickets.


Just in case I strike lucky one question I would have raised from the 
floor if I were there would have been "Does anyone read the Task 
Views?". Since I started mine I have received only a couple of 
suggestions for additions including a very abrupt one about a package 
which had been included for months but whose author clearly did not read 
before writing. So I would ask whether we need to focus much energy on 
the Task Views.


So, maybe see you there, maybe not.

On 16/01/2017 14:57, ProfJCNash wrote:

Navigating the Jungle of R Packages

The R ecosystem has many packages in various collections,
especially CRAN, Bioconductor, and GitHub. While this
richness of choice speaks to the popularity and
importance of R, the large number of contributed packages
makes it difficult for users to find appropriate tools for
their work.

A session on this subject has been approved for UseR! in
Brussels. The tentative structure is three short
introductory presentations, followed by discussion or
planning work to improve the tools available to help
users find the best R package and function for their needs.

The currently proposed topics are

- wrapper packages that allow diverse tools that perform
  similar functions to be accessed by unified calls

- collaborative mechanisms to create and update Task Views

- search and sort tools to find packages.

At the time of writing we have tentative presenters for
the topics, but welcome others. We hope these presentations
at useR! 2017 will be part of a larger discussion that will
contribute to an increased team effort after the conference
to improve the the support for R users in these areas.


John Nash, Julia Silge, Spencer Graves

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[R-pkg-devel] Use of \alias{} versus \concept{}

[Michael Dewey]

In my CRAN package metap I implement a number of techniques which have 
multiple names. So, for instance, what I call sumz is also called sum of 
normals, and Stouffer's method. I decided it would be kinder if they 
were documented under all the names I know. Looking at the trusty manual 
I see that \alias{x} does not need to just define an R object so that 
works OK and puts the name, x, in the package index. But I also notice 
that there is \concept{x} which does not index x but makes it findable 
by help.search.


Is the sole reason for \concept{} to enable documenting something which 
does not make it to the index or is there some subtlety which I am missing?


And of course any other advice, especially "Don't do that" is welcome.

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[R-pkg-devel] Is it possible to protect a word from the spell checker?

[Michael Dewey]

The spell checker is correct they are not correctly spelled English 
words but names. I searched the Writing R Extensions manual but did not 
find any solution. I know it is only a NOTE not more serious.


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Re: [R-pkg-devel] Package fails to build on Windows only, builds on GNU/Linux (parse issue)

[Michael Dewey]

Duncan Murdoch  wrote :

> On 02/02/2016 2:23 PM, Irucka Embry wrote:
> > https://gitlab.com/iembry/install.load/raw/master/R/install_load.R
> is
> > the link to raw R code for my package. I have been successful at
> > building the package on GNU/Linux, but building on Windows fails. I have
> > used R 3.2.3 in both cases.
> >
> > On Windows, using readLines, this is the result of the Line 1:
> >
> > [1] "#' Check, Install and Load CRAN & USGS GRAN Packages"
> >

When I view that line via my webmail and using Chrome browser on Windows I see 
a string which seems to start:

lower case i possibly with an umlaut
closing guillemet
inverted question mark
hash symbol

whereas the GNU/Linux example just starts hash symbol

Hope that helps someone

> >
> > On GNU/Linux, using readLines, this is the result of Line 1:
> >
> > [1] "#' Check, Install and Load CRAN & USGS GRAN Packages"
> >
> >
> > Can someone offer suggestions on how to fix this character issue for
> > Windows package development?
> 
> I can't see any difference there.  Is that the point, or do you see a 
> difference?
> 
> What is the exact error message you get when parsing?
> 
> Duncan Murdoch
> 
> >
> > I have created the R code with the Kate text editor. I have not had this
> > issue in the past with any of my R packages using the Kate text editor.
> >
> > I have a few packages that have the same issue.
> >
> > Thank you.
> >
> > Irucka Embry
> >
> >
> > ___Get
> the Free email that has everyone talking at   [[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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