Re: [R-pkg-devel] issues with SOfun - package upload
Dear Brian, Dear Uwe, Thank you for your replies. I wrote a function that does the same stuff that the suggested package does. Now there are no reference to suggested packages. Best, Luca 2017-11-08 18:03 GMT+01:00 Uwe Ligges : > And even this cannot work for strong dependencies, as sztrong deendencies > must be available from mainstream repositoreis. > > Best, > Uwe Ligges > > > > > > On 08.11.2017 17:59, Brian G. Peterson wrote: > >> I think you should be using: >> >> Additional_repositories: https://github.com/mrdwab/SOfun >> >> since that is the actual repository. >> >> Regards, >> >> Brian >> >> On Wed, 2017-11-08 at 17:01 +0100, LUCA BELMONTE wrote: >> >>> Good evening, >>> >>> I am trying to upload my package, called PdPDB 2.0. >>> When building and checking the package with R-studio with --as-cran >>> option >>> selected, everything looks ok but, once I tried to upload the package >>> to >>> CRAN I had the following reply: >>> >>> *"Strong dependencies not in mainstream repositories:* >>> * SOfun* >>> ** checking package namespace information ... OK* >>> ** checking package dependencies ... ERROR* >>> *Package required but not available: 'SOfun'"* >>> >>> I understand the issue it with SOfun that is a package I downloaded >>> and >>> installed from this github url: https://github.com/mrdwab/SOfun >>> >>> I came back to CARN policies and I have read: >>> >>> >>> *"Packages on which a CRAN package depends should be available from a >>> mainstream repository: if any mentioned in ‘Suggests’ or ‘Enhances’ >>> fields >>> are not from such a repository, where to obtain them at a repository >>> should >>> be specified in an ‘Additional_repositories’ field of the DESCRIPTION >>> file >>> (as a comma-separated list of repository URLs) or for other means of >>> access, described in the ‘Description’ field."* >>> >>> So, I updated the DESCRIPTION file as follows: >>> Additional_repositories: http://news.mrdwab.com/install_github.R >>> >>> Before to proceed to submission, I would like to know if this is the >>> right >>> way to proceed or I misinterpreted the submission procedure. >>> >>> Thank you for reading this email, >>> Best, >>> >>> >> __ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> >> -- Luca Belmonte, PhD Dept. Life Sciences, University of Modena and Reggio Emilia Mobile: +39 328 45 81 762 [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Macros in Rd files.
Note the % may be a comment?
Uwe
On 09.11.2017 06:05, Rolf Turner wrote:
I tried to define a macro to produce today's date (like unto the
"\today" command in LaTeX):
\newcommand{\today}{format(Sys.date(),"%d/%m/%Y")}
I put this into my *.Rd file just before invoking it. (Something like
"I don't think I will do any more work today (i.e. \today).")
When I did
R CMD build ldEst
to my package I got the warning:
Warning:
/tmp/RtmpL6sNnQ/Rbuild7f3036693218/ldEst/man/sampleCiLength.Rd:95:
unexpected END_OF_INPUT '\keyword{ datagen }
Clearly I'm stuffing something up. Can some kind soul please provide me
with guidance as to what I *should* be doing?
Ta.
cheers,
Rolf Turner
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Re: [R-pkg-devel] Macros in Rd files.
On 09/11/2017 5:06 AM, Uwe Ligges wrote:
Note the % may be a comment?
Yes, and the body should be written in Rd markup, not R. Working out
the appropriate number of escapes is painful; I recommend trial and error.
This worked for me:
\newcommand{\today}{\Sexpr{format(Sys.Date(),"\\\%d/\\\%m/\\\%Y")}}
Duncan Murdoch
Uwe
On 09.11.2017 06:05, Rolf Turner wrote:
I tried to define a macro to produce today's date (like unto the
"\today" command in LaTeX):
\newcommand{\today}{format(Sys.date(),"%d/%m/%Y")}
I put this into my *.Rd file just before invoking it. (Something like
"I don't think I will do any more work today (i.e. \today).")
When I did
R CMD build ldEst
to my package I got the warning:
Warning:
/tmp/RtmpL6sNnQ/Rbuild7f3036693218/ldEst/man/sampleCiLength.Rd:95:
unexpected END_OF_INPUT '\keyword{ datagen }
Clearly I'm stuffing something up. Can some kind soul please provide me
with guidance as to what I *should* be doing?
Ta.
cheers,
Rolf Turner
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Re: [R-pkg-devel] issues with SOfun - package upload
Did you write it from scratch or modify the function from the package you were referencing? There may be some licensing issues you need to consider either way. -Dason On Thu, Nov 9, 2017 at 3:53 AM, LUCA BELMONTE wrote: > Dear Brian, > Dear Uwe, > > Thank you for your replies. > > I wrote a function that does the same stuff that the suggested package > does. > Now there are no reference to suggested packages. > > Best, > Luca > > 2017-11-08 18:03 GMT+01:00 Uwe Ligges : > >> And even this cannot work for strong dependencies, as sztrong deendencies >> must be available from mainstream repositoreis. >> >> Best, >> Uwe Ligges >> >> >> >> >> >> On 08.11.2017 17:59, Brian G. Peterson wrote: >> >>> I think you should be using: >>> >>> Additional_repositories: https://github.com/mrdwab/SOfun >>> >>> since that is the actual repository. >>> >>> Regards, >>> >>> Brian >>> >>> On Wed, 2017-11-08 at 17:01 +0100, LUCA BELMONTE wrote: >>> Good evening, I am trying to upload my package, called PdPDB 2.0. When building and checking the package with R-studio with --as-cran option selected, everything looks ok but, once I tried to upload the package to CRAN I had the following reply: *"Strong dependencies not in mainstream repositories:* * SOfun* ** checking package namespace information ... OK* ** checking package dependencies ... ERROR* *Package required but not available: 'SOfun'"* I understand the issue it with SOfun that is a package I downloaded and installed from this github url: https://github.com/mrdwab/SOfun I came back to CARN policies and I have read: *"Packages on which a CRAN package depends should be available from a mainstream repository: if any mentioned in ‘Suggests’ or ‘Enhances’ fields are not from such a repository, where to obtain them at a repository should be specified in an ‘Additional_repositories’ field of the DESCRIPTION file (as a comma-separated list of repository URLs) or for other means of access, described in the ‘Description’ field."* So, I updated the DESCRIPTION file as follows: Additional_repositories: http://news.mrdwab.com/install_github.R Before to proceed to submission, I would like to know if this is the right way to proceed or I misinterpreted the submission procedure. Thank you for reading this email, Best, >>> __ >>> R-package-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel >>> >>> > > > -- > Luca Belmonte, PhD > > Dept. Life Sciences, > University of Modena and Reggio Emilia > > Mobile: +39 328 45 81 762 > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] R CMD INSTALL crashes with recent builds of r-devel
Dear list members,
I have three packages on CRAN (asremlPlus, dae and imageData).
The current versions of all three packages can be built and installed using
build of 2017-06-27 r72859 development snapshot of R. I am doing this on a
64-bit laptop and a 64-bit desktop, both running Windows 10.
However, in order to upload a new version to imageData, I have been attempting
since 23/10/2017 to build it with more recent builds of r-devel. For instance,
I have used several builds between Windows 32/64 bit binary build of the
2017-10-29 r73635 development snapshot of R and the build 2017-11-06 r73681
development snapshot of R. In every case it has failed.
When I use
devtools::check("imageData", manual=TRUE, check_dir="D:/Analyses/R",
document=FALSE,
args="--as-cran", build_args="--compact-docs")
I get the following output
* installing *source* package 'imageData' ...
** R
** data
** inst
** preparing package for lazy loading
In R CMD INSTALL
Running R CMD INSTALL gives similar output:
D:\Analyses\R>R CMD INSTALL --build --debug imageData
In R CMD INSTALL
processing 'imageData'
a directory
* installing to library 'D:/Analyses/R library'
* build_help_types=
* DBG: 'R CMD INSTALL' now doing do_install()
* created lock directory 'D:/Analyses/R library/00LOCK-imageData'
* installing *source* package 'imageData' ...
** backing up earlier installation
** R
** data
** inst
** preparing package for lazy loading
In addition a dialog box with the following error message is obtained:
R for Window terminal front-end has stopped working.
I have used rhub to test the installation for all the platforms with the
development version that are available on rhub with the same result.
I have reached a dead-end in that I do not know how I can get any further
information that would help to identify the problem.
Any suggestions as to how I might proceed towards a solution to this problem?
Cheers,
Chris Brien
Adjunct Senior Lecturer in Statistics
-
Phenomics and Bioinformatics Research Centre
University of South Australia
GPO Box 2471
ADELAIDE 5001 South Australia
Phone: +61 8 8302 5535 Fax: +61 8 8302 5785
Email: chris.br...@unisa.edu.au
WEB page:
CRICOS No 00121B
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Re: [R-pkg-devel] Macros in Rd files.
On 09/11/17 23:06, Uwe Ligges wrote: Note the % may be a comment? Ah, yes. Of course! Duh! (Slaps forehead vigorously!) Thanks. cheers, Rolf -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Macros in Rd files.
On 09/11/17 23:40, Duncan Murdoch wrote:
On 09/11/2017 5:06 AM, Uwe Ligges wrote:
Note the % may be a comment?
Yes, and the body should be written in Rd markup, not R. Working out
the appropriate number of escapes is painful; I recommend trial and error.
This worked for me:
\newcommand{\today}{\Sexpr{format(Sys.Date(),"\\\%d/\\\%m/\\\%Y")}}
Now that is a bit more subtle! I don't understand what "written in Rd
markup" really means, and I don't understand the "\Sexpr" construction.
I'd seen it when looking at the example macros in
/usr/local/lib64/R/share/Rd/macros/system.Rd
but I figured if you know nothing about it, don't mess with it.
Is there anywhere that I could read up about writing "in Rd markup"?
Anyway, thanks for giving me the recipe, which is what I really need.
cheers,
Rolf
--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
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Re: [R-pkg-devel] Macros in Rd files --- supplementary question ...
... Mr. Speaker.
On 09/11/17 23:40, Duncan Murdoch wrote:
On 09/11/2017 5:06 AM, Uwe Ligges wrote:
Note the % may be a comment?
Yes, and the body should be written in Rd markup, not R. Working out
the appropriate number of escapes is painful; I recommend trial and error.
This worked for me:
\newcommand{\today}{\Sexpr{format(Sys.Date(),"\\\%d/\\\%m/\\\%Y")}}
Did that, and it worked like a charm. However when I do the "R CMD
build" thing, when it comes to the "* building the PDF package manual"
step it says "Hmm ... looks like a package" (no shit, Sherlock!) and
emits a huge amount of verbose LaTeX diagnostics.
"Normally" one just gets the line "* building the PDF package manual"
and nothing else, and "R CMD build" just carries on cruising.
Evidently defining a macro in the *.Rd file triggers the extra elaboration.
It's no big deal of course, but I just thought I'd ask:
(a) Is there anything to worry about in this respect?
(b) Is there anything different that I should be doing?
(c) Is there anyway of suppressing the (ever-so-slightly annoying)
extra screen output?
I guess that's really three supplementary questions
Thanks for any pointers.
cheers,
Rolf
--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
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Re: [R-pkg-devel] Macros in Rd files --- supplementary question ...
On 09/11/2017 3:29 PM, Rolf Turner wrote:
... Mr. Speaker.
On 09/11/17 23:40, Duncan Murdoch wrote:
On 09/11/2017 5:06 AM, Uwe Ligges wrote:
Note the % may be a comment?
Yes, and the body should be written in Rd markup, not R. Working out
the appropriate number of escapes is painful; I recommend trial and error.
This worked for me:
\newcommand{\today}{\Sexpr{format(Sys.Date(),"\\\%d/\\\%m/\\\%Y")}}
Did that, and it worked like a charm. However when I do the "R CMD
build" thing, when it comes to the "* building the PDF package manual"
step it says "Hmm ... looks like a package" (no shit, Sherlock!) and
emits a huge amount of verbose LaTeX diagnostics.
"Normally" one just gets the line "* building the PDF package manual"
and nothing else, and "R CMD build" just carries on cruising.
Evidently defining a macro in the *.Rd file triggers the extra elaboration.
It's no big deal of course, but I just thought I'd ask:
(a) Is there anything to worry about in this respect?
Of course, never ignore diagnostics. Worry about every line that was
printed!
(b) Is there anything different that I should be doing?
Sounds like it...
(c) Is there anyway of suppressing the (ever-so-slightly annoying)
extra screen output?
Oooh, that's such a bad idea. Don't do that. Fix the problem that led
to the output.
Duncan
I guess that's really three supplementary questions
Thanks for any pointers.
cheers,
Rolf
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Re: [R-pkg-devel] Macros in Rd files.
On 09/11/2017 3:05 PM, Rolf Turner wrote:
On 09/11/17 23:40, Duncan Murdoch wrote:
On 09/11/2017 5:06 AM, Uwe Ligges wrote:
Note the % may be a comment?
Yes, and the body should be written in Rd markup, not R. Working out
the appropriate number of escapes is painful; I recommend trial and error.
This worked for me:
\newcommand{\today}{\Sexpr{format(Sys.Date(),"\\\%d/\\\%m/\\\%Y")}}
Now that is a bit more subtle! I don't understand what "written in Rd
markup" really means, and I don't understand the "\Sexpr" construction.
I'd seen it when looking at the example macros in
/usr/local/lib64/R/share/Rd/macros/system.Rd
but I figured if you know nothing about it, don't mess with it.
Is there anywhere that I could read up about writing "in Rd markup"?
Not sure this would be helpful, but there's
http://developer.r-project.org/parseRd.pdf
The short summary is this:
Rd files are a mess. There are several different modes of parsing that
apply: at the top level you have Rd code, and in different contexts you
may have R code (or something close to it), or verbatim code (just
kidding! There are ways to signal you want out). Table 1 in that
document says what syntax is expected within what macro. In
\newcommand, it says it wants "verbatim" input, but really it's going to
interpret that as Rd input, i.e. LaTeX-like.
Regret asking yet?
Duncan Murdoch
Anyway, thanks for giving me the recipe, which is what I really need.
cheers,
Rolf
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Re: [R-pkg-devel] Macros in Rd files.
On 09/11/2017 3:05 PM, Rolf Turner wrote:
On 09/11/17 23:40, Duncan Murdoch wrote:
On 09/11/2017 5:06 AM, Uwe Ligges wrote:
Note the % may be a comment?
Yes, and the body should be written in Rd markup, not R. Working out
the appropriate number of escapes is painful; I recommend trial and error.
This worked for me:
\newcommand{\today}{\Sexpr{format(Sys.Date(),"\\\%d/\\\%m/\\\%Y")}}
Now that is a bit more subtle! I don't understand what "written in Rd
markup" really means, and I don't understand the "\Sexpr" construction.
I'd seen it when looking at the example macros in
/usr/local/lib64/R/share/Rd/macros/system.Rd
but I figured if you know nothing about it, don't mess with it.
Is there anywhere that I could read up about writing "in Rd markup"?
Not sure this would be helpful, but there's
http://developer.r-project.org/parseRd.pdf
The short summary is this:
Rd files are a mess. There are several different modes of parsing that
apply: at the top level you have Rd code, and in different contexts you
may have R code (or something close to it), or verbatim code (just
kidding! There are ways to signal you want out). Table 1 in that
document says what syntax is expected within what macro. In
\newcommand, it says it wants "verbatim" input, but really it's going to
interpret that as Rd input, i.e. LaTeX-like.
Regret asking yet?
Duncan Murdoch
Anyway, thanks for giving me the recipe, which is what I really need.
cheers,
Rolf
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Re: [R-pkg-devel] Macros in Rd files --- supplementary question ...
On 10/11/17 12:00, Duncan Murdoch wrote: [Rolf Turner wrote:] ... when I do the "R CMD build" thing, when it comes to the "* building the PDF package manual" step it says "Hmm ... looks like a package" (no shit, Sherlock!) and emits a huge amount of verbose LaTeX diagnostics. "Normally" one just gets the line "* building the PDF package manual" and nothing else, and "R CMD build" just carries on cruising. Evidently defining a macro in the *.Rd file triggers the extra elaboration. It's no big deal of course, but I just thought I'd ask: (a) Is there anything to worry about in this respect? Of course, never ignore diagnostics. Worry about every line that was printed! (b) Is there anything different that I should be doing? Sounds like it... (c) Is there anyway of suppressing the (ever-so-slightly annoying) extra screen output? Oooh, that's such a bad idea. Don't do that. Fix the problem that led to the output. Trouble is, I don't (a) know if this really *is* a problem, or (b) if it is, any idea of how to work out how to fix it. I would like to know if it is "an expected phenomenon". Does it happen to other people? I.e. is there anyone out there who has defined their own macro in a *.Rd file, and if so, do *they* get a plethora of LaTeX messages when they do "R CMD build" to the package in question? I'd love to hear from you! :-) cheers, Rolf -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Macros in Rd files --- supplementary question ...
A github search might be helpful to identify packages that define macros in their Rd files: https://github.com/search?utf8=%E2%9C%93&q=user%3Acran+extension%3Ard+newcommand&type=Code On Thu, Nov 9, 2017 at 6:35 PM, Rolf Turner wrote: > > On 10/11/17 12:00, Duncan Murdoch wrote: > > [Rolf Turner wrote:] > >> ... when I do the "R CMD >> >>> build" thing, when it comes to the "* building the PDF package manual" >>> step it says "Hmm ... looks like a package" (no shit, Sherlock!) and >>> emits a huge amount of verbose LaTeX diagnostics. >>> >>> "Normally" one just gets the line "* building the PDF package manual" >>> and nothing else, and "R CMD build" just carries on cruising. >>> >>> Evidently defining a macro in the *.Rd file triggers the extra >>> elaboration. >>> >>> It's no big deal of course, but I just thought I'd ask: >>> >>> (a) Is there anything to worry about in this respect? >>> >> >> Of course, never ignore diagnostics. Worry about every line that was >> printed! >> >> >>> (b) Is there anything different that I should be doing? >>> >> >> Sounds like it... >> >>> >>> (c) Is there anyway of suppressing the (ever-so-slightly annoying) >>> extra screen output? >>> >> >> Oooh, that's such a bad idea. Don't do that. Fix the problem that led >> to the output. >> > > Trouble is, I don't (a) know if this really *is* a problem, or (b) if it > is, any idea of how to work out how to fix it. > > I would like to know if it is "an expected phenomenon". Does it happen to > other people? I.e. is there anyone out there who has defined their > own macro in a *.Rd file, and if so, do *they* get a plethora of LaTeX > messages when they do "R CMD build" to the package in question? > > I'd love to hear from you! :-) > > cheers, > > Rolf > > -- > Technical Editor ANZJS > Department of Statistics > University of Auckland > Phone: +64-9-373-7599 ext. 88276 > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Macros in Rd files --- supplementary question ...
On 10/11/17 13:10, François Michonneau wrote: A github search might be helpful to identify packages that define macros in their Rd files: https://github.com/search?utf8=%E2%9C%93&q=user%3Acran+extension%3Ard+newcommand&type=Code Thanks. Looking into it. cheers, Rolf -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
