On 03/11/2016 05:45 PM, Hartley, Stephen (NIH/NHGRI) [F] 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.
The right solution is to declare them in the Imports: line, too.
Martin
-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
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