If you have R-devel you can get those NOTEs using: R CMD check --as-cran *.tar.gz
(It's been reported by --as-cran since Oct 2015 or so). /Henrik On Fri, Mar 11, 2016 at 2:45 PM, Hartley, Stephen (NIH/NHGRI) [F] <stephen.hart...@nih.gov> wrote: > Thanks. I'll try that. I'm surprised, as my local R-Devel install isn't that > old. > > I used to have a few specific imports like this, but I was told to remove > them because BiocCheck did not like them (because these packages were not > declared in the "imports" line of the DESCRIPTION). I don't know if the > newest version of BiocCheck still complains about them now. > > -Steve > > -----Original Message----- > From: Martin Morgan [mailto:martin.mor...@roswellpark.org] > Sent: Friday, March 11, 2016 2:24 PM > To: Hartley, Stephen (NIH/NHGRI) [F]; bioc-devel > Subject: Re: [Bioc-devel] Odd behavior by R CMD check > > > > On 03/11/2016 02:17 PM, Hartley, Stephen (NIH/NHGRI) [F] wrote: >> I'm seeing some odd behavior by the R CMD check command for my package, >> JunctionSeq. >> >> http://bioconductor.org/checkResults/3.3/bioc-LATEST/JunctionSeq/zin2- >> checksrc.html >> >> It's not technically throwing warnings (just a "NOTE"), but it is claiming >> that there's no global definition for functions belonging to the default R >> packages (grDevices, utils, stats, and graphics). >> >> So I get lines like this: >> drawGene: no visible global function definition for 'plot.new' >> >> drawGene: no visible global function definition for 'plot.window' >> >> drawGene: no visible global function definition for 'par' >> >> drawGene: no visible global function definition for 'strwidth' >> >> drawGene: no visible global function definition for 'lines' >> >> drawGene: no visible global function definition for 'rect' >> >> drawGene: no visible global function definition for 'segments' >> >> drawGene: no visible global function definition for 'strheight' >> >> Since it's still able to compile the vignette and everything it's clearly >> not actually having a problem finding these functions at runtime, but I >> can't figure out what would cause it to throw these notes. I don't get these >> notes when I run R CMD check locally on any of my test machines (windows, >> CentOS5 linux and scientific linux 6). And I've had it build with no issues >> before. I can't see how my recent changes could possibly have caused this ... >> >> Has anyone ever seen this before? > > This is the behavior with a recent version of R-devel; likely you are using > an older version or R-3.2.*. Things 'work' because the relevant packages are > on the search path, but would fail if for instance the user or another > package were to define a 'strheight' function that did something different > from graphics::strheight. > > The solution is to import the relevant functions, as indicated in the build > report. > > importFrom("grDevices", "cairo_ps", "col2rgb", "colorRamp", "dev.off", > "png", "rgb", "svg", "tiff", "x11") > importFrom("graphics", "abline", "axis", "box", "hist", "layout", > "legend", "lines", "par", "plot", "plot.new", "plot.window", > "points", "rect", "segments", "smoothScatter", "strheight", > "strwidth", "text", "title") > importFrom("stats", "Gamma", "as.formula", "coef", "coefficients", > "deviance", "dnbinom", "fitted.values", "formula", "glm", > "loess", "model.matrix", "optimize", "p.adjust", "pchisq", > "predict", "qf", "rchisq", "rnorm", "runif", "terms", > "weighted.mean") > importFrom("utils", "object.size", "packageVersion", "read.delim", > "read.table", "write.table") > > Martin > >> >> Regards, >> Steve Hartley >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
