Dear All,
I understand the R CMD checks with only the base package attached,
everything else (including the other packages bundled with the base R)
should be imported and most importantly declared in the Imports field from
the DESCRIPTION file.
However, I do use functions from other packages than base (utils,
grDevices, stats, graphics), for which it is sufficient to declare
importFrom() in the NAMESPACE file.
For instance, it is not required to specify utils in the Imports: field
from DESCRIPTION, when using importFrom("utils",
"packageDescription") in
NAMESPACE.
The opposite happens for importFrom("methods", "is"), which
ends up in the
error: Namespace dependency not required: ?methods?
Is there a special reason for which package methods is treated differently
from all other packages bundled with the base R?
Thank you,
Adrian
--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
Soseaua Panduri nr. 90-92
050663 Bucharest sector 5
Romania
https://adriandusa.eu
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>>>>> Adrian Du?a <dusa.adrian at unibuc.ro> >>>>> on Fri, 9 Mar 2018 10:34:30 +0200 writes:> Dear All, > I understand the R CMD checks with only the base package attached, > everything else (including the other packages bundled with the base R) > should be imported and most importantly declared in the Imports field from > the DESCRIPTION file. > However, I do use functions from other packages than base (utils, > grDevices, stats, graphics), for which it is sufficient to declare > importFrom() in the NAMESPACE file. > For instance, it is not required to specify utils in the Imports: field > from DESCRIPTION, when using importFrom("utils", "packageDescription") in > NAMESPACE. Is that so? Not according to my reading of the 'Writing R Extensions' manual, nor according to what I have been doing in all of my packages for ca. 2 years: The rule I have in my mind is 1) NAMESPACE Import(s|From) \ ............................ <==> DESCRIPTION -> 'Imports:' 2) .. using "::" in R code / If you really found that you did not have to import from say 'utils', I think this was a *un*lucky coincidence. Even R's own "stats" package has a line importFrom(utils, count.fields, flush.console, str, tail) in its NAMESPACE. > The opposite happens for importFrom("methods", "is"), which ends up in the > error: Namespace dependency not required: ?methods? > Is there a special reason for which package methods is treated differently > from all other packages bundled with the base R? > Thank you, > Adrian > -- > Adrian Dusa > University of Bucharest > Romanian Social Data Archive > Soseaua Panduri nr. 90-92 > 050663 Bucharest sector 5 > Romania > https://adriandusa.eu There are places in the R source where it is treated specially, indeed, part of 'methods' may be needed when it is neither loaded nor attached (e.g., when R runs with only base, say, and suddenly encounters an S4 object), and there still are situations where 'methods' needs to be in the search() path and not just loaded, but these cases should be unrelated to the above DESCRIPTION-Imports vs NAMESPACE-Imports correspondence. Martin Maechler ETH Zurich & R Core Team
On Mon, Mar 12, 2018 at 2:18 PM, Martin Maechler <maechler at stat.math.ethz.ch> wrote:> [...] > Is that so? Not according to my reading of the 'Writing R > Extensions' manual, nor according to what I have been doing in > all of my packages for ca. 2 years: > > The rule I have in my mind is > > 1) NAMESPACE Import(s|From) \ > ............................ <==> DESCRIPTION -> 'Imports:' > 2) .. using "::" in R code / > > > If you really found that you did not have to import from say > 'utils', I think this was a *un*lucky coincidence.Of course, the importFrom() is mandatory in NAMESPACE otherwise the package does not pass the checks. The question was related to the relation between the packages mentioned in the NAMESPACE and the packages mentioned in the Imports: field from DESCRIPTION. For instance, the current version 3.1 of package QCA on CRAN mentions in the DESCRIPTION: Imports: venn (? 1.2), shiny, methods, fastdigest while the NAMESPACE file has: import(shiny) import(venn) import(fastdigest) importFrom("utils", "packageDescription", "remove.packages", "capture.output") importFrom("stats", "glm", "predict", "quasibinomial", "binom.test", "cutree", "dist", "hclust", "na.omit", "dbinom", "setNames") importFrom("grDevices", "dev.cur", "dev.new", "dev.list") importFrom("graphics", "abline", "axis", "box", "mtext", "par", "title", "text") importFrom("methods", "is") There are functions from packages utils, stats, grDevices and graphics for which the R checks do not require a specific entry in the Imports: field. I suspect because all of these packages are part of the base R, but so is package methods. The question is why is it not mandatory for those packages to be mentioned in the Imports: field from DESCRIPTION, while removing package methods from that field runs into an error, despite maintaining the package in the NAMESPACE's importFrom().> [...] > There are places in the R source where it is treated specially, > indeed, part of 'methods' may be needed when it is neither > loaded nor attached (e.g., when R runs with only base, say, and > suddenly encounters an S4 object), and there still are > situations where 'methods' needs to be in the search() path and > not just loaded, but these cases should be unrelated to the > above DESCRIPTION-Imports vs NAMESPACE-Imports correspondence.This is what I had expected myself, then the above behavior has to have another explanation. It is just a curiosity, there is naturally nothing wrong with maintaining package methods in the Imports: field. Only odd why some base R packages are treated differently than other base R packages, at the package checks stage. Thank you, Adrian -- Adrian Dusa University of Bucharest Romanian Social Data Archive Soseaua Panduri nr. 90-92 050663 Bucharest sector 5 Romania https://adriandusa.eu [[alternative HTML version deleted]]