Hi,
I used roxygen2 v5.0.1 to document my package, and all was ok. I have
just updated to roxygen2 v6.0.0 and my script is broken and I can't find
why.
I have done a simple version of a package folder as a test with 3 files:
chr.R, essai-package.R and DESCRIPTION.
Previously, I did:
package.skeleton("essai",code_files=c('chr.R',"essai-package.R"))
roxygenize("essai")
system(paste0("R CMD build '", getwd(), "/essai'"))
install.packages(file.path(getwd(), "essai_1.0.tar.gz"), repos = NULL,
type="source")
And it worked well.
Now I get an error at the second line: roxygenize("essai")
> roxygenize("essai")
First time using roxygen2. Upgrading automatically...
Updating roxygen version in
/Users/marcgirondot/Documents/Espace_de_travail_R/Package_Essai/essai/DESCRIPTION
Warning: The existing 'NAMESPACE' file was not generated by roxygen2,
and will not be overwritten.
Warning: The existing 'chr.Rd' file was not generated by roxygen2, and
will not be overwritten.
Warning: The existing 'essai-package.Rd' file was not generated by
roxygen2, and will not be overwritten.
And of course it fails after.
Are you aware of this situation ? And do you have a solution ?
Thanks a lot
Marc
A file DESCRIPTION:
Package: essai
Type: Package
Title: Package Used For Try
Version: 1.0
Date: 2017-02-06
Author: Marc Girondot <marc.girondot at u-psud.fr>
Maintainer: Marc Girondot <marc.girondot at u-psud.fr>
Description: Trying package.
Depends: R (>= 2.14.2)
License: GPL-2
LazyData: yes
LazyLoad: yes
Encoding: UTF-8
RoxygenNote: 6.0.0
A file essai-package.R (essai=try in French):
#' Trying package
#'
#' \tabular{ll}{
#' Package: \tab essai\cr
#' Type: \tab Package\cr
#' Version: \tab 1.0 - build 1\cr
#' Date: \tab 2017-02-06\cr
#' License: \tab GPL (>= 2)\cr
#' LazyLoad: \tab yes\cr
#' }
#' @title The package essai
#' @author Marc Girondot \email{marc.girondot@@u-psud.fr}
#' @docType package
#' @name essai-package
NULL
A file chr.R:
#' chr returns the characters defined by the codes
#' @title Return the characters defined by the codes
#' @author Based on this blog:
http://datadebrief.blogspot.com/2011/03/ascii-code-table-in-r.html
#' @return A string with characters defined by the codes
#' @param n The vector with codes
#' @description Return a string with characters defined by the codes.
J'essaye avec un code utf-8: ?.
#' @examples
#' chr(65:75)
#' chr(unlist(tapply(144:175, 144:175, function(x) {c(208, x)})))
#' @encoding UTF-8
#' @export
chr <- function(n) {
rawToChar(as.raw(n))
}
If your package source is version controlled (meaning you are free to regret any time), I'd recommend you to delete the three files NAMESPACE, chr.Rd, and essai-package.Rd. Then try to roxygenize again. Basically the warnings you saw indicates that roxygen2 failed to find the line % Generated by roxygen2: do not edit by hand in your NAMESPACE and .Rd files, so it thinks these files were probably not previously generated by roxygen2. I think the cause is package.skeleton(), which generated the Rd files. Seriously, friends don't let friends use package.skeleton()... (it is 2017 now) Regards, Yihui -- Yihui Xie <xieyihui at gmail.com> Web: http://yihui.name On Mon, Feb 6, 2017 at 9:46 AM, Marc Girondot via R-help <r-help at r-project.org> wrote:> Hi, > > I used roxygen2 v5.0.1 to document my package, and all was ok. I have just > updated to roxygen2 v6.0.0 and my script is broken and I can't find why. > > I have done a simple version of a package folder as a test with 3 files: > chr.R, essai-package.R and DESCRIPTION. > > Previously, I did: > > package.skeleton("essai",code_files=c('chr.R',"essai-package.R")) > roxygenize("essai") > system(paste0("R CMD build '", getwd(), "/essai'")) > install.packages(file.path(getwd(), "essai_1.0.tar.gz"), repos = NULL, > type="source") > > And it worked well. > > Now I get an error at the second line: roxygenize("essai") > >> roxygenize("essai") > First time using roxygen2. Upgrading automatically... > Updating roxygen version in > /Users/marcgirondot/Documents/Espace_de_travail_R/Package_Essai/essai/DESCRIPTION > Warning: The existing 'NAMESPACE' file was not generated by roxygen2, and > will not be overwritten. > Warning: The existing 'chr.Rd' file was not generated by roxygen2, and will > not be overwritten. > Warning: The existing 'essai-package.Rd' file was not generated by roxygen2, > and will not be overwritten. > > And of course it fails after. > > Are you aware of this situation ? And do you have a solution ? > > Thanks a lot > > Marc > > > A file DESCRIPTION: > > Package: essai > Type: Package > Title: Package Used For Try > Version: 1.0 > Date: 2017-02-06 > Author: Marc Girondot <marc.girondot at u-psud.fr> > Maintainer: Marc Girondot <marc.girondot at u-psud.fr> > Description: Trying package. > Depends: R (>= 2.14.2) > License: GPL-2 > LazyData: yes > LazyLoad: yes > Encoding: UTF-8 > RoxygenNote: 6.0.0 > > A file essai-package.R (essai=try in French): > > #' Trying package > #' > #' \tabular{ll}{ > #' Package: \tab essai\cr > #' Type: \tab Package\cr > #' Version: \tab 1.0 - build 1\cr > #' Date: \tab 2017-02-06\cr > #' License: \tab GPL (>= 2)\cr > #' LazyLoad: \tab yes\cr > #' } > #' @title The package essai > #' @author Marc Girondot \email{marc.girondot@@u-psud.fr} > #' @docType package > #' @name essai-package > > NULL > > A file chr.R: > > #' chr returns the characters defined by the codes > #' @title Return the characters defined by the codes > #' @author Based on this blog: > http://datadebrief.blogspot.com/2011/03/ascii-code-table-in-r.html > #' @return A string with characters defined by the codes > #' @param n The vector with codes > #' @description Return a string with characters defined by the codes. > J'essaye avec un code utf-8: ?. > #' @examples > #' chr(65:75) > #' chr(unlist(tapply(144:175, 144:175, function(x) {c(208, x)}))) > #' @encoding UTF-8 > #' @export > > > chr <- function(n) { > rawToChar(as.raw(n)) > } > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Le 06/02/2017 ? 17:14, Yihui Xie a ?crit :> If your package source is version controlled (meaning you are free to > regret any time), I'd recommend you to delete the three files > NAMESPACE, chr.Rd, and essai-package.Rd. Then try to roxygenize again. > Basically the warnings you saw indicates that roxygen2 failed to find > the line > > % Generated by roxygen2: do not edit by hand > > in your NAMESPACE and .Rd files, so it thinks these files were > probably not previously generated by roxygen2. I think the cause is > package.skeleton(), which generated the Rd files. Seriously, friends > don't let friends use package.skeleton()... (it is 2017 now)Thanks ! It works perfectly after removing the /man/ folder and the NAMESPACE file. I didn't know that package.skeleton() was out-of-age ! That's true that it is easy to generate the skeleton manually. Marc> > Regards, > Yihui > -- > Yihui Xie <xieyihui at gmail.com> > Web: http://yihui.name > > > On Mon, Feb 6, 2017 at 9:46 AM, Marc Girondot via R-help > <r-help at r-project.org> wrote: >> Hi, >> >> I used roxygen2 v5.0.1 to document my package, and all was ok. I have just >> updated to roxygen2 v6.0.0 and my script is broken and I can't find why. >> >> I have done a simple version of a package folder as a test with 3 files: >> chr.R, essai-package.R and DESCRIPTION. >> >> Previously, I did: >> >> package.skeleton("essai",code_files=c('chr.R',"essai-package.R")) >> roxygenize("essai") >> system(paste0("R CMD build '", getwd(), "/essai'")) >> install.packages(file.path(getwd(), "essai_1.0.tar.gz"), repos = NULL, >> type="source") >> >> And it worked well. >> >> Now I get an error at the second line: roxygenize("essai") >> >>> roxygenize("essai") >> First time using roxygen2. Upgrading automatically... >> Updating roxygen version in >> /Users/marcgirondot/Documents/Espace_de_travail_R/Package_Essai/essai/DESCRIPTION >> Warning: The existing 'NAMESPACE' file was not generated by roxygen2, and >> will not be overwritten. >> Warning: The existing 'chr.Rd' file was not generated by roxygen2, and will >> not be overwritten. >> Warning: The existing 'essai-package.Rd' file was not generated by roxygen2, >> and will not be overwritten. >> >> And of course it fails after. >> >> Are you aware of this situation ? And do you have a solution ? >> >> Thanks a lot >> >> Marc >> >> >> A file DESCRIPTION: >> >> Package: essai >> Type: Package >> Title: Package Used For Try >> Version: 1.0 >> Date: 2017-02-06 >> Author: Marc Girondot <marc.girondot at u-psud.fr> >> Maintainer: Marc Girondot <marc.girondot at u-psud.fr> >> Description: Trying package. >> Depends: R (>= 2.14.2) >> License: GPL-2 >> LazyData: yes >> LazyLoad: yes >> Encoding: UTF-8 >> RoxygenNote: 6.0.0 >> >> A file essai-package.R (essai=try in French): >> >> #' Trying package >> #' >> #' \tabular{ll}{ >> #' Package: \tab essai\cr >> #' Type: \tab Package\cr >> #' Version: \tab 1.0 - build 1\cr >> #' Date: \tab 2017-02-06\cr >> #' License: \tab GPL (>= 2)\cr >> #' LazyLoad: \tab yes\cr >> #' } >> #' @title The package essai >> #' @author Marc Girondot \email{marc.girondot@@u-psud.fr} >> #' @docType package >> #' @name essai-package >> >> NULL >> >> A file chr.R: >> >> #' chr returns the characters defined by the codes >> #' @title Return the characters defined by the codes >> #' @author Based on this blog: >> http://datadebrief.blogspot.com/2011/03/ascii-code-table-in-r.html >> #' @return A string with characters defined by the codes >> #' @param n The vector with codes >> #' @description Return a string with characters defined by the codes. >> J'essaye avec un code utf-8: ?. >> #' @examples >> #' chr(65:75) >> #' chr(unlist(tapply(144:175, 144:175, function(x) {c(208, x)}))) >> #' @encoding UTF-8 >> #' @export >> >> >> chr <- function(n) { >> rawToChar(as.raw(n)) >> } >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code.