Hi Kevin. Sorry, this is pretty much all my fault. The definition of the S3 method /rescale/ now lives in /phytools/. /rescale/ is still exported by the namespace of /geiger/ on CRAN, so I suspect you're working with the GitHub version.
The easiest thing to do is add /phytools (>1.5-1)/ to *Depends:* in your DESCRIPTION file and /importFrom(phytools, rescale)/ to NAMESPACE. (This should work immediately because currently on CRAN /rescale/ is defined & exported by both /phytools/ and /geiger/.) Please let me know if that works. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> (/Princeton University Press/, 2022) On 2/28/2023 9:33 AM, Kevin Arbuckle wrote: > CAUTION: EXTERNAL SENDER > > 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, arbucklekevin.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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat%2F&data=05%7C01%7Cliam.revell%40umb.edu%7Ce4f266c4a3d14c5772b508db1998ddc1%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C638131916601335049%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0%2F%2Baqb9sSHXRSdTsmAK0kXJb2hQA33PqjFzKAxbzyoQ%3D&reserved=0 >> .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://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.m%2F&data=05%7C01%7Cliam.revell%40umb.edu%7Ce4f266c4a3d14c5772b508db1998ddc1%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C638131916601335049%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UmVgtr3Nwa8ERzmDcwQEPddQ%2FhhVwf9lVSOv57I5DEk%3D&reserved=0 >> 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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C01%7Cliam.revell%40umb.edu%7Ce4f266c4a3d14c5772b508db1998ddc1%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C638131916601335049%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pGB0gmL%2FB5NljwFkNn%2B4t8bh5OZpO1G88azy9q4gjFA%3D&reserved=0 > Searchable archive > athttps://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C01%7Cliam.revell%40umb.edu%7Ce4f266c4a3d14c5772b508db1998ddc1%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C638131916601335049%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JVuh6Laiff5fRhVAJdpCNX60yymeOPTxnqMo4HabNW4%3D&reserved=0 [[alternative HTML version deleted]] _______________________________________________ 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/
