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))
}
roxygen2 v6.0.0
4 messages · Marc Girondot, Yihui Xie, Bert Gunter
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.
Marc: You miss Yihui's point I think: roxygen2 will generate the (Namespace and other) files for you. See its documentation for how (the directives to put in your comments). -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Mon, Feb 6, 2017 at 9:38 AM, Marc Girondot via R-help
<r-help at r-project.org> wrote:
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.
______________________________________________ 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.