On Jan 30, 2017, at 8:58 PM, Kevin Ushey <kevinushey at gmail.com> wrote:
Most importantly, this _is_ a recent-ish change in R CMD check. Previously, R CMD check did not warn about missing imports from 'base' R packages (that is, R packages distributed with R, having priority 'base'); now it correctly does. While packages with priority 'base' are loaded by default in most R installations, it's possible for the user to customize that behavior, and so packages that don't import the functions they use from these packages will break if they are detached (or their order on the search path is changed).
The correct thing to do is indeed import any functions from any R packages you use, base or otherwise. The simplest fix, if you don't want to selectively import such a large range of functions, is to simply add e.g.
import(utils)
import(stats)
... etc ...
to your NAMESPACE file.
Best,
Kevin
On Mon, Jan 30, 2017 at 9:21 AM, Brian G. Peterson <brian at braverock.com> wrote:
See the link in my email below. It says:
"Packages implicitly import the base namespace. Variables exported from
other packages with namespaces need to be imported explicitly using the
directives import and importFrom."
Regards,
Brian
On Mon, 2017-01-30 at 11:04 -0600, Cathy Lee Gierke wrote:
That is the obvious solution, but it doesn't seem correct: I have
pdf included in the description, and namespace files, yet it is being
called out. Additionally, aren't most of these pkgs in the packages
included by default?
And up until yesterday, I didn't have any of these problems. I've
been compiling and running this for several years. But now I want to
release to CRAN, so I've been fixing minor issues....and suddenly
this mass of Notes.
Thank you,
Cathy Lee Gierke
?Darkness cannot drive out darkness: only light can do that. Hate
cannot drive out hate: only love can do that.?
?The arc of the moral universe is long, but it bends towards
justice.?
?Nothing in the world is more dangerous than sincere ignorance and
conscientious stupidity.?
?Never forget that everything Hitler did in Germany was legal.?
?Forgiveness is not an occasional act, it is a constant attitude.?
?Injustice anywhere is a threat to justice everywhere.?
? Martin Luther King Jr.
On Mon, Jan 30, 2017 at 10:52 AM, Brian G. Peterson <brian at braverock.
com> wrote:
Yes, that seemed to get rid of the NOTE....but it doesn't seem to
make much difference other than that. i.e., it seems to process
the same using CATkit vs CATkit_2.06.tar.gz!
Here is the main error that I am getting. I just upgraded to the
latest R version, fyi.
Everything was fine, a few minor warnings...now this.
Description and namespace are proper. These pkgs should all be
part of the R base, aren't they? Anyone know why I should get
these errors? Thanks!
* checking R code for possible problems ... NOTE
Actogram: no visible global function definition for ?par?
Actogram: no visible global function definition for ?barplot?
Actogram: no visible global function definition for ?box?
Actogram: no visible global function definition for ?text?
Actogram: no visible global function definition for ?mtext?
Actogram: no visible binding for global variable ?end?
AutoCorr: no visible global function definition for ?par?
AutoCorr: no visible global function definition for ?layout?
AutoCorr: no visible global function definition for ?acf?
AutoCorr: no visible global function definition for ?abline?
AutoCorr: no visible global function definition for ?title?
AutoCorr: no visible global function definition for ?mtext?
AutoCorr: no visible global function definition for ?var?
AutoCorr: no visible binding for global variable ?end?
CATCosinor: no visible global function definition for ?par?
CATCosinor: no visible global function definition for ?pdf?
CATCosinor: no visible global function definition for ?jpeg?
CATCosinor: no visible global function definition for ?png?
CATCosinor: no visible global function definition for ?tiff?
......... A zillion more for every function I have......
periCosinor: no visible global function definition for ?par?
periCosinor: no visible global function definition for ?fft?
Undefined global functions or variables:
TukeyHSD abline acf aov as.raster axis barplot box boxplot ccf
coefficients dev.cur dev.off drop1 end fft gray heat.colors
image
jpeg layout legend lines median model.tables mtext na.action
na.omit
palette par pdf pf plot plot.new png points rainbow rasterImage
read.table str strwidth tail terrain.colors text tiff title ts
var
write.table
Consider adding
importFrom("grDevices", "as.raster", "dev.cur", "dev.off",
"gray",
"heat.colors", "jpeg", "palette", "pdf", "png",
"rainbow",
"terrain.colors", "tiff")
importFrom("graphics", "abline", "axis", "barplot", "box",
"boxplot",
"image", "layout", "legend", "lines", "mtext",
"par",
"plot", "plot.new", "points", "rasterImage",
"strwidth",
"text", "title")
importFrom("stats", "TukeyHSD", "acf", "aov", "ccf",
"coefficients",
"drop1", "end", "fft", "median", "model.tables",
"na.action", "na.omit", "pf", "ts", "var")
importFrom("utils", "read.table", "str", "tail", "write.table")
to your NAMESPACE file.
Cathy Lee Gierke
?Darkness cannot drive out darkness: only light can do that. Hate
cannot drive out hate: only love can do that.?
?The arc of the moral universe is long, but it bends towards
justice.?
?Nothing in the world is more dangerous than sincere ignorance
and conscientious stupidity.?
?Never forget that everything Hitler did in Germany was legal.?
?Forgiveness is not an occasional act, it is a constant
attitude.?
?Injustice anywhere is a threat to justice everywhere.?
? Martin Luther King Jr.
On Mon, Jan 30, 2017 at 10:05 AM, Brian G. Peterson <brian at braver
ock.com> wrote:
On Mon, 2017-01-30 at 09:45 -0600, Cathy Lee Gierke wrote:
building ?CATkit_2.06.tar.gz?
R CMD build creates a tarball
x-134-84-0-217:CATkit user$ *R CMD check CATkit*
but you are checknig the directory, not the tarball.
do
R CMD check CATkit_2.06.tar.gz
instead.
Regards,
Brian