Hi Emmanuel, Strangely enough it was a Windows machine I used to check it and it runs fine. The log files from the checks all come back fine except for the note in my original email, but as the info in the log file only say what the problem is but gives no indication how to address it in this case I'm struggling with it. I assume it is something to do with the NAMESPACE file (or, plausibly, the DESCRIPTION file) but as I can't figure out what's going on and nothing has changed with imported functions from the geiger package I was hoping someone might be able to spot issues in those files, or maybe has come across a similar issue and knows how to resolve it.
Cheers, Kev Dr Kevin Arbuckle Athro Cyswllt (Darllenydd) mewn Biowyddorau (Bioleg Esblygiadol) / Associate Professor (Reader) in Biosciences (Evolutionary Biology) Adran Biowyddorau / Department of Biosciences Cyfadran Gwyddoniaeth a Pheirianneg / Faculty of Science and Engineering Prifysgol Abertawe / Swansea University Abertawe / Swansea SA2 8PP UK Rhowch wybod i ni os hoffech dderbyn eich gohebiaeth yn Gymraeg. Rydym yn croesawu gohebiaeth yn Gymraeg neu yn Saesneg. Ni fydd gohebu yn Gymraeg yn arwain at oedi. -----Original Message----- From: Emmanuel Paradis <emmanuel.para...@ird.fr> Sent: 28 February 2023 11:03 To: Kevin Arbuckle <kevin.arbuc...@swansea.ac.uk> Cc: r-sig-phylo <r-sig-phylo@r-project.org> Subject: Re: [R-sig-phylo] NAMESPACE issue Hi Kevin, Do you run the checks of a new version of windex on this site: win-builder.r-project.org/ ? It runs the checks both on Debian and Windowns with several choices of R versions, and you can access the detailed log files. Best, Emmanuel ----- Le 28 Fév 23, à 17:38, Arbuckle kevin.arbuc...@swansea.ac.uk a écrit : > Hi all, > > I realise this might not be strictly a phylogeny-related issue, but it > might be as it relates to geiger and in any case the CRAN Core Team > have left me at an impasse trying to get an update to windex through > to CRAN (just repeating the error message then ignoring messages > asking for clarification or advice on fixing it). Hopefully it's relevant > enough to this list to be OK. > > When trying to submit an update to the package, all Debian checks are > coming back fine, but there is one note in the Windows checks that is > stopping the process. The note reads:- > > "windex: no visible global function definition for 'rescale' > Undefined global functions or variables: > rescale" > > However, geiger (the package which contains rescale) is listed as a > dependency in the DESCRIPTION and is imported in the NAMESPACE, so > rescale should definitely be there. Combined with the lack of issue > flagged by Debian checks (which presumably would also check basic > things like 'do the functions exist') and the fact that this issue > hasn't occurred in previous version submitted to CRAN (nothing has > changed with respect to the use of the rescale function), I am at a loss. > > In case it helps, the contents of the DESCRIPTION and NAMESPACE files > are as > follows:- > > DESCRIPTION file: > Package: windex > Type: Package > Title: Analysing Convergent Evolution using the Wheatsheaf Index > Version: 2.0.4 > Date: 2023-02-23 > Author: Kevin Arbuckle and Amanda Minter > Maintainer: Kevin Arbuckle > kevin.arbuc...@swansea.ac.uk<mailto:kevin.arbuc...@swansea.ac.uk> > Description: Analysing convergent evolution using the Wheatsheaf > index, described in Arbuckle et al. (2014) <doi: > 10.1111/2041-210X.12195>, and some other unrelated but perhaps useful > functions. > License: GPL-2 > Depends: phytools, geiger (>= 2.0), ape (>= 4.0), phangorn, > scatterplot3d, utils, methods, R (>= 3.0.0) > Packaged: 2023-02-23 12:36:50 UTC; karbuckle > > NAMESPACE file: > exportPattern("^[^\\.]") > import(ape,utils,scatterplot3d) > importFrom("graphics", "abline", "hist", "legend", "points", "arrows", > "plot","text","polygon") > importFrom("stats", "dist", "quantile", "sd", "var", "AIC", "BIC", > "logLik", "na.omit", "pchisq", "shapiro.test","model.frame","density") > importFrom("methods", "is") > importFrom("phytools", "findMRCA", "nodeHeights") importFrom("geiger", > "rescale", "ratematrix", "sim.char") importFrom("phangorn", "CI", > "as.phyDat", "Children", "Descendants") > > > Any advice on how to resolve this would be welcome. Note that > originally I had imported geiger (and phangorn) as import rather than > importFrom in the NAMESPACE, but the current version was an attempt to > resolve the issue and didn't work in that the same note is coming back every > time. > > Best wishes, > Kev > > Dr Kevin Arbuckle > Athro Cyswllt (Darllenydd) mewn Biowyddorau (Bioleg Esblygiadol) / > Associate Professor (Reader) in Biosciences (Evolutionary Biology) > Adran Biowyddorau / Department of Biosciences Cyfadran Gwyddoniaeth a > Pheirianneg / Faculty of Science and Engineering Prifysgol Abertawe / > Swansea University Abertawe / Swansea > SA2 8PP > UK > > Rhowch wybod i ni os hoffech dderbyn eich gohebiaeth yn Gymraeg. Rydym > yn croesawu gohebiaeth yn Gymraeg neu yn Saesneg. Ni fydd gohebu yn > Gymraeg yn arwain at oedi. > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat > .ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C01%7CKevin.Arbuc > kle%40Swansea.ac.uk%7C8fb40ec68c054cceca3508db197b7139%7Cbbcab52e9fbe4 > 3d6a2f39f66c43df268%7C0%7C0%7C638131790186270163%7CUnknown%7CTWFpbGZsb > 3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D% > 7C3000%7C%7C%7C&sdata=P2lMsc8QxwQPh%2Bgtk%2Bj6YRL%2FaPBb58Sam5huKul4fR > U%3D&reserved=0 Searchable archive at > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.m > ail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C01%7CKevin. > Arbuckle%40Swansea.ac.uk%7C8fb40ec68c054cceca3508db197b7139%7Cbbcab52e > 9fbe43d6a2f39f66c43df268%7C0%7C0%7C638131790186270163%7CUnknown%7CTWFp > bGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn > 0%3D%7C3000%7C%7C%7C&sdata=VxuDpZGDagj2g6cp14zV7G02F2PKSWkT0n1psYbs8V8 > %3D&reserved=0 _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
