Also note that William's suggestion is documented at the bottom of the "Generic Functions and Methods" section of Writing R Extensions. https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Generic-functions-and-methods
"... as a package can take over a function in the base package and make it generic by something like foo <- function(object, ...) UseMethod("foo") foo.default <- function(object, ...) base::foo(object) "Earlier versions of this manual suggested assigning foo.default <- base::foo. This is not a good idea, as it captures the base function at the time of installation and it might be changed as R is patched or updated." Best, Josh On Wed, Nov 7, 2018 at 10:45 AM Rampal S. Etienne <rampaletie...@gmail.com> wrote: > > The problem was resolved by installing again a new version of devtools. > > However, this new version gives other problems: devtools::check() says > the DESCRIPTION file is missing a License field, but there IS a license > field in this file. > > > On 7-11-2018 16:59, William Dunlap wrote: > > After installing a new version of R the OP may have to rebuild (and > > retest) packages like pkgload that define functions by grabbing > > functions from the base package and modifying them, as in > > pkgload/R/namespace-env.r: > > > > onload_assign("makeNamespace", > > eval( > > modify_lang( > > extract_lang(body(loadNamespace), > > > > # Find makeNamespace definition > > comp_lang, y = quote(makeNamespace <- NULL), idx = 1:2)[[3]], > > > > # Replace call to .Internal(registerNamespace()) is replaced by > > a call to > > # register_namespace > > function(x) { > > if (comp_lang(x, quote(.Internal(registerNamespace(name, > > env))))) { > > quote(register_namespace(name, env)) > > } else { > > x > > } > > })) > > ) > > > > > > > > > > Bill Dunlap > > TIBCO Software > > wdunlap tibco.com <http://tibco.com> > > > > On Wed, Nov 7, 2018 at 3:45 AM, Georgi Boshnakov > > <georgi.boshna...@manchester.ac.uk > > <mailto:georgi.boshna...@manchester.ac.uk>> wrote: > > > > Without code we are guessing. A bug is possible but I will make > > another guess suggestion. > > > > Delete all binary files created by devtools during compilation in > > your package directory. > > devtools::load_all() is so fast partly because it recompiles the > > C/Fortran files only when necessary > > but sometimes compilation may be needed even if devtools thinks > > otherwise. > > > > Georgi Boshnakov > > > > > > -----Original Message----- > > From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com > > <mailto:murdoch.dun...@gmail.com>] > > Sent: 07 November 2018 00:26 > > To: Rampal Etienne; Georgi Boshnakov; > > r-package-devel@r-project.org <mailto:r-package-devel@r-project.org> > > Subject: Re: [R-pkg-devel] nativeRoutines error when using > > roxygen2 in RStudio > > > > On 06/11/2018 5:17 PM, Rampal Etienne wrote: > > > Dear Duncan, > > > > > > I don't get it when using R CMD check. > > > > > > I only get it when building/loading using roxygen2 or when I call > > > load_all (which roxygen2 does too, I think). load_all calls load_dll > > > which then throws this error. I have registered my routines in > > > R_init_secsse.c: > > > > > > void R_init_secsse(DllInfo *dll) > > > { > > > R_registerRoutines(dll, NULL, NULL, FortranEntries, NULL); > > > R_useDynamicSymbols(dll, FALSE); > > > } > > > > > > Any suggestions? > > > > Nope! Sounds like a bug in devtools/roxygen2, but I don't know > > either > > of those packages well. > > > > Duncan Murdoch > > > > > > > > Cheers, Rampal > > > > > > > > > On 06-Nov-18 22:50, Duncan Murdoch wrote: > > >> On 06/11/2018 3:27 PM, Rampal Etienne wrote: > > >>> Dear Georgi, > > >>> > > >>> Thanks for your suggestions. I have tried to install the > > development > > >>> version of roxygen2, but to no avail. > > >>> > > >>> I don't have a Collate field in DESCRIPTION. > > >>> > > >>> devtools::check() gives me: > > >>> > > >>> Updating secsse documentation Loading secsse Registered S3 method > > >>> overwritten by 'dplyr': method from as.data.frame.tbl_df tibble > > >>> Registered S3 method overwritten by 'geiger': method from > > >>> unique.multiPhylo ape Error in nativeRoutines[[lib]] <- routines : > > >>> object 'nativeRoutines' not found > > >> > > >> Do you get that error if you run "R CMD check" on the tarball > > of your > > >> package? > > >> > > >> If so, how comfortable are you with debugging R code? I can > > tell you > > >> how to debug the check process, but it's a little tricky. > > >> > > >> Duncan Murdoch > > >> > > >>> > > >>> > > >>> Any other suggestions? > > >>> > > >>> Cheers, Rampal > > >>> > > >>> On 02-Nov-18 08:33, Georgi Boshnakov wrote: > > >>>> Try installing the latest development version of roxygen2, if you > > >>>> are not using it already. > > >>>> There was a bug in the released version preventing > > installation in > > >>>> some cases. > > >>>> If you don't want to use development version of roxygen2, > > >>>> try putting all filenames in the Collate field in DESCRIPTION > > on one > > >>>> line and make sure that there is a single space > > >>>> between them. This should work if your problem is what I think. > > >>>> > > >>>> By the way, in such cases you will get more informative > > messages if > > >>>> you run devtools::check(). > > >>>> > > >>>> -- > > >>>> Georgi Boshnakov > > >>>> > > >>>> > > >>>> ________________________________________ > > >>>> From: R-package-devel [r-package-devel-boun...@r-project.org > > <mailto:r-package-devel-boun...@r-project.org>] on > > >>>> behalf of Rampal Etienne [rampaletie...@gmail.com > > <mailto:rampaletie...@gmail.com>] > > >>>> Sent: 01 November 2018 22:40 > > >>>> To: r-package-devel@r-project.org > > <mailto:r-package-devel@r-project.org> > > >>>> Subject: [R-pkg-devel] nativeRoutines error when using > > roxygen2 in > > >>>> RStudio > > >>>> > > >>>> Since a few weeks (after updating R-devel and Rtools) I get the > > >>>> following error when trying to build a package or document > > it, when > > >>>> using roxygen2 in RStudio: > > >>>> > > >>>> In R CMD INSTALL Error in nativeRoutines[[lib]] <- routines : > > object > > >>>> 'nativeRoutines' not found Calls: > > suppressPackageStartupMessages ... > > >>>> withCallingHandlers -> <Anonymous> -> load_all -> load_dll > > Execution > > >>>> halted > > >>>> > > >>>> When I disable roxygen2, I do not get this error, but of > > course the > > >>>> documentation is not created. > > >>>> > > >>>> I have installed the latest versions of RStudio, Rtools, R-devel, > > >>>> roxygen2, pkgload, but the problem persists. > > >>>> > > >>>> Does anybody have a clue what is causing this? I am using > > Windows 10, > > >>>> and the package contains Fortran code. > > >>>> > > >>>> Kind regards, > > >>>> Rampal Etienne > > >>>> > > >>>> [[alternative HTML version deleted]] > > >>>> > > >>>> ______________________________________________ > > >>>> R-package-devel@r-project.org > > <mailto:R-package-devel@r-project.org> mailing list > > >>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > <https://stat.ethz.ch/mailman/listinfo/r-package-devel> > > >>> > > >>> > > >>> [[alternative HTML version deleted]] > > >>> > > >>> ______________________________________________ > > >>> R-package-devel@r-project.org > > <mailto:R-package-devel@r-project.org> mailing list > > >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > <https://stat.ethz.ch/mailman/listinfo/r-package-devel> > > >>> > > >> > > > > > > > ______________________________________________ > > R-package-devel@r-project.org > > <mailto:R-package-devel@r-project.org> mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > <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 -- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com R/Finance 2018 | www.rinfinance.com ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel