[R-pkg-devel] Help - Shiny app on CRAN
Dear team, I have submitted the package GreymodelsPackage_1.0.tar.gz to CRAN and it's a shiny app. However, I received the following * using log directory 'd:/RCompile/CRANincoming/R-devel/GreymodelsPackage.Rcheck' * using R Under development (unstable) (2022-09-25 r82916 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * checking for file 'GreymodelsPackage/DESCRIPTION' ... OK * checking extension type ... ERROR Extensions with Type 'Shiny application' cannot be checked. * DONE Status: 1 ERROR I am not sure how to fix the problems and I would appreciate your help on how to resolve this issue. Thanks and regards, Havisha Jahajeeah [[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] Help - Shiny app on CRAN
В Mon, 26 Sep 2022 19:14:04 +0400 "Jahajeeah, Havisha" пишет: > * checking extension type ... ERROR > Extensions with Type 'Shiny application' cannot be checked. Since you're writing a package, you can either specify Type: Package in the DESCRIPTION file, or omit the field entirely: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-types -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Help - Shiny app on CRAN
On 26.09.2022 17:14, Jahajeeah, Havisha wrote: Dear team, I have submitted the package GreymodelsPackage_1.0.tar.gz to CRAN and it's a shiny app. However, I received the following * using log directory 'd:/RCompile/CRANincoming/R-devel/GreymodelsPackage.Rcheck' * using R Under development (unstable) (2022-09-25 r82916 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * checking for file 'GreymodelsPackage/DESCRIPTION' ... OK * checking extension type ... ERROR Extensions with Type 'Shiny application' cannot be checked. You apparently declared it as Type "Shiny application" rather than "Package" in the DESCRIPTION field? Simply omit the Type field or decalre it as Package. Best, Uwe Ligges * DONE Status: 1 ERROR I am not sure how to fix the problems and I would appreciate your help on how to resolve this issue. Thanks and regards, Havisha Jahajeeah [[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
Re: [R-pkg-devel] Unable to create manual
So I am looking at the R Installation and Administration section,
specifically section 3 for windows. . I have some inquiries.
1. Where do I run "make check"?
2. I got this when I was running the make check:
C:\Users\edmon\Documents\R\RFIN> R CMD make check
make: *** No rule to make target 'check'. Stop.
I'm guessing I'm running it incorrectly.
3. I get this back when I run the "tools::testInstalledPackages(scope =
"base")" on my RGUI.
Error: testing 'utils' failed
Where may I find the error log for this?
Best regards,
On Sat, Sep 17, 2022 at 3:27 AM Tomas Kalibera
wrote:
>
> On 9/16/22 20:17, Edward Wei wrote:
> > That is an interesting thought. I don't think I have downloaded LaTex
> > explicitly, however, I do have MikTex and I added that file to PATH
> > manually.
> >
> > This is what my current PATH calls:
> >
> "c:/rtools42/x86_64-w64-mingw32.static.posix/bin;c:/rtools42/usr/bin;C:\\Program
> > Files\\R\\R-4.2.0\\bin\\x64;C:\\Program Files (x86)\\Common
> >
> Files\\Oracle\\Java\\javapath;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\WINDOWS\\System32\\OpenSSH\\;C:\\Program
> > Files\\Wolfram Research\\WolframScript\\;C:\\Program
> >
> Files\\Git\\cmd;C:\\Users\\edmon\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\edmon\\AppData\\Local\\GitHubDesktop\\bin;C:\\Users\\edmon\\AppData\\Local\\Programs\\MiKTeX\\miktex\\bin\\x64\\;C:/Program
> > Files/RStudio/bin/quarto/bin"
> >
> > I have been able to generate a PDF of my package by entering :
> > tools::texi2pdf(file = "avfintools.Rcheck/avfintools-manual.tex")
> > on the console.
> >
> > Is there a way to submit the manual manually rather than have it
> compiled?
> > Or is it a requirement for the manual to be able to be compiled from the
> > package?
> >
> > Thanks for your help,
>
> MikTeX is fine and common choice and works with R.
>
> R Admin manual has "Installing R under Windows" with more details there
> and in the linked documents, including
> Howto: Building R 4.2 and packages on Windows.
>
> There must be something special set up on your system that probably only
> debugging could reveal. Possibly some customization in any of the R
> startup files. Or some conflicting tool on the PATH (e.g. in Git?).
>
> Tomas
>
> >
> > On Wed, Sep 14, 2022 at 3:14 PM Uwe Ligges <
> lig...@statistik.tu-dortmund.de>
> > wrote:
> >
> >>
> >> On 14.09.2022 23:54, Duncan Murdoch wrote:
> >>> On 12/09/2022 9:09 a.m., Edward Wei wrote:
> This is the following error message I get from R CMD check:
>
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
> * checking PDF version of manual without index ... ERROR
> Re-running with no redirection of stdout/stderr.
> Hmm ... looks like a package
> Converting parsed Rd's to LaTeX ...
> Creating pdf output from LaTeX ...
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
> quiet, :
> pdflatex is not available
> >>> This looks like a problem in the way tools::texi2dvi detects pdflatex.
> >>> If you have a valid LaTeX file, try running
> >>>
> >>> tools::texi2dvi(filename, pdf = TRUE)
> >>>
> >>> If that gives the same message, then debug(tools::texi2dvi), and
> repeat,
> >>> single stepping through the function to see what test it uses, and
> >>> figure out why it fails on your system.
> >> Or the env var PATH is overwritten once R get started, perhaps you have
> >> it in one of the files R process it at startup?
> >> Does Sys.getenv("PATH") show the pat to the LaTeX binary?
> >>
> >> Best,
> >> Uwe Ligges
> >>
> >>
> >>> Duncan Murdoch
> >>>
> >>>
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
> quiet, :
> pdflatex is not available
> Error in running tools::texi2pdf()
> You may want to clean up by 'rm -Rf
> C:/Users/edmon/AppData/Local/Temp/RtmpWkD7Iy/Rd2pdf35d81e3e188c'
> * DONE
>
> Status: 1 ERROR, 1 WARNING, 2 NOTEs
>
>
> Then, I tried debugging by isolating errors from the Rd to PDF
> conversion.
>
>
> C:\Users\edmon\Documents\R\RFIN> R CMD Rd2pdf avfintools --no-clean
> Hmm ... looks like a package
> Converting Rd files to LaTeX ...
> Creating pdf output from LaTeX ...
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
> quiet, :
> pdflatex is not available
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
> quiet, :
> pdflatex is not available
> Error in running tools::texi2pdf()
> You may want to clean up by 'rm -Rf .Rd2pdf27964'
>
>
> In this folder is the file Rd2.tex which I tried to complie into a
> pdf. But
> this error returns and PDF cannot be compiled. :
>
>
> LaTeX Error: File `Rd.sty' not found.
>
> Type X to quit or to proceed,
> or enter new name. (Default
Re: [R-pkg-devel] Help - Shiny app on CRAN
Dear team, My second attempt at submitting the package GreymodelsPackage_1.0.tar.gz to CRAN. Grateful if you could please assist me with the following issues: CIvalue2: no visible global function definition for 'qt' andgm11: no visible binding for global variable 'ParticleSwarm' andgm11: no visible global function definition for 'tail' app: no visible global function definition for 'shinyApp' dbgm12: no visible binding for global variable 'ParticleSwarm' dbgm12: no visible global function definition fo lotegm: no visible global function definition for 'geom_point' plotegm: no visible global function definition for 'aes' plotegm: no visible binding for global variable 'x' plotegm: no visible binding for global variable 'y' plotegm: no visible global function definition for 'geom_line' plotegm: no visible global function definition for 'scale_color_manual' plotegm: no visible global function definition for 'ggplot Also, Objects in \usage without \alias in documentation object 'Multivariable': 'dbgm12' Objects in \usage without \alias in documentation object 'Plots': 'plots' Bad \usage lines found in documentation object 'BackgroundValues': gm11(x0), epgm11(x0), tbgm11(x0), igm11(x0), gm114(x0) Bad \usage lines found in documentation object 'CombinedModels': ngbm11(x0), ggvm11(x0), tfdgm11(x0) Thanks and Regards, Havisha Jahajeeah On Mon, Sep 26, 2022 at 7:14 PM Jahajeeah, Havisha wrote: > Dear team, > > I have submitted the package GreymodelsPackage_1.0.tar.gz to CRAN and it's > a shiny app. > > However, I received the following > > * using log directory > 'd:/RCompile/CRANincoming/R-devel/GreymodelsPackage.Rcheck' > * using R Under development (unstable) (2022-09-25 r82916 ucrt) > * using platform: x86_64-w64-mingw32 (64-bit) > * using session charset: UTF-8 > * checking for file 'GreymodelsPackage/DESCRIPTION' ... OK > * checking extension type ... ERROR > Extensions with Type 'Shiny application' cannot be checked. > * DONE > Status: 1 ERROR > > I am not sure how to fix the problems and I would appreciate your help on > how to resolve this issue. > > Thanks and regards, > > Havisha Jahajeeah > > [[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] Unable to create manual
On Mon, 26 Sep 2022 10:50:01 -0700 Edward Wei wrote: > 1. Where do I run "make check"? In the directory where R is built from source. If you're using a binary build of R, this isn't applicable. > 3. I get this back when I run the "tools::testInstalledPackages(scope > = "base")" on my RGUI. > > Error: testing 'utils' failed > > Where may I find the error log for this? testInstalledPackages() creates output files in the current directory. Does list.files(pattern = 'utils|Rout\\.fail') give you anything useful? -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Help - Shiny app on CRAN
Hello, are you aware of https://win-builder.r-project.org/? It'll allow you to validate that your package passes all the requirements before submitting it to CRAN. My $.02 /Henrik On Mon, Sep 26, 2022 at 11:23 AM Jahajeeah, Havisha wrote: > > Dear team, > > My second attempt at submitting the package GreymodelsPackage_1.0.tar.gz to > CRAN. > > Grateful if you could please assist me with the following issues: > > CIvalue2: no visible global function definition for 'qt' > andgm11: no visible binding for global variable 'ParticleSwarm' > andgm11: no visible global function definition for 'tail' > app: no visible global function definition for 'shinyApp' > dbgm12: no visible binding for global variable 'ParticleSwarm' > dbgm12: no visible global function definition fo > > lotegm: no visible global function definition for 'geom_point' > plotegm: no visible global function definition for 'aes' > plotegm: no visible binding for global variable 'x' > plotegm: no visible binding for global variable 'y' > plotegm: no visible global function definition for 'geom_line' > plotegm: no visible global function definition for 'scale_color_manual' > plotegm: no visible global function definition for 'ggplot > > Also, > > Objects in \usage without \alias in documentation object 'Multivariable': > 'dbgm12' > > Objects in \usage without \alias in documentation object 'Plots': > 'plots' > > Bad \usage lines found in documentation object 'BackgroundValues': > gm11(x0), epgm11(x0), tbgm11(x0), igm11(x0), gm114(x0) > Bad \usage lines found in documentation object 'CombinedModels': > ngbm11(x0), ggvm11(x0), tfdgm11(x0) > > > > Thanks and Regards, > > Havisha Jahajeeah > > > On Mon, Sep 26, 2022 at 7:14 PM Jahajeeah, Havisha > wrote: > > > Dear team, > > > > I have submitted the package GreymodelsPackage_1.0.tar.gz to CRAN and it's > > a shiny app. > > > > However, I received the following > > > > * using log directory > > 'd:/RCompile/CRANincoming/R-devel/GreymodelsPackage.Rcheck' > > * using R Under development (unstable) (2022-09-25 r82916 ucrt) > > * using platform: x86_64-w64-mingw32 (64-bit) > > * using session charset: UTF-8 > > * checking for file 'GreymodelsPackage/DESCRIPTION' ... OK > > * checking extension type ... ERROR > > Extensions with Type 'Shiny application' cannot be checked. > > * DONE > > Status: 1 ERROR > > > > I am not sure how to fix the problems and I would appreciate your help on > > how to resolve this issue. > > > > Thanks and regards, > > > > Havisha Jahajeeah > > > > > > [[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
Re: [R-pkg-devel] Help - Shiny app on CRAN
It might be easier to help you if you show us your package by
publishing the source code somewhere.
On Mon, 26 Sep 2022 22:22:48 +0400
"Jahajeeah, Havisha" wrote:
> CIvalue2: no visible global function definition for 'qt'
> andgm11: no visible binding for global variable 'ParticleSwarm'
> andgm11: no visible global function definition for 'tail'
> app: no visible global function definition for 'shinyApp'
> dbgm12: no visible binding for global variable 'ParticleSwarm'
It sounds like your NAMESPACE file isn't properly set up to import the
functions you're using. For the package to work correctly, it should
contain lines
importFrom(stats, qt)
importFrom(utils, tail)
importFrom(shiny, shinyApp)
and so on for every function you use that's not in base.
See Writing R Extensions section 1.5:
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Specifying-imports-and-exports
> Objects in \usage without \alias in documentation object 'Plots':
> 'plots'
A single Rd file can describe multiple functions, but they should be
both mentioned in the \usage{} section and as an \alias{}. Do you
export two different objects (functions?) named "plots" and "Plots", or
is one of those an error?
> Bad \usage lines found in documentation object 'BackgroundValues':
> gm11(x0), epgm11(x0), tbgm11(x0), igm11(x0), gm114(x0)
The \usage{} section must exactly match the definition of the function
(but you can omit default values of the arguments if they're too large
and not very informative), without any other words or punctuation.
Once your package passes the automated tests, a human volunteer will go
over your package to make sure that it fits the CRAN policy (not
providing a link because you've already read it when you submitted the
package), which includes having good documentation for every function
you export.
See Writing R Extensions section 2 for more information on this:
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-R-documentation-files
I've also noticed that you're showing us an error message from the CRAN
pre-test infrastructure. You can get these errors (and start fixing
them) faster without spending time waiting for the test result by
running R CMD check --as-cran your_package.tar.gz on your own machine.
--
Best regards,
Ivan
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[R-pkg-devel] R build fail without a message
Hi, One of my CRAN packages gets an ARM-64 build fail, visible at https://www.r-project.org/nosvn/R.check/r-oldrel-macos-arm64/EdSurvey-00check.html It ends: checking replacement functions ... OK checking foreign function calls ... It looks like someone tripped over the power chord, but I have no way of knowing what actually happened. I cannot reproduce this on Rhub for R-release on ARM-64 nor on my coworker's m1 on R-release. Any ideas on what I can do to diagnose this before resubmitting? Best, Paul Bailey, Ph.D. Senior Economist, AIR 202-403-5694 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Inquiry
Hi there, I am writing to aks your help for an issuue arising when I am writing my R package using R studio 1.2.1335 as follows. ``checking for missing documentation entries ... WARNING Undocumented code objects: 'r2' All user-level objects in a package should have documentation entries." The function r2.r is among .r files within R folder of my package. I am not interested to present "r2" in the R topics documented: as a part of first page of built pdf help file of my package. I appreciate highly if you could help me to solve this issue. -- This email was Anti Virus checked by Security Gateway. [[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] Inquiry
This issue isn't related to RStudio. The issue is that you're exporting an object without providing any documentation for it. It sounds like you don't want to export it, so you need to go to your NAMESPACE file and remove the part was export(r2). If you do want to export it, then you need to document it, there's no way around that. The documentation doesn't need to be very detailed. On Mon., Sep. 26, 2022, 20:01 , wrote: > Hi there, > I am writing to aks your help for an issuue arising when I am writing my R > package using R studio 1.2.1335 as follows. > ``checking for missing documentation entries ... WARNING > Undocumented code objects: > 'r2' > All user-level objects in a package should have documentation entries." > The function r2.r is among .r files within R folder of my package. > I am not interested to present "r2" in the R topics documented: as a part > of first page of built pdf help file of my package. > I appreciate highly if you could help me to solve this issue. > > -- > This email was Anti Virus checked by Security Gateway. > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R build fail without a message
Paul, I wouldn't worry about oldrel - that's likely an incomplete run (I don't see that error anymore), but I would worry about the failure on R-release: https://www.r-project.org/nosvn/R.check/r-release-macos-arm64/EdSurvey-00check.html You can always check with the Mac Builder before you submit it to CRAN: https://mac.r-project.org/macbuilder/submit.html Cheers, Simon > On 27/09/2022, at 10:03 AM, Bailey, Paul wrote: > > Hi, > > One of my CRAN packages gets an ARM-64 build fail, visible at > https://www.r-project.org/nosvn/R.check/r-oldrel-macos-arm64/EdSurvey-00check.html > > > It ends: > >checking replacement functions ... OK >checking foreign function calls ... > > It looks like someone tripped over the power chord, but I have no way of > knowing what actually happened. > > I cannot reproduce this on Rhub for R-release on ARM-64 nor on my coworker's > m1 on R-release. Any ideas on what I can do to diagnose this before > resubmitting? > > Best, > Paul Bailey, Ph.D. > Senior Economist, AIR > 202-403-5694 > > __ > 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
Re: [R-pkg-devel] Inquiry
On Mon, 26 Sep 2022 20:07:28 -0400
Andrew Simmons wrote:
> This issue isn't related to RStudio.
>
> The issue is that you're exporting an object without providing any
> documentation for it. It sounds like you don't want to export it, so
> you need to go to your NAMESPACE file and remove the part was
> export(r2). If you do want to export it, then you need to document
> it, there's no way around that. The documentation doesn't need to be
> very detailed.
>
>
> On Mon., Sep. 26, 2022, 20:01 , wrote:
>
> > Hi there,
> > I am writing to aks your help for an issuue arising when I am
> > writing my R package using R studio 1.2.1335 as follows.
> > ``checking for missing documentation entries ... WARNING
> > Undocumented code objects:
> > 'r2'
> > All user-level objects in a package should have documentation
> > entries." The function r2.r is among .r files within R folder of
> > my package. I am not interested to present "r2" in the R topics
> > documented: as a part of first page of built pdf help file of my
> > package. I appreciate highly if you could help me to solve this
> > issue.
My understanding is that functions, that are not meant to be called
directly by users, should be documented in a file named
-internal.Rd. It should have a structure something like:
> \name{pkgnm-internal}
> \alias{pkgnm-internal}
> \alias{foo}
> \alias{bar}
> \alias{clyde}
> \title{Internal pkgnm functions}
> \description{
> Internal pkgnm functions.
> }
> \usage{
> foo(x,y,z)
> bar(melvin,irving,...)
> clyde(arrgh)
> }
> \details{
> These functions are not intended to be called directly by the
> user.
> }
> \author{Hoo Hee
> \email{hoo@somewhere.otr}
> }
> \keyword{internal}
Then if someone types, e.g., "help(clyde)" they get the processed
form of the forgoing *.Rd file displayed, and are thereby told that
they probably should not mess with clyde().
cheers,
Rolf Turner
P.S. I always export everything.
R. T.
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Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
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