----- Original Message ----- > From: "Hartley, Stephen (NIH/NHGRI) [F]" <[email protected]> > To: "Henrik Bengtsson" <[email protected]> > Cc: "bioc-devel" <[email protected]> > Sent: Monday, March 14, 2016 6:58:04 AM > Subject: Re: [Bioc-devel] Odd behavior by R CMD check
> Why didn't this show up before in the SPB reports until recently? Is > "--as-cran" > a new addition to the SPB? > No. SPB does not use "--as-cran". As was pointed out earlier in this thread, R-devel is now emitting this information by default (i.e. with or without the --as-cran flag). Dan > -----Original Message----- > From: Henrik Bengtsson [mailto:[email protected]] > Sent: Friday, March 11, 2016 6:06 PM > To: Hartley, Stephen (NIH/NHGRI) [F] > Cc: Martin Morgan; bioc-devel > Subject: Re: [Bioc-devel] Odd behavior by R CMD check > > 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] > <[email protected]> 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:[email protected]] >> 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]] >>> >>> _______________________________________________ >>> [email protected] 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. >> >> _______________________________________________ >> [email protected] mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
