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
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