Thanks a lot Hervé.
Your suggestions are perfect. I fully imported these classes because I
realized that it would be less chances of errors, as you say here.
I used that, and it is true that I am using these functions for dplyr.
The reason I tried to do with dplyr is was to summarize quicker.
Previously I was using data.table. I will just import the used functions
for dplyr, since, as you say, I am not using many functions.
Thanks for your help, really appreciate it.
On 08/17/2015 03:19 PM, Hervé Pagès wrote:
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
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