similar to: R CMD check and missing imports from base packages

On Wed, Apr 29, 2015 at 12:53 PM, Winston Chang <winstonchang1 at gmail.com> wrote: > On Tue, Apr 28, 2015 at 3:04 PM, G?bor Cs?rdi <csardi.gabor at gmail.com> > wrote: > > > > > > E.g. if package 'ggplot2' uses 'stats::density()', and package 'igraph' > > also defines 'density()', and 'igraph' is on the search

> And in general a developer would avoid masking a function > in a base package, so as not to require the user to distinguish > between stats::density() and igraph::density(). Maybe the > example is not meant literally. The 'filter' function in the popular 'dplyr' package masks the one that has been in the stats package forever, and they have nothing in common, so that

On Wed, Apr 29, 2015 at 1:45 PM, Gabriel Becker <gmbecker at ucdavis.edu> wrote: > Gabor, > > To play devil's advocate a bit, why not just have the package formally > import the functions it wants to use (or the whole package if that is > easier)? > This is exactly my goal. And to facilitate this, R CMD check could remind you if you forgot to do the formal import.

Gabor, To play devil's advocate a bit, why not just have the package formally import the functions it wants to use (or the whole package if that is easier)? Also, if your package Depends on another package, instead of importing it (e.g. because the end user will need functions in it in order to meaningfully use your functions), I imagine you *want* to hit symbols in that package before base,

All, Here are two ideas on this: 1. have R CMD check show how every external function reference gets resolved. 2. have R CMD check warn anytime there is a potential name conflict, e.g. density( ) coming from either igraph or stats, and show how it was resolved. Either could be an option. I guess there are potential problems with conditional loading of libraries where a function could be

On 04/28/2015 01:04 PM, G?bor Cs?rdi wrote: > When a symbol in a package is resolved, R looks into the package's > environment, and then into the package's imports environment. Then, if the > symbol is still not resolved, it looks into the base package. So far so > good. > > If still not found, it follows the 'search()' path, starting with the > global

On 04/29/2015 05:38 PM, William Dunlap wrote: >> And in general a developer would avoid masking a function >> in a base package, so as not to require the user to distinguish >> between stats::density() and igraph::density(). Maybe the >> example is not meant literally. > > The 'filter' function in the popular 'dplyr' package masks the one > that has

Dear All, before its latest version my package had 'Imports: Matrix' in its DESCRIPTION file, but it did not import anything in NAMESPACE. Rather, some functions explicitly loaded Matrix, as they needed. The reason for this was that importing Matrix is really slow, and only very few igraph functions need it. (I guess Matrix is slow because of the many registered names, but that is another

Dear R developers, I am seeking advice on some $subject matter. My package will have an update soon, that is not backward compatible with the current version. It will likely break much of the existing code. Many (~50) packages depend on 'igraph' and they, too, will most probably break with the new version. My intended solution is, that I create a snapshot of the current package, under

Hello R Help Team, I have created graph from weighted adjecency matrix .Is there a way I can find highly connected nodes in Igraph like the Package RBGL does. nathan -- View this message in context: http://www.nabble.com/Highly-Connected-Nodes-in-Igraph-tp22377522p22377522.html Sent from the R help mailing list archive at Nabble.com.

Dear all, It is my understanding that using 'importFrom' in the NAMESPACE of a package allows to avoid conflicts between different packages defining objects with identical names. However, I can still see conflicts while loading the package using 'library'. Here is a toy example, with a package 'foo' importing 'as.igraph' from the igraph package, and 'nj'

Hi All, I am not sure why this happens, but apparently an old binary is installed by default. Downloading and installing the new binary by hand works fine. Is this the intended behavior? If yes, may I ask what is the reason for it? Thanks, Gabor > install.packages("igraph") There is a binary version available (and will be installed) but the source version is later:

Hi to all, does anybody knows whether there is a package to plot those http://www.equine-science.de/temp/graph.jpg graphs. the thickness of the points and/or the lines should be represent the numbers of behaviours With kind regards Knut

On Wed, Apr 29, 2015 at 8:12 PM, Paul Gilbert <pgilbert902 at gmail.com> wrote: > > As I recall, several packages mask the simulate generic in stats, if you > are looking for examples. > FWIW, here is a list of base* functions masked** by CRAN packages: https://github.com/gaborcsardi/rfunctions/blob/master/rfunctions.md Look at the long table in the end. simulate indeed comes up

Dear colleagues, I'm trying to have a look at the Assortative and Disassortative ( http://en.wikipedia.org/wiki/Assortative_mixing) of the network I have. But it seems that the igraph hasn't mentioned that yet. I have to get the in/out degree of the vertices of each edge and calculate the Pearson's Correlation coefficient which seems to be quite a huge task for me. :( So I wonder if

I'm trying to draw an arrow with a curved shaft on the graph as a straight one looks messy on a detailed graph. I've looked in arrows but it doesn't seem to give an option. larrows doesn't look much more promising. I had a look in the archive and couldn't find anything. Any thoughts? Thanks Paul -- View this message in context:

I'm getting an R CMD check warning with a package (call it package A) that defines an S3 method but not the generic. The generic is defined in another package (package B). Package A imports the S3 generic from B. And there's one additional detail: the generic overrides a function in the stats package. I've created a minimal test package which reproduces the problem:

On 29/04/2015 1:57 PM, G?bor Cs?rdi wrote: > On Wed, Apr 29, 2015 at 1:45 PM, Gabriel Becker <gmbecker at ucdavis.edu> > wrote: > > > Gabor, > > > > To play devil's advocate a bit, why not just have the package formally > > import the functions it wants to use (or the whole package if that is > > easier)? > > > > This is exactly my

Hi Consider the following graph: x <- rnorm(1000) x <- x + exp(-x/2) layout(matrix(rep(c(1,1,2), 2), 2, 3, byrow=TRUE)) boxplot(x) rug(jitter(x), side=2) plot(density(x)) What I would really like to do is to have the density plot rotated by 90 degrees so that I can see it line up with the rug plot on the side axis. I cant seem to do this. I have seen references to the grid

> On Jun 14, 2017, at 1:53 PM, Rolf Turner <r.turner at auckland.ac.nz> wrote: > > On 15/06/17 05:29, David Winsemius wrote: >>> On Jun 14, 2017, at 10:18 AM, David Winsemius <dwinsemius at comcast.net> wrote: >>> >>> >>>> On Jun 14, 2017, at 9:46 AM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote: >>>>