[Bioc-devel] help with imports for new package and other questions

Hi Lorena,

In your particular case it seems to me that you're using dplyr
internally for convenient data frame transformations (nothing that
couldn't be done with plain R BTW), and that you're only using a few
dplyr symbols for this. The codetoolsBioC package could be useful to
help you identify these things and import them selectively. It seems
to me that these things are: %>%, group_by, filter, and summarise,
but I could be missing some. OTOH your package defines the IsomirDataSeq
class which extends the SummarizedExperiment class, and thus relies
largely on the GenomicRanges/SummarizedExperiment infrastructure.
So I would highly recommend that you *fully* import BiocGenerics,
S4Vectors, IRanges, and SummarizedExperiment. That will make the
maintenance of your NAMESPACE file much easier in the long run than
importing selectively from these packages.

I also remember seeing selective imports from the methods package
in NAMESPACE files generated with codetoolsBioC. Unless there is a
good reason for doing so, these should be avoided and the methods
package fully imported.

Cheers,
H.

On 08/14/2015 06:57 AM, Lo wrote:

Hi,

I am trying to get right my new package
(http://github.com/lpantano/isomiRs). But I am having some problems with
the packages I import.

The main problem is that I get warnings while loading my packages
because some dplyr replaces functions in others packages like S4Vectors
and others.

This is my NAMESPACE

import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomicRanges)
import(SummarizedExperiment)
import(dplyr)
importFrom(plyr, join_all)
import(DESeq2)
import(methods)
import(RColorBrewer)
import(gplots)
import(ggplot2)
import(GGally)
import(DiscriMiner)

and these are the warnings:

** preparing package for lazy loading
Warning: replacing previous import by ?dplyr::slice? when loading 
?isomiRs?
Warning: replacing previous import by ?dplyr::collapse? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::intersect? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::setdiff? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::union? when loading 
?isomiRs?
Warning: replacing previous import by ?dplyr::rename? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::combine? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::desc? when loading 
?isomiRs?
Warning: replacing previous import by ?gplots::space? when loading
?isomiRs?
** help


I need to solve this to avoid warnings. I tried something like use
`importFrom` to only import some functions but don't know if importFrom
is something I shouldn't use or I should.

I would also appreciate very much if some one can point me to the right
way to solve the following:

* I failed to create good documentation for some functions, data of my
package. Can anyone point me to a good example of a dataset
documentation, so I could create a good one for my dataset example.

* I have some problems with my coding style, like sometimes I have `=`
insted of `<-` and I forgot to add spaces like this ` <- `. Any one
knows of a plugin for any editor to help me find that. Because I am
always missing some of them by eye.

Thanks a lot in advance for any help in any point.

Lorena