date:20170130

Re: [R-pkg-devel] Encoding problem

2017-01-30 Thread Thierry Onkelinx

Dear David,

Have you tried removing the exclamation mark in %!\VignetteEncoding{UTF-8}?
I think it should be %\VignetteEncoding{UTF-8}

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2017-01-29 13:40 GMT+01:00 David Scott :

> I am trying to add a vignette to xtable showing how to incorporate some
> Chinese characters following an enquiry from a user.
>
> I can create the vignette satisfactorily just processing the knitr file
> normally, with the resulting pdf displaying Chinese characters in the R
> code and also as headings when I produce a table. However when I try to
> build the package with the vignette included, I get:
>
> * creating vignettes ...Warning: running command
> '"C:/PROGRA~1/R/R-33~1.2/bin/x64/Rscript" --vanilla
>  ERROR
> Error: Vignette 'ChineseCharacters.Rnw' is non-ASCII but has no declared
> encoding
> Execution halted
> make: *** [build] Error 1
>
> I updated R to 3.3.2 and Rtools to 33 before running the build.
>
> The vignette starts as follows:
>
> %\VignetteIndexEntry{xtable Chinese Characters}
> %\VignetteDepends{xtable}
> %\VignetteKeywords{LaTeX, HTML, table}
> %\VignettePackage{xtable}
> % !Rnw weave = knitr
> % \VignetteEngine{knitr::knitr}
> %!\VignetteEncoding{UTF-8}
> %***
> ***
> \documentclass{ctexart}
> \usepackage{longtable}
> \usepackage{booktabs}
> \usepackage{array}
> \usepackage{hyperref}
> \usepackage{inputenx}
>
> The section of the file which is not ASCII is:
>
> <>=
> ### Prepare data
> library(knitr)
> library(xtable)
>
> tbl <- data.frame(positivePairs = 0, negativePairs = 0,
>   avePositiveSpread = NA,
>   aveNegativeSpread = NA,
>   PnL = 435, sumPnL = 144358.7)
> names(tbl) <- c("ÕýÏò¿ª²Ö", "¸ºÏò¿ª²Ö", "ÕýÏò¿ª²ÖÆ½¾ù¼Û²î",
> "¸ºÏò¿ª²ÖÆ½¼Û¼Û²î", "µ±ÈÕËðÒæ", "ÀÛ¼ÆËðÒæ")
> @
>
> I am a bit of a novice at encodings, and know nothing about Chinese
> characters so any advice is welcome.
>
> David Scott
>
>
>
> --
> _
> David Scott Department of Statistics
> The University of Auckland, PB 92019
> Auckland 1142,NEW ZEALAND
> Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
> Email:  d.sc...@auckland.ac.nz,  Fax: +64 9 373 7018
>
> Volunteer Arena Manager:
> Orienteering Sprint Final at University of Auckland
> World Masters Games 2017
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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[R-pkg-devel] Description Meta Information Note

2017-01-30 Thread Cathy Lee Gierke

I'm getting a Note that I don't understandand I think it may be the
cause of other errors later  I have copied all of the output up to the
error for context.  The error line is at the end.  It seems to say that I
have not done a Build before doing the Check, but I did

x-134-84-0-217:~ user$ cd '/Users/user/CATkit'

x-134-84-0-217:CATkit user$ *R CMD build CATkit*

* checking for file ‘CATkit/DESCRIPTION’ ... OK

* preparing ‘CATkit’:

* checking DESCRIPTION meta-information ... OK

* checking for LF line-endings in source and make files

* checking for empty or unneeded directories

* building ‘CATkit_2.06.tar.gz’


x-134-84-0-217:CATkit user$ *R CMD check CATkit*

* using log directory ‘/Users/user/CATkit/CATkit.Rcheck’

* using R version 3.3.2 (2016-10-31)

* using platform: x86_64-apple-darwin13.4.0 (64-bit)

* using session charset: UTF-8

* checking for file ‘CATkit/DESCRIPTION’ ... OK

* checking extension type ... Package

* this is package ‘CATkit’ version ‘2.06’

* 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 ... NOTE

Found the following hidden files and directories:

  .DS_Store

  inst/.DS_Store

  inst/extdata/.DS_Store

  inst/extdata/.Rapp.history

  man/.DS_Store

These were most likely included in error. See section ‘Package

structure’ in the ‘Writing R Extensions’ manual.

* checking for portable file names ... OK

* checking for sufficient/correct file permissions ... OK

* checking whether package ‘CATkit’ can be installed ... OK

* checking installed package size ... OK

* checking package directory ... OK

** checking DESCRIPTION meta-information ... NOTE*

*Checking should be performed on sources prepared by ‘R CMD build’.*
Thanks,

Cathy Lee Gierke




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Re: [R-pkg-devel] Description Meta Information Note

2017-01-30 Thread Brian G. Peterson

On Mon, 2017-01-30 at 09:45 -0600, Cathy Lee Gierke wrote:
>  building ‘CATkit_2.06.tar.gz’

R CMD build creates a tarball

> x-134-84-0-217:CATkit user$ *R CMD check CATkit*

but you are checknig the directory, not the tarball.

do 

R CMD check CATkit_2.06.tar.gz

instead.

Regards,

Brian

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[R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Cathy Lee Gierke

Yes, that seemed to get rid of the NOTEbut it doesn't seem to make much
difference other than that.  i.e., it seems to process the same using
CATkit vs CATkit_2.06.tar.gz!

Here is the main error that I am getting.  I just upgraded to the latest R
version, fyi.

Everything was fine, a few minor warnings...now this.  Description and
namespace are proper.  These pkgs should all be part of the R base, aren't
they? Anyone know why I should get these errors?  Thanks!

* checking R code for possible problems ... NOTE

Actogram: no visible global function definition for ‘par’

Actogram: no visible global function definition for ‘barplot’

Actogram: no visible global function definition for ‘box’

Actogram: no visible global function definition for ‘text’

Actogram: no visible global function definition for ‘mtext’

Actogram: no visible binding for global variable ‘end’

AutoCorr: no visible global function definition for ‘par’

AutoCorr: no visible global function definition for ‘layout’

AutoCorr: no visible global function definition for ‘acf’

AutoCorr: no visible global function definition for ‘abline’

AutoCorr: no visible global function definition for ‘title’

AutoCorr: no visible global function definition for ‘mtext’

AutoCorr: no visible global function definition for ‘var’

AutoCorr: no visible binding for global variable ‘end’

CATCosinor: no visible global function definition for ‘par’

CATCosinor: no visible global function definition for ‘pdf’

CATCosinor: no visible global function definition for ‘jpeg’

CATCosinor: no visible global function definition for ‘png’

CATCosinor: no visible global function definition for ‘tiff’

. A zillion more for every function I have..

periCosinor: no visible global function definition for ‘par’

periCosinor: no visible global function definition for ‘fft’

Undefined global functions or variables:

  TukeyHSD abline acf aov as.raster axis barplot box boxplot ccf

  coefficients dev.cur dev.off drop1 end fft gray heat.colors image

  jpeg layout legend lines median model.tables mtext na.action na.omit

  palette par pdf pf plot plot.new png points rainbow rasterImage

  read.table str strwidth tail terrain.colors text tiff title ts var

  write.table

Consider adding

  importFrom("grDevices", "as.raster", "dev.cur", "dev.off", "gray",

 "heat.colors", "jpeg", "palette", "pdf", "png", "rainbow",

 "terrain.colors", "tiff")

  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",

 "image", "layout", "legend", "lines", "mtext", "par",

 "plot", "plot.new", "points", "rasterImage", "strwidth",

 "text", "title")

  importFrom("stats", "TukeyHSD", "acf", "aov", "ccf", "coefficients",

 "drop1", "end", "fft", "median", "model.tables",

 "na.action", "na.omit", "pf", "ts", "var")

  importFrom("utils", "read.table", "str", "tail", "write.table")

to your NAMESPACE file.

Cathy Lee Gierke


*“Darkness cannot drive out darkness: only light can do that. Hate cannot
drive out hate: only love can do that.” *
*“The arc of the moral universe is long, but it bends towards justice.”*
*“Nothing in the world is more dangerous than sincere ignorance and
conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.”   *
*“Forgiveness is not an occasional act, it is a constant attitude.” *
*“Injustice anywhere is a threat to justice everywhere.”  *

― Martin Luther King Jr.



On Mon, Jan 30, 2017 at 10:05 AM, Brian G. Peterson 
wrote:

> On Mon, 2017-01-30 at 09:45 -0600, Cathy Lee Gierke wrote:
> >  building ‘CATkit_2.06.tar.gz’
>
> R CMD build creates a tarball
>
> > x-134-84-0-217:CATkit user$ *R CMD check CATkit*
>
> but you are checknig the directory, not the tarball.
>
> do
>
> R CMD check CATkit_2.06.tar.gz
>
> instead.
>
> Regards,
>
> Brian
>

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Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Dirk Eddelbuettel


On 30 January 2017 at 10:39, Cathy Lee Gierke wrote:
| Everything was fine, a few minor warnings...now this.  Description and
| namespace are proper.  These pkgs should all be part of the R base, aren't
| they? Anyone know why I should get these errors?  Thanks!

Just read what it says and do that:

| Consider adding
| 
|   importFrom("grDevices", "as.raster", "dev.cur", "dev.off", "gray",
|  "heat.colors", "jpeg", "palette", "pdf", "png", "rainbow",
|  "terrain.colors", "tiff")
|   importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
|  "image", "layout", "legend", "lines", "mtext", "par",
|  "plot", "plot.new", "points", "rasterImage", "strwidth",
|  "text", "title")
|   importFrom("stats", "TukeyHSD", "acf", "aov", "ccf", "coefficients",
|  "drop1", "end", "fft", "median", "model.tables",
|  "na.action", "na.omit", "pf", "ts", "var")
|   importFrom("utils", "read.table", "str", "tail", "write.table")
| 
| to your NAMESPACE file.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Brian G. Peterson

The error you reference below is pretty clear, I think.
You need to add imports for all the functions you're using from other
packages.  
See: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Speci
fying-imports-and-exports
Regards,
Brian


On Mon, 2017-01-30 at 10:39 -0600, Cathy Lee Gierke wrote:
> Yes, that seemed to get rid of the NOTEbut it doesn't seem to
> make much difference other than that.  i.e., it seems to process the
> same using CATkit vs CATkit_2.06.tar.gz!
> 
> Here is the main error that I am getting.  I just upgraded to the
> latest R version, fyi.
> 
> Everything was fine, a few minor warnings...now this.  Description
> and namespace are proper.  These pkgs should all be part of the R
> base, aren't they? Anyone know why I should get these errors? 
> Thanks!
> 
> * checking R code for possible problems ... NOTE
> Actogram: no visible global function definition for ‘par’
> Actogram: no visible global function definition for ‘barplot’
> Actogram: no visible global function definition for ‘box’
> Actogram: no visible global function definition for ‘text’
> Actogram: no visible global function definition for ‘mtext’
> Actogram: no visible binding for global variable ‘end’
> AutoCorr: no visible global function definition for ‘par’
> AutoCorr: no visible global function definition for ‘layout’
> AutoCorr: no visible global function definition for ‘acf’
> AutoCorr: no visible global function definition for ‘abline’
> AutoCorr: no visible global function definition for ‘title’
> AutoCorr: no visible global function definition for ‘mtext’
> AutoCorr: no visible global function definition for ‘var’
> AutoCorr: no visible binding for global variable ‘end’
> CATCosinor: no visible global function definition for ‘par’
> CATCosinor: no visible global function definition for ‘pdf’
> CATCosinor: no visible global function definition for ‘jpeg’
> CATCosinor: no visible global function definition for ‘png’
> CATCosinor: no visible global function definition for ‘tiff’
> . A zillion more for every function I have..
> periCosinor: no visible global function definition for ‘par’
> periCosinor: no visible global function definition for ‘fft’
> Undefined global functions or variables:
>   TukeyHSD abline acf aov as.raster axis barplot box boxplot ccf
>   coefficients dev.cur dev.off drop1 end fft gray heat.colors image
>   jpeg layout legend lines median model.tables mtext na.action
> na.omit
>   palette par pdf pf plot plot.new png points rainbow rasterImage
>   read.table str strwidth tail terrain.colors text tiff title ts var
>   write.table
> Consider adding
>   importFrom("grDevices", "as.raster", "dev.cur", "dev.off", "gray",
>              "heat.colors", "jpeg", "palette", "pdf", "png",
> "rainbow",
>              "terrain.colors", "tiff")
>   importFrom("graphics", "abline", "axis", "barplot", "box",
> "boxplot",
>              "image", "layout", "legend", "lines", "mtext", "par",
>              "plot", "plot.new", "points", "rasterImage", "strwidth",
>              "text", "title")
>   importFrom("stats", "TukeyHSD", "acf", "aov", "ccf",
> "coefficients",
>              "drop1", "end", "fft", "median", "model.tables",
>              "na.action", "na.omit", "pf", "ts", "var")
>   importFrom("utils", "read.table", "str", "tail", "write.table")
> to your NAMESPACE file.
> 
> Cathy Lee Gierke      
> “Darkness cannot drive out darkness: only light can do that. Hate
> cannot drive out hate: only love can do that.” 
> 
> “The arc of the moral universe is long, but it bends towards
> justice.”
> “Nothing in the world is more dangerous than sincere ignorance and
> conscientious stupidity.” 
> “Never forget that everything Hitler did in Germany was legal.”   
> “Forgiveness is not an occasional act, it is a constant attitude.” 
> “Injustice anywhere is a threat to justice everywhere.”  
> 
>   
>   ―
> Martin Luther King Jr.
> 
> 
> 
> On Mon, Jan 30, 2017 at 10:05 AM, Brian G. Peterson  com> wrote:
> > On Mon, 2017-01-30 at 09:45 -0600, Cathy Lee Gierke wrote:
> > 
> > >  building ‘CATkit_2.06.tar.gz’
> > 
> > 
> > 
> > R CMD build creates a tarball
> > 
> > 
> > 
> > > x-134-84-0-217:CATkit user$ *R CMD check CATkit*
> > 
> > 
> > 
> > but you are checknig the directory, not the tarball.
> > 
> > 
> > 
> > do
> > 
> > 
> > 
> > R CMD check CATkit_2.06.tar.gz
> > 
> > 
> > 
> > instead.
> > 
> > 
> > 
> > Regards,
> > 
> > 
> > 
> > Brian
> > 
> > 
-- 
Brian G. Peterson
http://braverock.com/brian/
Ph: 773-459-4973
IM: bgpbraverock

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Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Cathy Lee Gierke

That is the obvious solution, but it doesn't seem correct:  I have pdf
included in the description, and namespace files, yet it is being called
out.  Additionally, aren't most of these pkgs in the packages included by
default?

And up until yesterday, I didn't have any of these problems.  I've been
compiling and running this for several years.  But now I want to release to
CRAN, so I've been fixing minor issuesand suddenly this mass of Notes.

Thank you,

Cathy Lee Gierke


*“Darkness cannot drive out darkness: only light can do that. Hate cannot
drive out hate: only love can do that.” *
*“The arc of the moral universe is long, but it bends towards justice.”*
*“Nothing in the world is more dangerous than sincere ignorance and
conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.”   *
*“Forgiveness is not an occasional act, it is a constant attitude.” *
*“Injustice anywhere is a threat to justice everywhere.”  *

― Martin Luther King Jr.



On Mon, Jan 30, 2017 at 10:52 AM, Brian G. Peterson 
wrote:

> The error you reference below is pretty clear, I think.
>
> You need to add imports for all the functions you're using from other
> packages.
>
> See: https://cran.r-project.org/doc/manuals/r-release/R-exts.
> html#Specifying-imports-and-exports
>
> Regards,
>
> Brian
>
>
> --
> Brian G. Petersonhttp://braverock.com/brian/
> Ph: 773-459-4973 <(773)%20459-4973>
> IM: bgpbraverock
>
>
> On Mon, 2017-01-30 at 10:39 -0600, Cathy Lee Gierke wrote:
>
> Yes, that seemed to get rid of the NOTEbut it doesn't seem to make
> much difference other than that.  i.e., it seems to process the same using
> CATkit vs CATkit_2.06.tar.gz!
>
> Here is the main error that I am getting.  I just upgraded to the latest R
> version, fyi.
>
> Everything was fine, a few minor warnings...now this.  Description and
> namespace are proper.  These pkgs should all be part of the R base, aren't
> they? Anyone know why I should get these errors?  Thanks!
>
> * checking R code for possible problems ... NOTE
>
> Actogram: no visible global function definition for ‘par’
>
> Actogram: no visible global function definition for ‘barplot’
>
> Actogram: no visible global function definition for ‘box’
>
> Actogram: no visible global function definition for ‘text’
>
> Actogram: no visible global function definition for ‘mtext’
>
> Actogram: no visible binding for global variable ‘end’
>
> AutoCorr: no visible global function definition for ‘par’
>
> AutoCorr: no visible global function definition for ‘layout’
>
> AutoCorr: no visible global function definition for ‘acf’
>
> AutoCorr: no visible global function definition for ‘abline’
>
> AutoCorr: no visible global function definition for ‘title’
>
> AutoCorr: no visible global function definition for ‘mtext’
>
> AutoCorr: no visible global function definition for ‘var’
>
> AutoCorr: no visible binding for global variable ‘end’
>
> CATCosinor: no visible global function definition for ‘par’
>
> CATCosinor: no visible global function definition for ‘pdf’
>
> CATCosinor: no visible global function definition for ‘jpeg’
>
> CATCosinor: no visible global function definition for ‘png’
>
> CATCosinor: no visible global function definition for ‘tiff’
>
> . A zillion more for every function I have..
>
> periCosinor: no visible global function definition for ‘par’
>
> periCosinor: no visible global function definition for ‘fft’
>
> Undefined global functions or variables:
>
>   TukeyHSD abline acf aov as.raster axis barplot box boxplot ccf
>
>   coefficients dev.cur dev.off drop1 end fft gray heat.colors image
>
>   jpeg layout legend lines median model.tables mtext na.action na.omit
>
>   palette par pdf pf plot plot.new png points rainbow rasterImage
>
>   read.table str strwidth tail terrain.colors text tiff title ts var
>
>   write.table
>
> Consider adding
>
>   importFrom("grDevices", "as.raster", "dev.cur", "dev.off", "gray",
>
>  "heat.colors", "jpeg", "palette", "pdf", "png", "rainbow",
>
>  "terrain.colors", "tiff")
>
>   importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
>
>  "image", "layout", "legend", "lines", "mtext", "par",
>
>  "plot", "plot.new", "points", "rasterImage", "strwidth",
>
>  "text", "title")
>
>   importFrom("stats", "TukeyHSD", "acf", "aov", "ccf", "coefficients",
>
>  "drop1", "end", "fft", "median", "model.tables",
>
>  "na.action", "na.omit", "pf", "ts", "var")
>
>   importFrom("utils", "read.table", "str", "tail", "write.table")
>
> to your NAMESPACE file.
>
> Cathy Lee Gierke
>
>
> *“Darkness cannot drive out darkness: only light can do that. Hate cannot
> drive out hate: only love can do that.” *
> *“The arc of the moral universe is long, but it bends towards justice.”*
> *“Nothing in the world is more dangerous than sincere ignorance and
> conscienti

Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Brian G. Peterson

See the link in my email below.  It says:
"Packages implicitly import the base namespace. Variables exported from
other packages with namespaces need to be imported explicitly using the
directives import and importFrom."

Regards,

Brian

On Mon, 2017-01-30 at 11:04 -0600, Cathy Lee Gierke wrote:
> That is the obvious solution, but it doesn't seem correct:  I have
> pdf included in the description, and namespace files, yet it is being
> called out.  Additionally, aren't most of these pkgs in the packages
> included by default?
> 
> And up until yesterday, I didn't have any of these problems.  I've
> been compiling and running this for several years.  But now I want to
> release to CRAN, so I've been fixing minor issuesand suddenly
> this mass of Notes.  
> 
> Thank you,
> 
> Cathy Lee Gierke
>       
> “Darkness cannot drive out darkness: only light can do that. Hate
> cannot drive out hate: only love can do that.” 
> 
> “The arc of the moral universe is long, but it bends towards
> justice.”
> “Nothing in the world is more dangerous than sincere ignorance and
> conscientious stupidity.” 
> “Never forget that everything Hitler did in Germany was legal.”   
> “Forgiveness is not an occasional act, it is a constant attitude.” 
> “Injustice anywhere is a threat to justice everywhere.”  
> 
> ― Martin Luther King Jr.
> 
> 
> On Mon, Jan 30, 2017 at 10:52 AM, Brian G. Peterson  com> wrote:
> > The error you reference below is pretty clear, I think.
> > 
> > You need to add imports for all the functions you're using from
> > other packages. 
> > 
> > See: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#S
> > pecifying-imports-and-exports
> > 
> > Regards,
> > 
> > Brian
> > 
> > 
> > -- 
> > Brian G. Peterson
> > http://braverock.com/brian/
> > Ph: 773-459-4973
> > IM: bgpbraverock
> > 
> > On Mon, 2017-01-30 at 10:39 -0600, Cathy Lee Gierke wrote:
> > > Yes, that seemed to get rid of the NOTEbut it doesn't seem to
> > > make much difference other than that.  i.e., it seems to process
> > > the same using CATkit vs CATkit_2.06.tar.gz!
> > > 
> > > Here is the main error that I am getting.  I just upgraded to the
> > > latest R version, fyi.
> > > 
> > > Everything was fine, a few minor warnings...now this. 
> > > Description and namespace are proper.  These pkgs should all be
> > > part of the R base, aren't they? Anyone know why I should get
> > > these errors?  Thanks!
> > > 
> > > * checking R code for possible problems ... NOTE
> > > Actogram: no visible global function definition for ‘par’
> > > Actogram: no visible global function definition for ‘barplot’
> > > Actogram: no visible global function definition for ‘box’
> > > Actogram: no visible global function definition for ‘text’
> > > Actogram: no visible global function definition for ‘mtext’
> > > Actogram: no visible binding for global variable ‘end’
> > > AutoCorr: no visible global function definition for ‘par’
> > > AutoCorr: no visible global function definition for ‘layout’
> > > AutoCorr: no visible global function definition for ‘acf’
> > > AutoCorr: no visible global function definition for ‘abline’
> > > AutoCorr: no visible global function definition for ‘title’
> > > AutoCorr: no visible global function definition for ‘mtext’
> > > AutoCorr: no visible global function definition for ‘var’
> > > AutoCorr: no visible binding for global variable ‘end’
> > > CATCosinor: no visible global function definition for ‘par’
> > > CATCosinor: no visible global function definition for ‘pdf’
> > > CATCosinor: no visible global function definition for ‘jpeg’
> > > CATCosinor: no visible global function definition for ‘png’
> > > CATCosinor: no visible global function definition for ‘tiff’
> > > . A zillion more for every function I have..
> > > periCosinor: no visible global function definition for ‘par’
> > > periCosinor: no visible global function definition for ‘fft’
> > > Undefined global functions or variables:
> > >   TukeyHSD abline acf aov as.raster axis barplot box boxplot ccf
> > >   coefficients dev.cur dev.off drop1 end fft gray heat.colors
> > > image
> > >   jpeg layout legend lines median model.tables mtext na.action
> > > na.omit
> > >   palette par pdf pf plot plot.new png points rainbow rasterImage
> > >   read.table str strwidth tail terrain.colors text tiff title ts
> > > var
> > >   write.table
> > > Consider adding
> > >   importFrom("grDevices", "as.raster", "dev.cur", "dev.off",
> > > "gray",
> > >              "heat.colors", "jpeg", "palette", "pdf", "png",
> > > "rainbow",
> > >              "terrain.colors", "tiff")
> > >   importFrom("graphics", "abline", "axis", "barplot", "box",
> > > "boxplot",
> > >              "image", "layout", "legend", "lines", "mtext",
> > > "par",
> > >              "plot", "plot.new", "points", "rasterImage",
> > > "strwidth",
> > >              "text", "title")
> > >   importFrom("stats", "TukeyHSD", "acf", "aov", "ccf",
> > > "coefficients",
> > >              "dr

Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Kasper Daniel Hansen

On Mon, Jan 30, 2017 at 12:04 PM, Cathy Lee Gierke  wrote:

> That is the obvious solution, but it doesn't seem correct:  I have pdf
> included in the description, and namespace files, yet it is being called
> out.  Additionally, aren't most of these pkgs in the packages included by
> default?
>

No, they are not. Read the documentation and see the error

And up until yesterday, I didn't have any of these problems.  I've been
> compiling and running this for several years.  But now I want to release to
> CRAN, so I've been fixing minor issuesand suddenly this mass of Notes.
>

I have no idea what you did previously to ignore this. But the
behaviour/error you see is always caused by an incomplete NAMESPACE; its
very common.

Perhaps follow the advice from all the other replies.

Best,
Kasper



> Thank you,
>
> Cathy Lee Gierke
>
>
> *“Darkness cannot drive out darkness: only light can do that. Hate cannot
> drive out hate: only love can do that.” *
> *“The arc of the moral universe is long, but it bends towards justice.”*
> *“Nothing in the world is more dangerous than sincere ignorance and
> conscientious stupidity.” *
> *“Never forget that everything Hitler did in Germany was legal.”   *
> *“Forgiveness is not an occasional act, it is a constant attitude.” *
> *“Injustice anywhere is a threat to justice everywhere.”  *
>
> ― Martin Luther King Jr.
>
> 
>
> On Mon, Jan 30, 2017 at 10:52 AM, Brian G. Peterson 
> wrote:
>
> > The error you reference below is pretty clear, I think.
> >
> > You need to add imports for all the functions you're using from other
> > packages.
> >
> > See: https://cran.r-project.org/doc/manuals/r-release/R-exts.
> > html#Specifying-imports-and-exports
> >
> > Regards,
> >
> > Brian
> >
> >
> > --
> > Brian G. Petersonhttp://braverock.com/brian/
> > Ph: 773-459-4973 <(773)%20459-4973>
> > IM: bgpbraverock
> >
> >
> > On Mon, 2017-01-30 at 10:39 -0600, Cathy Lee Gierke wrote:
> >
> > Yes, that seemed to get rid of the NOTEbut it doesn't seem to make
> > much difference other than that.  i.e., it seems to process the same
> using
> > CATkit vs CATkit_2.06.tar.gz!
> >
> > Here is the main error that I am getting.  I just upgraded to the latest
> R
> > version, fyi.
> >
> > Everything was fine, a few minor warnings...now this.  Description and
> > namespace are proper.  These pkgs should all be part of the R base,
> aren't
> > they? Anyone know why I should get these errors?  Thanks!
> >
> > * checking R code for possible problems ... NOTE
> >
> > Actogram: no visible global function definition for ‘par’
> >
> > Actogram: no visible global function definition for ‘barplot’
> >
> > Actogram: no visible global function definition for ‘box’
> >
> > Actogram: no visible global function definition for ‘text’
> >
> > Actogram: no visible global function definition for ‘mtext’
> >
> > Actogram: no visible binding for global variable ‘end’
> >
> > AutoCorr: no visible global function definition for ‘par’
> >
> > AutoCorr: no visible global function definition for ‘layout’
> >
> > AutoCorr: no visible global function definition for ‘acf’
> >
> > AutoCorr: no visible global function definition for ‘abline’
> >
> > AutoCorr: no visible global function definition for ‘title’
> >
> > AutoCorr: no visible global function definition for ‘mtext’
> >
> > AutoCorr: no visible global function definition for ‘var’
> >
> > AutoCorr: no visible binding for global variable ‘end’
> >
> > CATCosinor: no visible global function definition for ‘par’
> >
> > CATCosinor: no visible global function definition for ‘pdf’
> >
> > CATCosinor: no visible global function definition for ‘jpeg’
> >
> > CATCosinor: no visible global function definition for ‘png’
> >
> > CATCosinor: no visible global function definition for ‘tiff’
> >
> > . A zillion more for every function I have..
> >
> > periCosinor: no visible global function definition for ‘par’
> >
> > periCosinor: no visible global function definition for ‘fft’
> >
> > Undefined global functions or variables:
> >
> >   TukeyHSD abline acf aov as.raster axis barplot box boxplot ccf
> >
> >   coefficients dev.cur dev.off drop1 end fft gray heat.colors image
> >
> >   jpeg layout legend lines median model.tables mtext na.action na.omit
> >
> >   palette par pdf pf plot plot.new png points rainbow rasterImage
> >
> >   read.table str strwidth tail terrain.colors text tiff title ts var
> >
> >   write.table
> >
> > Consider adding
> >
> >   importFrom("grDevices", "as.raster", "dev.cur", "dev.off", "gray",
> >
> >  "heat.colors", "jpeg", "palette", "pdf", "png", "rainbow",
> >
> >  "terrain.colors", "tiff")
> >
> >   importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
> >
> >  "image", "layout", "legend", "lines", "mtext", "par",
> >
> >  "plot", "plot.new", "points", "rasterImage", "strwidth",
> >
> >  "text"

Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Kevin Ushey

Most importantly, this _is_ a recent-ish change in R CMD check. Previously,
R CMD check did not warn about missing imports from 'base' R packages (that
is, R packages distributed with R, having priority 'base'); now it
correctly does. While packages with priority 'base' are loaded by default
in most R installations, it's possible for the user to customize that
behavior, and so packages that don't import the functions they use from
these packages will break if they are detached (or their order on the
search path is changed).

The correct thing to do is indeed import any functions from any R packages
you use, base or otherwise. The simplest fix, if you don't want to
selectively import such a large range of functions, is to simply add e.g.

import(utils)
import(stats)
... etc ...

to your NAMESPACE file.

Best,
Kevin

On Mon, Jan 30, 2017 at 9:21 AM, Brian G. Peterson 
wrote:

> See the link in my email below.  It says:
> "Packages implicitly import the base namespace. Variables exported from
> other packages with namespaces need to be imported explicitly using the
> directives import and importFrom."
>
> Regards,
>
> Brian
>
> On Mon, 2017-01-30 at 11:04 -0600, Cathy Lee Gierke wrote:
> > That is the obvious solution, but it doesn't seem correct:  I have
> > pdf included in the description, and namespace files, yet it is being
> > called out.  Additionally, aren't most of these pkgs in the packages
> > included by default?
> >
> > And up until yesterday, I didn't have any of these problems.  I've
> > been compiling and running this for several years.  But now I want to
> > release to CRAN, so I've been fixing minor issuesand suddenly
> > this mass of Notes.
> >
> > Thank you,
> >
> > Cathy Lee Gierke
> >
> > “Darkness cannot drive out darkness: only light can do that. Hate
> > cannot drive out hate: only love can do that.”
> >
> > “The arc of the moral universe is long, but it bends towards
> > justice.”
> > “Nothing in the world is more dangerous than sincere ignorance and
> > conscientious stupidity.”
> > “Never forget that everything Hitler did in Germany was legal.”
> > “Forgiveness is not an occasional act, it is a constant attitude.”
> > “Injustice anywhere is a threat to justice everywhere.”
> >
> > ― Martin Luther King Jr.
> >
> >
> > On Mon, Jan 30, 2017 at 10:52 AM, Brian G. Peterson  > com> wrote:
> > > The error you reference below is pretty clear, I think.
> > >
> > > You need to add imports for all the functions you're using from
> > > other packages.
> > >
> > > See: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#S
> > > pecifying-imports-and-exports
> > >
> > > Regards,
> > >
> > > Brian
> > >
> > >
> > > --
> > > Brian G. Peterson
> > > http://braverock.com/brian/
> > > Ph: 773-459-4973
> > > IM: bgpbraverock
> > >
> > > On Mon, 2017-01-30 at 10:39 -0600, Cathy Lee Gierke wrote:
> > > > Yes, that seemed to get rid of the NOTEbut it doesn't seem to
> > > > make much difference other than that.  i.e., it seems to process
> > > > the same using CATkit vs CATkit_2.06.tar.gz!
> > > >
> > > > Here is the main error that I am getting.  I just upgraded to the
> > > > latest R version, fyi.
> > > >
> > > > Everything was fine, a few minor warnings...now this.
> > > > Description and namespace are proper.  These pkgs should all be
> > > > part of the R base, aren't they? Anyone know why I should get
> > > > these errors?  Thanks!
> > > >
> > > > * checking R code for possible problems ... NOTE
> > > > Actogram: no visible global function definition for ‘par’
> > > > Actogram: no visible global function definition for ‘barplot’
> > > > Actogram: no visible global function definition for ‘box’
> > > > Actogram: no visible global function definition for ‘text’
> > > > Actogram: no visible global function definition for ‘mtext’
> > > > Actogram: no visible binding for global variable ‘end’
> > > > AutoCorr: no visible global function definition for ‘par’
> > > > AutoCorr: no visible global function definition for ‘layout’
> > > > AutoCorr: no visible global function definition for ‘acf’
> > > > AutoCorr: no visible global function definition for ‘abline’
> > > > AutoCorr: no visible global function definition for ‘title’
> > > > AutoCorr: no visible global function definition for ‘mtext’
> > > > AutoCorr: no visible global function definition for ‘var’
> > > > AutoCorr: no visible binding for global variable ‘end’
> > > > CATCosinor: no visible global function definition for ‘par’
> > > > CATCosinor: no visible global function definition for ‘pdf’
> > > > CATCosinor: no visible global function definition for ‘jpeg’
> > > > CATCosinor: no visible global function definition for ‘png’
> > > > CATCosinor: no visible global function definition for ‘tiff’
> > > > . A zillion more for every function I have..
> > > > periCosinor: no visible global function definition for ‘par’
> > > > periCosinor: no visible global function definition for ‘fft’
> > > > Undefined globa

Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Duncan Murdoch


On 30/01/2017 12:04 PM, Cathy Lee Gierke wrote:

That is the obvious solution, but it doesn't seem correct:  I have pdf
included in the description, and namespace files, yet it is being called
out.  Additionally, aren't most of these pkgs in the packages included by
default?

And up until yesterday, I didn't have any of these problems.  I've been
compiling and running this for several years.  But now I want to release to
CRAN, so I've been fixing minor issuesand suddenly this mass of Notes.


For several years R would allow functions from base packages to be 
assumed to be on the search list, but it no longer does so (and hasn't 
since R 3.3.0).  This is a good thing:  if your user says library(foo), 
and the foo package happens to export a pdf() function, your package may 
end up using that one, even though you really mean grDevices::pdf().  If 
you explicitly import pdf() from grDevices, that won't happen.


Duncan Murdoch



Thank you,

Cathy Lee Gierke


*“Darkness cannot drive out darkness: only light can do that. Hate cannot
drive out hate: only love can do that.” *
*“The arc of the moral universe is long, but it bends towards justice.”*
*“Nothing in the world is more dangerous than sincere ignorance and
conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.”   *
*“Forgiveness is not an occasional act, it is a constant attitude.” *
*“Injustice anywhere is a threat to justice everywhere.”  *

― Martin Luther King Jr.



On Mon, Jan 30, 2017 at 10:52 AM, Brian G. Peterson 
wrote:


The error you reference below is pretty clear, I think.

You need to add imports for all the functions you're using from other
packages.

See: https://cran.r-project.org/doc/manuals/r-release/R-exts.
html#Specifying-imports-and-exports

Regards,

Brian


--
Brian G. Petersonhttp://braverock.com/brian/
Ph: 773-459-4973 <(773)%20459-4973>
IM: bgpbraverock


On Mon, 2017-01-30 at 10:39 -0600, Cathy Lee Gierke wrote:

Yes, that seemed to get rid of the NOTEbut it doesn't seem to make
much difference other than that.  i.e., it seems to process the same using
CATkit vs CATkit_2.06.tar.gz!

Here is the main error that I am getting.  I just upgraded to the latest R
version, fyi.

Everything was fine, a few minor warnings...now this.  Description and
namespace are proper.  These pkgs should all be part of the R base, aren't
they? Anyone know why I should get these errors?  Thanks!

* checking R code for possible problems ... NOTE

Actogram: no visible global function definition for ‘par’

Actogram: no visible global function definition for ‘barplot’

Actogram: no visible global function definition for ‘box’

Actogram: no visible global function definition for ‘text’

Actogram: no visible global function definition for ‘mtext’

Actogram: no visible binding for global variable ‘end’

AutoCorr: no visible global function definition for ‘par’

AutoCorr: no visible global function definition for ‘layout’

AutoCorr: no visible global function definition for ‘acf’

AutoCorr: no visible global function definition for ‘abline’

AutoCorr: no visible global function definition for ‘title’

AutoCorr: no visible global function definition for ‘mtext’

AutoCorr: no visible global function definition for ‘var’

AutoCorr: no visible binding for global variable ‘end’

CATCosinor: no visible global function definition for ‘par’

CATCosinor: no visible global function definition for ‘pdf’

CATCosinor: no visible global function definition for ‘jpeg’

CATCosinor: no visible global function definition for ‘png’

CATCosinor: no visible global function definition for ‘tiff’

. A zillion more for every function I have..

periCosinor: no visible global function definition for ‘par’

periCosinor: no visible global function definition for ‘fft’

Undefined global functions or variables:

  TukeyHSD abline acf aov as.raster axis barplot box boxplot ccf

  coefficients dev.cur dev.off drop1 end fft gray heat.colors image

  jpeg layout legend lines median model.tables mtext na.action na.omit

  palette par pdf pf plot plot.new png points rainbow rasterImage

  read.table str strwidth tail terrain.colors text tiff title ts var

  write.table

Consider adding

  importFrom("grDevices", "as.raster", "dev.cur", "dev.off", "gray",

 "heat.colors", "jpeg", "palette", "pdf", "png", "rainbow",

 "terrain.colors", "tiff")

  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",

 "image", "layout", "legend", "lines", "mtext", "par",

 "plot", "plot.new", "points", "rasterImage", "strwidth",

 "text", "title")

  importFrom("stats", "TukeyHSD", "acf", "aov", "ccf", "coefficients",

 "drop1", "end", "fft", "median", "model.tables",

 "na.action", "na.omit", "pf", "ts", "var")

  importFrom("utils", "read.table", "str", "tail", "write.table")

to your NA

Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Cathy Lee Gierke

Thank you. That will be why I didn't see them previously. Helps my sanity ;-)

Sent from my iPhone

> On Jan 30, 2017, at 8:58 PM, Kevin Ushey  wrote:
> 
> Most importantly, this _is_ a recent-ish change in R CMD check. Previously, R 
> CMD check did not warn about missing imports from 'base' R packages (that is, 
> R packages distributed with R, having priority 'base'); now it correctly 
> does. While packages with priority 'base' are loaded by default in most R 
> installations, it's possible for the user to customize that behavior, and so 
> packages that don't import the functions they use from these packages will 
> break if they are detached (or their order on the search path is changed).
> 
> The correct thing to do is indeed import any functions from any R packages 
> you use, base or otherwise. The simplest fix, if you don't want to 
> selectively import such a large range of functions, is to simply add e.g.
> 
> import(utils)
> import(stats)
> ... etc ...
> 
> to your NAMESPACE file.
> 
> Best,
> Kevin
> 
>> On Mon, Jan 30, 2017 at 9:21 AM, Brian G. Peterson  
>> wrote:
>> See the link in my email below.  It says:
>> "Packages implicitly import the base namespace. Variables exported from
>> other packages with namespaces need to be imported explicitly using the
>> directives import and importFrom."
>> 
>> Regards,
>> 
>> Brian
>> 
>> On Mon, 2017-01-30 at 11:04 -0600, Cathy Lee Gierke wrote:
>> > That is the obvious solution, but it doesn't seem correct:  I have
>> > pdf included in the description, and namespace files, yet it is being
>> > called out.  Additionally, aren't most of these pkgs in the packages
>> > included by default?
>> >
>> > And up until yesterday, I didn't have any of these problems.  I've
>> > been compiling and running this for several years.  But now I want to
>> > release to CRAN, so I've been fixing minor issuesand suddenly
>> > this mass of Notes.  
>> >
>> > Thank you,
>> >
>> > Cathy Lee Gierke
>> >   
>> > “Darkness cannot drive out darkness: only light can do that. Hate
>> > cannot drive out hate: only love can do that.” 
>> >
>> > “The arc of the moral universe is long, but it bends towards
>> > justice.”
>> > “Nothing in the world is more dangerous than sincere ignorance and
>> > conscientious stupidity.” 
>> > “Never forget that everything Hitler did in Germany was legal.”   
>> > “Forgiveness is not an occasional act, it is a constant attitude.” 
>> > “Injustice anywhere is a threat to justice everywhere.”  
>> >
>> > ― Martin Luther King Jr.
>> >
>> >
>> > On Mon, Jan 30, 2017 at 10:52 AM, Brian G. Peterson > > com> wrote:
>> > > The error you reference below is pretty clear, I think.
>> > >
>> > > You need to add imports for all the functions you're using from
>> > > other packages. 
>> > >
>> > > See: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#S
>> > > pecifying-imports-and-exports
>> > >
>> > > Regards,
>> > >
>> > > Brian
>> > >
>> > >
>> > > -- 
>> > > Brian G. Peterson
>> > > http://braverock.com/brian/
>> > > Ph: 773-459-4973
>> > > IM: bgpbraverock
>> > >
>> > > On Mon, 2017-01-30 at 10:39 -0600, Cathy Lee Gierke wrote:
>> > > > Yes, that seemed to get rid of the NOTEbut it doesn't seem to
>> > > > make much difference other than that.  i.e., it seems to process
>> > > > the same using CATkit vs CATkit_2.06.tar.gz!
>> > > >
>> > > > Here is the main error that I am getting.  I just upgraded to the
>> > > > latest R version, fyi.
>> > > >
>> > > > Everything was fine, a few minor warnings...now this. 
>> > > > Description and namespace are proper.  These pkgs should all be
>> > > > part of the R base, aren't they? Anyone know why I should get
>> > > > these errors?  Thanks!
>> > > >
>> > > > * checking R code for possible problems ... NOTE
>> > > > Actogram: no visible global function definition for ‘par’
>> > > > Actogram: no visible global function definition for ‘barplot’
>> > > > Actogram: no visible global function definition for ‘box’
>> > > > Actogram: no visible global function definition for ‘text’
>> > > > Actogram: no visible global function definition for ‘mtext’
>> > > > Actogram: no visible binding for global variable ‘end’
>> > > > AutoCorr: no visible global function definition for ‘par’
>> > > > AutoCorr: no visible global function definition for ‘layout’
>> > > > AutoCorr: no visible global function definition for ‘acf’
>> > > > AutoCorr: no visible global function definition for ‘abline’
>> > > > AutoCorr: no visible global function definition for ‘title’
>> > > > AutoCorr: no visible global function definition for ‘mtext’
>> > > > AutoCorr: no visible global function definition for ‘var’
>> > > > AutoCorr: no visible binding for global variable ‘end’
>> > > > CATCosinor: no visible global function definition for ‘par’
>> > > > CATCosinor: no visible global function definition for ‘pdf’
>> > > > CATCosinor: no visible global function definition for ‘jpeg’
>> > > > CATCosinor: no visible global f

Re: [R-pkg-devel] Encoding problem

2017-01-30 Thread David Scott

Thanks Thierry, that indeed was the problem.

I am not sure who to advise to correct the documentation in Writing R 
Extensions though because I was following the instructions there:

"... the encoding may be declared using a comment like

%!\VignetteEncoding{UTF-8}

If the encoding is UTF-8, this can also be declared using the declaration

%!\SweaveUTF8"


The same instruction appears in all the versions of WRE that I checked, 
HTML and PDF, R-release, R-patched and R-devel.

I have copied in Duncan and Martin in the expectation they might ensure 
a correction.

David

On 31/01/2017 4:10 a.m., Thierry Onkelinx wrote:
> Dear David,
>
> Have you tried removing the exclamation mark in 
> %!\VignetteEncoding{UTF-8}? I think it should be %\VignetteEncoding{UTF-8}
>
> Best regards,
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature 
> and Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
>
> To call in the statistician after the experiment is done may be no 
> more than asking him to perform a post-mortem examination: he may be 
> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does 
> not ensure that a reasonable answer can be extracted from a given body 
> of data. ~ John Tukey
>
> 2017-01-29 13:40 GMT+01:00 David Scott  >:
>
> I am trying to add a vignette to xtable showing how to incorporate
> some Chinese characters following an enquiry from a user.
>
> I can create the vignette satisfactorily just processing the knitr
> file normally, with the resulting pdf displaying Chinese
> characters in the R code and also as headings when I produce a
> table. However when I try to build the package with the vignette
> included, I get:
>
> * creating vignettes ...Warning: running command
> '"C:/PROGRA~1/R/R-33~1.2/bin/x64/Rscript" --vanilla
>  ERROR
> Error: Vignette 'ChineseCharacters.Rnw' is non-ASCII but has no
> declared encoding
> Execution halted
> make: *** [build] Error 1
>
> I updated R to 3.3.2 and Rtools to 33 before running the build.
>
> The vignette starts as follows:
>
> %\VignetteIndexEntry{xtable Chinese Characters}
> %\VignetteDepends{xtable}
> %\VignetteKeywords{LaTeX, HTML, table}
> %\VignettePackage{xtable}
> % !Rnw weave = knitr
> % \VignetteEngine{knitr::knitr}
> %!\VignetteEncoding{UTF-8}
> 
> %**
> \documentclass{ctexart}
> \usepackage{longtable}
> \usepackage{booktabs}
> \usepackage{array}
> \usepackage{hyperref}
> \usepackage{inputenx}
>
> The section of the file which is not ASCII is:
>
> <>=
> ### Prepare data
> library(knitr)
> library(xtable)
>
> tbl <- data.frame(positivePairs = 0, negativePairs = 0,
>   avePositiveSpread = NA,
>   aveNegativeSpread = NA,
>   PnL = 435, sumPnL = 144358.7)
> names(tbl) <- c("ÕýÏò¿ª²Ö", "¸ºÏò¿ª²Ö", "ÕýÏò¿ª²ÖÆ½¾ù¼Û²î",
> "¸ºÏò¿ª²ÖÆ½¼Û¼Û²î", "µ±ÈÕËðÒæ", "ÀÛ¼ÆËðÒæ")
> @
>
> I am a bit of a novice at encodings, and know nothing about
> Chinese characters so any advice is welcome.
>
> David Scott
>
>
>
> -- 
> _
> David Scott Department of Statistics
> The University of Auckland, PB 92019
> Auckland 1142,NEW ZEALAND
> Phone: +64 9 923 5055 , or +64 9 373
> 7599 ext 85055 
> Email: d.sc...@auckland.ac.nz ,
> Fax: +64 9 373 7018 
>
> Volunteer Arena Manager:
> Orienteering Sprint Final at University of Auckland
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>
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-- 
_
David Scott Department of Statistics
The University of Auckland, PB 92019
Auckland 1142,NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email:  d.sc...@auckland.ac.nz,  Fax: +64 9 373 7018

Volunteer Arena Manager:
Orienteering Sprint Final at University of Auckland
World Masters Games 2017



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Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-30 Thread Dirk Eddelbuettel


On 30 January 2017 at 09:58, Kevin Ushey wrote:
| The correct thing to do is indeed import any functions from any R packages
| you use, base or otherwise. The simplest fix, if you don't want to
| selectively import such a large range of functions, is to simply add e.g.
| 
| import(utils)
| import(stats)
| ... etc ...
| 
| to your NAMESPACE file.

Or do what R CMD check suggested and import the ones used, rather than all.

Which is what I had quoted earlier:

| Consider adding
| 
|   importFrom("grDevices", "as.raster", "dev.cur", "dev.off", "gray",
|  "heat.colors", "jpeg", "palette", "pdf", "png", "rainbow",
|  "terrain.colors", "tiff")
|   importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
|  "image", "layout", "legend", "lines", "mtext", "par",
|  "plot", "plot.new", "points", "rasterImage", "strwidth",
|  "text", "title")
|   importFrom("stats", "TukeyHSD", "acf", "aov", "ccf", "coefficients",
|  "drop1", "end", "fft", "median", "model.tables",
|  "na.action", "na.omit", "pf", "ts", "var")
|   importFrom("utils", "read.table", "str", "tail", "write.table")
| 
| to your NAMESPACE file.

I find this preferable and quite appreciate that R CMD check provides it.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] Encoding problem

[R-pkg-devel] Description Meta Information Note

Re: [R-pkg-devel] Description Meta Information Note

[R-pkg-devel] no visible global function definition for ‘par’

Re: [R-pkg-devel] no visible global function definition for ‘par’

Re: [R-pkg-devel] no visible global function definition for ‘par’

Re: [R-pkg-devel] no visible global function definition for ‘par’

Re: [R-pkg-devel] no visible global function definition for ‘par’

Re: [R-pkg-devel] no visible global function definition for ‘par’

Re: [R-pkg-devel] no visible global function definition for ‘par’

Re: [R-pkg-devel] no visible global function definition for ‘par’

Re: [R-pkg-devel] no visible global function definition for ‘par’

Re: [R-pkg-devel] Encoding problem

Re: [R-pkg-devel] no visible global function definition for ‘par’

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