From yurii.aulchenko at gmail.com Fri Jul 3 18:03:57 2015 From: yurii.aulchenko at gmail.com (Yury Aulchenko) Date: Fri, 3 Jul 2015 18:03:57 +0200 Subject: [GenABEL-dev] Fwd: CRAN packages maintained by you References: <21909.1101.132120.323584@fangorn.hornik.net> Message-ID: FYI ---------------- Sent from mobile device, please excuse possible typos Begin forwarded message: > From: Kurt Hornik > Date: 2 Jul 2015 11:28:45 CEST > To: CRAN at R-project.org > Subject: CRAN packages maintained by you > Reply-To: Kurt.Hornik at wu.ac.at > > > Dear CRAN package maintainers, > > You may already have seen the following news item for r-devel: > > * 'R CMD check --as-cran' now checks code usage (via 'codetools') > with only the base package attached, so that functions from > default packages other than base which are used in the package > code but not imported are reported as undefined globals. > > This may result in lots of notes about undefined globals which can be > found in the default packages. The change was made because even though > the default packages (stats, graphics, ...) are typically loaded and > attached, bindings not found in the package code itself, the imports or > base are searched for along the search path starting with the global > environment, and there is no control over what is actually found there. > Therefore, undefined globals corresponding to functions or variables in > the default packages, really need to be imported into the package > namespace. > > With current versions of r-devel, one can get a convenient summary of > all undefined globals, which can be used for programmatically generating > the missing imports as follows. > > One package currently gives > > * checking R code for possible problems ... NOTE > choose_palette : SaveColorsToFile: no visible global function > definition for ?write.table? > choose_palette : ShowExample: no visible global function definition for > ?dev.list? > choose_palette : ShowExample: no visible global function definition for > ?dev.new? > choose_palette : ShowExample: no visible global function definition for > ?dev.cur? > choose_palette : ShowExample: no visible global function definition for > ?par? > choose_palette : RegenExample: no visible global function definition > for ?dev.list? > choose_palette : RegenExample: no visible global function definition > for ?dev.set? > choose_palette : PlotMap: no visible global function definition for > ?polygon? > <...................................................................> > choose_palette : PlotMosaic: no visible global function definition for > ?image? > choose_palette : PlotLines: no visible global function definition for > ?segments? > choose_palette: no visible global function definition for > ?compareVersion? > choose_palette: no visible global function definition for ?dev.list? > choose_palette: no visible global function definition for ?dev.off? > desaturate: no visible global function definition for ?col2rgb? > Undefined global functions or variables: > barplot col2rgb compareVersion cutree dev.cur dev.list dev.new > dev.off dev.set dist dnorm hclust head image na.omit par persp pie > polygon rect rnorm runif segments volcano write.table > > Using the above output, do > > txt <- "barplot col2rgb compareVersion cutree dev.cur dev.list dev.new > dev.off dev.set dist dnorm hclust head image na.omit par persp pie > polygon rect rnorm runif segments volcano write.table" > > and use > > imports_for_undefined_globals <- > function(txt, lst, selective = TRUE) > { > if(!missing(txt)) > lst <- scan(what = character(), text = txt, quiet = TRUE) > nms <- lapply(lst, find) > ind <- sapply(nms, length) > 0L > imp <- split(lst[ind], substring(unlist(nms[ind]), 9L)) > if(selective) { > sprintf("importFrom(%s)", > vapply(Map(c, names(imp), imp), > function(e) > paste0("\"", e, "\"", collapse = ", "), > "")) > } else { > sprintf("import(\"%s\")", names(imp)) > } > } > > to get > > R> writeLines(imports_for_undefined_globals(txt)) > importFrom("datasets", "volcano") > importFrom("grDevices", "col2rgb", "dev.cur", "dev.list", "dev.new", "dev.off", "dev.set") > importFrom("graphics", "barplot", "image", "par", "persp", "pie", "polygon", "rect", "segments") > importFrom("stats", "cutree", "dist", "dnorm", "hclust", "na.omit", "rnorm", "runif") > importFrom("utils", "compareVersion", "head", "write.table") > > For non-selective importing, use > > R> writeLines(imports_for_undefined_globals(txt, selective = FALSE)) > import("datasets") > import("grDevices") > import("graphics") > import("stats") > import("utils") > > Of course, namespaces newly imported from also need to be listed in the > Imports: field of DESCRIPTION. > > Please make sure you make the necessary changes before you submit new > versions of your package to CRAN. > > Best > -k > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yurii.aulchenko at gmail.com Wed Jul 8 17:50:35 2015 From: yurii.aulchenko at gmail.com (Yurii Aulchenko) Date: Wed, 8 Jul 2015 17:50:35 +0200 Subject: [GenABEL-dev] [Genabel-commits] r2000 - pkg/GenABEL/R In-Reply-To: <20150708154449.1C9C21861AB@r-forge.r-project.org> References: <20150708154449.1C9C21861AB@r-forge.r-project.org> Message-ID: <8627980E-F069-4A90-BC22-36D7E36E16E3@gmail.com> Hi nd_0001! (Yakov?) ?no/one measurement? as diagnostic comment may be confusing for the user; and then you say ?number of points is too small?, apparently also relating to the npt Looking in the documentation, I assume that npt is length of data: Input vector of Chi square statistic so why not calling it the way people know form the doc? e.g. ?input vector ?data? has zero-length? and so on? Yurii > On 08 Jul 2015, at 17:44, noreply at r-forge.r-project.org wrote: > > Author: nd_0001 > Date: 2015-07-08 17:44:48 +0200 (Wed, 08 Jul 2015) > New Revision: 2000 > > Modified: > pkg/GenABEL/R/VIFGC_ovdom.R > Log: > Minor changes in GC functions, need to rewrite. Also catched 2000th revision=) > > Modified: pkg/GenABEL/R/VIFGC_ovdom.R > =================================================================== > --- pkg/GenABEL/R/VIFGC_ovdom.R 2015-07-08 07:36:58 UTC (rev 1999) > +++ pkg/GenABEL/R/VIFGC_ovdom.R 2015-07-08 15:44:48 UTC (rev 2000) > @@ -136,8 +136,9 @@ > if (ntp < 1) > stop("no valid measurments") > if (ntp == 1) { > - warning(paste("One measurment, Lambda = 1 returned")) > - return(list(estimate = 1, se = 999.99)) > + stop("Only one measurment. Stoped.") > + #warning(paste("One measurment, Lambda = 1 returned")) > + #return(list(estimate = 1, se = 999.99)) > } > if (ntp < 10) > warning(paste("number of points is too small:", ntp)) > > _______________________________________________ > Genabel-commits mailing list > Genabel-commits at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits From drosophila.simulans at gmail.com Wed Jul 8 18:39:39 2015 From: drosophila.simulans at gmail.com (Yakov Tsepilov) Date: Wed, 8 Jul 2015 22:39:39 +0600 Subject: [GenABEL-dev] [Genabel-commits] r2000 - pkg/GenABEL/R In-Reply-To: <8627980E-F069-4A90-BC22-36D7E36E16E3@gmail.com> References: <20150708154449.1C9C21861AB@r-forge.r-project.org> <8627980E-F069-4A90-BC22-36D7E36E16E3@gmail.com> Message-ID: Hi Yurii, Good suggestion, anyway I will rewrite scripts in proper way (according to Genabel standards for code formatting). With kind regards, Yakov Tsepilov. 2015-07-08 21:50 GMT+06:00 Yurii Aulchenko : > Hi nd_0001! (Yakov?) > > ?no/one measurement? as diagnostic comment may be confusing for the user; > and then you say ?number of points is too small?, apparently also relating > to the npt > > Looking in the documentation, I assume that npt is length of > > data: Input vector of Chi square statistic > > so why not calling it the way people know form the doc? e.g. > > ?input vector ?data? has zero-length? and so on? > > Yurii > > > On 08 Jul 2015, at 17:44, noreply at r-forge.r-project.org wrote: > > > > Author: nd_0001 > > Date: 2015-07-08 17:44:48 +0200 (Wed, 08 Jul 2015) > > New Revision: 2000 > > > > Modified: > > pkg/GenABEL/R/VIFGC_ovdom.R > > Log: > > Minor changes in GC functions, need to rewrite. Also catched 2000th > revision=) > > > > Modified: pkg/GenABEL/R/VIFGC_ovdom.R > > =================================================================== > > --- pkg/GenABEL/R/VIFGC_ovdom.R 2015-07-08 07:36:58 UTC (rev 1999) > > +++ pkg/GenABEL/R/VIFGC_ovdom.R 2015-07-08 15:44:48 UTC (rev 2000) > > @@ -136,8 +136,9 @@ > > if (ntp < 1) > > stop("no valid measurments") > > if (ntp == 1) { > > - warning(paste("One measurment, Lambda = 1 returned")) > > - return(list(estimate = 1, se = 999.99)) > > + stop("Only one measurment. Stoped.") > > + #warning(paste("One measurment, Lambda = 1 returned")) > > + #return(list(estimate = 1, se = 999.99)) > > } > > if (ntp < 10) > > warning(paste("number of points is too small:", ntp)) > > > > _______________________________________________ > > Genabel-commits mailing list > > Genabel-commits at lists.r-forge.r-project.org > > > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits > > _______________________________________________ > Genabel-commits mailing list > Genabel-commits at lists.r-forge.r-project.org > > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits > -------------- next part -------------- An HTML attachment was scrubbed... URL: From l.c.karssen at polyomica.com Wed Jul 8 22:46:22 2015 From: l.c.karssen at polyomica.com (L.C. Karssen) Date: Wed, 08 Jul 2015 22:46:22 +0200 Subject: [GenABEL-dev] The GenABEL tutorial now has a DOI Message-ID: <559D8C1E.2050703@polyomica.com> Dear GenABEL followers, We are pleased to announce that today we uploaded the current version of the GenABEL tutorial to Zenodo [1], a service for sharing multidisciplinary research results (data and publications). As a result, the tutorial has been given a DOI (Digital Object Identifier) and is more easily citable [2]. So if you need to cite the tutorial in a paper or on a poster, or if you'd like to point it out to a colleague, please use the DOI. Moreover, I've also created a "The GenABEL Project" community on Zenodo, so please enter that community when uploading GenABEL-related materials to Zenodo. Best regards, Lennart Karssen. [1] http://www.zenodo.org [2] http://dx.doi.org/10.5281/zenodo.19738 -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Lennart C. Karssen PolyOmica Groningen The Netherlands l.c.karssen at polyomica.com GPG key ID: 1A15AF2A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 819 bytes Desc: OpenPGP digital signature URL: From yurii.aulchenko at gmail.com Thu Jul 9 09:45:58 2015 From: yurii.aulchenko at gmail.com (Yury Aulchenko) Date: Thu, 9 Jul 2015 09:45:58 +0200 Subject: [GenABEL-dev] The GenABEL tutorial now has a DOI In-Reply-To: <559D8C1E.2050703@polyomica.com> References: <559D8C1E.2050703@polyomica.com> Message-ID: Great! Thank you very much, Lennart, for arranging this! So would the proper reference now look like: Yurii S Aulchenko, Lennart C. Karssen, the GenABEL project developers: "The GenABEL Tutorial", doi:10.5281/zenodo.19738 Should we also add this reference to http://www.genabel.org/tutorials? Yurii ---------------- Sent from mobile device, please excuse possible typos > On 08 Jul 2015, at 22:46, L.C. Karssen wrote: > > Dear GenABEL followers, > > We are pleased to announce that today we uploaded the current version of > the GenABEL tutorial to Zenodo [1], a service for sharing > multidisciplinary research results (data and publications). > As a result, the tutorial has been given a DOI (Digital Object > Identifier) and is more easily citable [2]. > > So if you need to cite the tutorial in a paper or on a poster, or if > you'd like to point it out to a colleague, please use the DOI. Moreover, > I've also created a "The GenABEL Project" community on Zenodo, so please > enter that community when uploading GenABEL-related materials to Zenodo. > > > Best regards, > > Lennart Karssen. > > > [1] http://www.zenodo.org > [2] http://dx.doi.org/10.5281/zenodo.19738 > -- > *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* > Lennart C. Karssen > PolyOmica > Groningen > The Netherlands > > l.c.karssen at polyomica.com > GPG key ID: 1A15AF2A > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel From yurii.aulchenko at gmail.com Thu Jul 9 09:54:04 2015 From: yurii.aulchenko at gmail.com (Yury Aulchenko) Date: Thu, 9 Jul 2015 09:54:04 +0200 Subject: [GenABEL-dev] The GenABEL tutorial now has a DOI In-Reply-To: <559D8C1E.2050703@polyomica.com> References: <559D8C1E.2050703@polyomica.com> Message-ID: <6AB70C46-FC20-4E9D-AEC9-DABCCE4CE0FE@gmail.com> Great! Thank you very much, Lennart, for arranging this! So would the proper reference now look like: Yurii S. Aulchenko, Lennart C. Karssen, the GenABEL project developers: "The GenABEL Tutorial", doi:10.5281/zenodo.19738 Should we also add this reference to http://www.genabel.org/tutorials? Yurii ---------------- Sent from mobile device, please excuse possible typos > On 08 Jul 2015, at 22:46, L.C. Karssen wrote: > > Dear GenABEL followers, > > We are pleased to announce that today we uploaded the current version of > the GenABEL tutorial to Zenodo [1], a service for sharing > multidisciplinary research results (data and publications). > As a result, the tutorial has been given a DOI (Digital Object > Identifier) and is more easily citable [2]. > > So if you need to cite the tutorial in a paper or on a poster, or if > you'd like to point it out to a colleague, please use the DOI. Moreover, > I've also created a "The GenABEL Project" community on Zenodo, so please > enter that community when uploading GenABEL-related materials to Zenodo. > > > Best regards, > > Lennart Karssen. > > > [1] http://www.zenodo.org > [2] http://dx.doi.org/10.5281/zenodo.19738 > -- > *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* > Lennart C. Karssen > PolyOmica > Groningen > The Netherlands > > l.c.karssen at polyomica.com > GPG key ID: 1A15AF2A > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From lennart at karssen.org Thu Jul 9 22:22:16 2015 From: lennart at karssen.org (L.C. Karssen) Date: Thu, 09 Jul 2015 22:22:16 +0200 Subject: [GenABEL-dev] The GenABEL tutorial now has a DOI In-Reply-To: <6AB70C46-FC20-4E9D-AEC9-DABCCE4CE0FE@gmail.com> References: <559D8C1E.2050703@polyomica.com> <6AB70C46-FC20-4E9D-AEC9-DABCCE4CE0FE@gmail.com> Message-ID: <559ED7F8.2020509@karssen.org> On 09-07-15 09:54, Yury Aulchenko wrote: > Great! Thank you very much, Lennart, for arranging this! You're welcome! > So would the > proper reference now look like: > > Yurii S. Aulchenko, Lennart C. Karssen, the GenABEL project developers: > "The GenABEL Tutorial", doi:10.5281/zenodo.19738 Yes. See also the "Cite as" box in the menu on the right (below the social media icons). There you can select your citation style or do an export to e.g. BibTeX or EndNote. > > Should we also add this reference to http://www.genabel.org/tutorials? Done. Lennart. > > Yurii > > ---------------- > Sent from mobile device, please excuse possible typos > > On 08 Jul 2015, at 22:46, L.C. Karssen > wrote: > >> Dear GenABEL followers, >> >> We are pleased to announce that today we uploaded the current version of >> the GenABEL tutorial to Zenodo [1], a service for sharing >> multidisciplinary research results (data and publications). >> As a result, the tutorial has been given a DOI (Digital Object >> Identifier) and is more easily citable [2]. >> >> So if you need to cite the tutorial in a paper or on a poster, or if >> you'd like to point it out to a colleague, please use the DOI. Moreover, >> I've also created a "The GenABEL Project" community on Zenodo, so please >> enter that community when uploading GenABEL-related materials to Zenodo. >> >> >> Best regards, >> >> Lennart Karssen. >> >> >> [1] http://www.zenodo.org >> [2] http://dx.doi.org/10.5281/zenodo.19738 >> -- >> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >> Lennart C. Karssen >> PolyOmica >> Groningen >> The Netherlands >> >> l.c.karssen at polyomica.com >> GPG key ID: 1A15AF2A >> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >> >> >> _______________________________________________ >> genabel-devel mailing list >> genabel-devel at lists.r-forge.r-project.org >> >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel > > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen Utrecht The Netherlands lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: