[R-pkg-devel] checking S3 generic/method consistency ... NOTE
Hi, I would like to know how you are calming down the R check. I've an issue
with the `head` method. I'm incorporating a head for data base, but nothing
that I add in the function file seems to be able to silence the R check. Below
is what I have:
checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
head.SQLiteConnection
#' Return the first n elements of a SQLiteConnection object
#'
#' If a database connection is selected, returns a dataframe of table names.
#' If a table name is also supplied, the first n rows from the table are
returned.
#'
#' @param x A database connection object or a table name.
#' @param \dots Additional arguments
#' @param table character specifying a table
#' @param n integer: Number of rows to output
#' @param temp logical should the function list the temp tables
#'
#' @export head.SQLiteConnection
#' @method head SQLiteConnection
#' @importFrom RSQLite dbGetQuery
#' @importFrom utils head
#' @rdname head
head.SQLiteConnection <- function(x, table = NULL, n = 10L, temp = FALSE, ...){
if(is.null(table)){
if(temp){
RSQLite::dbGetQuery(x, "SELECT type, name, tbl_name FROM
sqlite_temp_master;", ...)
} else RSQLite::dbGetQuery(x, "SELECT type, name, tbl_name FROM
sqlite_master;", ...)
} else {
RSQLite::dbGetQuery(x, sprintf("SELECT * FROM %s LIMIT %d;", table, n), ...)
}
}
Daniel
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Re: [R-pkg-devel] checking S3 generic/method consistency ... NOTE
That should work then, I confused myself how to properly document S3 methods
using Roxygen. Thanks for this.
Daniel
> Date: Thu, 23 Jul 2015 16:41:37 -0600
> Subject: Re: [R-pkg-devel] checking S3 generic/method consistency ... NOTE
> From: ucfa...@gmail.com
> To: dmarcel...@live.com
> CC: r-package-devel@r-project.org
>
> Hi Daniel
>
> You should only neee
>
> #' @export
>
> in your roxygen markup as roxygen (well recent versions anyway) are
> able to do the right thing and work out what needs to go into the
> NAMESPACE file. You don't need @method now, except in cases where there
> is ambiguity about the method/class, which shouldn;t be the case here.
>
> See: http://r-pkgs.had.co.nz/namespace.html#exports
>
> HTH
>
> G
>
> On 23 July 2015 at 15:21, Daniel Marcelino
> mailto:dmarcel...@live.com>> wrote:
> Hi, I would like to know how you are calming down the R check. I've an
> issue with the `head` method. I'm incorporating a head for data base,
> but nothing that I add in the function file seems to be able to
> silence the R check. Below is what I have:
>
> checking S3 generic/method consistency ... NOTE
> Found the following apparent S3 methods exported but not registered:
> head.SQLiteConnection
>
>
> #' Return the first n elements of a SQLiteConnection object
> #'
> #' If a database connection is selected, returns a dataframe of table names.
> #' If a table name is also supplied, the first n rows from the table
> are returned.
> #'
> #' @param x A database connection object or a table name.
> #' @param \dots Additional arguments
> #' @param table character specifying a table
> #' @param n integer: Number of rows to output
> #' @param temp logical should the function list the temp tables
> #'
> #' @export head.SQLiteConnection
> #' @method head SQLiteConnection
> #' @importFrom RSQLite dbGetQuery
> #' @importFrom utils head
> #' @rdname head
> head.SQLiteConnection <- function(x, table = NULL, n = 10L, temp =
> FALSE, ...){
> if(is.null(table)){
> if(temp){
> RSQLite::dbGetQuery(x, "SELECT type, name, tbl_name FROM
> sqlite_temp_master;", ...)
> } else RSQLite::dbGetQuery(x, "SELECT type, name, tbl_name FROM
> sqlite_master;", ...)
>
> } else {
> RSQLite::dbGetQuery(x, sprintf("SELECT * FROM %s LIMIT %d;", table,
> n), ...)
> }
> }
>
>
>
> Daniel
> __
> R-package-devel@r-project.org<mailto:R-package-devel@r-project.org>
> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>
> --
> Gavin Simpson, PhD
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[R-pkg-devel] Build fails on Mavericks
Hi, I'm having this error when building C functions from a package: clang: error: no such file or directory: '/usr/local/lib/libreadline.a' Apparently, it's a path issue caused by xcode/gfortran, but I couldn't figure out how to solve it. "which gcc" points to "/usr/bin/gcc" Does someone have any idea on how on this? Thanks, Daniel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Build fails on Mavericks
Yes, I do use homebrew for installing almost everything. I ended up solving the issue with $ brew link readline --forc e Daniel On Thu, Nov 19, 2015 at 2:37 PM, Rainer M Krug wrote: > Duncan Murdoch writes: > >> On 19/11/2015 9:05 AM, Daniel Marcelino wrote: >>> Hi, I'm having this error when building C functions from a package: >>> >>> clang: error: no such file or directory: '/usr/local/lib/libreadline.a' >>> >>> Apparently, it's a path issue caused by xcode/gfortran, but I couldn't >>> figure out how to solve it. >>> "which gcc" points to "/usr/bin/gcc" >>> Does someone have any idea on how on this? >> >> You didn't say what system you're on, but the message is coming from >> clang, not gcc, so it looks like OSX, and "which gcc" is irrelevant. >> If so, you probably want to ask on the R-sig-mac group. If not, give >> more details. > > Also: did you use the official R installer or installed it using homebrew? > > The path looks very much like homebrew. If yes, try installing readline > From homebrew. > > Cheers, > > Rainer > >> >> Duncan Murdoch >> >> __ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > -- > Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, > UCT), Dipl. Phys. (Germany) > > Centre of Excellence for Invasion Biology > Stellenbosch University > South Africa > > Tel : +33 - (0)9 53 10 27 44 > Cell: +33 - (0)6 85 62 59 98 > Fax : +33 - (0)9 58 10 27 44 > > Fax (D):+49 - (0)3 21 21 25 22 44 > > email: rai...@krugs.de > > Skype: RMkrug > > PGP: 0x0F52F982 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Previous messageNext messageBack to messages The following files should probably not be installed
Hi, I used to have some pictures in ‘inst/doc’ for decoration of the README.MD text, most for the Github repository. I was able to build the package without any NOTE on this, but since I updated to R 3.2.3 and created a vignette folder I'm receiving the following message. Am I missing something from the last R release? * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... NOTE The following files should probably not be installed: ‘Rlogo.png’, ‘SciencesPo_logo.png’, ‘butterfly.png’ Daniel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Previous messageNext messageBack to messages The following files should probably not be installed
Thanks for this Dirk. Daniel Sent from my iPhone > On Jan 20, 2016, at 3:55 PM, Dirk Eddelbuettel wrote: > > > On 20 January 2016 at 14:10, Daniel Marcelino wrote: > | Hi, I used to have some pictures in ‘inst/doc’ for decoration of the > README.MD text, most for the Github repository. > | I was able to build the package without any NOTE on this, but since I > updated to R 3.2.3 and created a vignette folder I'm receiving the following > message. Am I missing something from the last R release? > | > | * checking sizes of PDF files under ‘inst/doc’ ... OK > | * checking installed files from ‘inst/doc’ ... NOTE > | The following files should probably not be installed: > | ‘Rlogo.png’, ‘SciencesPo_logo.png’, ‘butterfly.png’ > > Just list them in .Rbuildignore --- they will still be in the GH repo but not > be part of the resulting .tar.gz. Hemce R CMD check will be no longer > complain. > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Build fails at Travis CI
Hi, I wonder if anyone has experienced this issue with Travis CI. The package I'm committing is just fine, it passes all the CRAN devel checks, but fails at Travis building checks. I realized that if I git commit without the "Collate" section, it passes. However, I've no clue why. I will appreciate any help on this. Daniel "Nam et ipsa scientia potestas est" __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Build fails at Travis CI
Sure, it's indeed open source. https://github.com/danielmarcelino/SciencesPo ThanksDaniel ---"Nam et ipsa scientia potestas est" Date: Sun, 5 Jun 2016 16:32:27 +0100 Subject: Re: [R-pkg-devel] Build fails at Travis CI From: jeblund...@doctors.org.uk To: dmarcel...@live.com CC: r-package-devel@r-project.org If it's open source, would you mind posting the link to github/travis? On 4 Jun 2016 21:13, "Daniel Marcelino" wrote: Hi, I wonder if anyone has experienced this issue with Travis CI. The package I'm committing is just fine, it passes all the CRAN devel checks, but fails at Travis building checks. I realized that if I git commit without the "Collate" section, it passes. However, I've no clue why. I will appreciate any help on this. Daniel "Nam et ipsa scientia potestas est" __ 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
[R-pkg-devel] Problem with \Sexpr{} expressions
Hi, I'm receiving the following note from CRAN check.
Package has help file(s) containing install/render-stage \Sexpr{}
expressions but no prebuilt PDF manual.
I went through all files having the expression, but couldn't find
where the offending part is. Is there any way I could try to pin-down
where this issue occurs?
Daniel
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Re: [R-pkg-devel] Package update submission to CRAN fails on pretest
Daniel Marcelino "Small steps toward a much better world" From: R-package-devel on behalf of Wolfgang Lenhard Sent: December 7, 2018 2:15 PM To: Georgi Boshnakov; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] Package update submission to CRAN fails on pretest Many thanks for the remark. It seems, it has something to do with submitting via the devtools (maybe I did something wrong with tagging the prior release). Submitting it manually at least does not result in pretest rejection. I guess there is something out of sync which resulted in rechecking and old version. Am 07.12.2018 um 13:46 schrieb Georgi Boshnakov: > The link you gave, https://cran.r-project.org/web/checks/check_results_cNORM.html, > is to the check results for the package currently on CRAN and it is indeed v. 1.0.1 > (it is linked from https://CRAN.R-project.org/package=cNORM). > > Was this really the link you got from CRAN's pretest? Sometimes they ask if care has been taken about NOTEs/WARNINGs for the current CRAN version, since some tests are not done during submission, but this doesn't seem the case here. > > Georgi Boshnakov > > > -Original Message- > From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf Of Wolfgang Lenhard > Sent: 07 December 2018 07:55 > To: r-package-devel@r-project.org > Subject: [R-pkg-devel] Package update submission to CRAN fails on pretest > > Dear list, > I am getting problems when trying to submit an update of the package > cNORM to CRAN. I am developing the package with RStudio and devtools and > I am using Travis for automatic testing. The package is tested locally > on Win10 and Mac OS X and on Travis with Ubuntu and Mac both for > development and release versions of R. All local tests and tests on > Travis work flawlessly - no errors, warning or notes. When submitting to > CRAN, a note and an error show up on some of the Linux OS (Fedora & > Solaris) and Mac OS X, while others display an 'OK' (Win, Debian). The > results: https://cran.r-project.org/web/checks/check_results_cNORM.html > > - error: This seems to be related to the vignette with the following > message: >> * checking examples ... ERROR >> Running examples in ‘cNORM-Ex.R’ failed > I can however not identify the location of the error > > - Note: Check: data for non-ASCII characters > > The strange thing is: I checked all data files multiple times. They > mainly consist of data.frames with numerics and all colnames are ASCII. > I am not able to replicate the issue. The same is true for the error, > which does not show up on Travis and as well locally. And finally, the > results state, that the version of the package is 1.0.1, which had been > the first submission to CRAN a month ago. The current version of the > package is 1.1.1. Could this be the reason for the problem? > > Do you have an idea how to progress with the testing or how to locate > the errors? Any help is welcome. > > Best regards, > Wolfgang Lenhard > > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Prof. Dr. Wolfgang Lenhard Lehrstuhl Psychologie IV Raum 02.130 Wittelsbacherplatz 1 D-97070 Würzburg Tel.: 0931 3189791 FAX: 0931 3184891 URL: https://go.uniwue.de/lenhard Map: https://go.uni-wuerzburg.de/3b __ 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
