[Bioc-devel] BiocGenerics attach when GenomicFeatures imported

[Marcin Cieślik]

Dear Herve,

Thank you for your response and apologies for not being sufficiently clear.

> Are you saying that before you add that call, when you install and load
your package BiocGenerics doesn't get attached (only
loaded via a namespace), but after you add the call to genes() and
re-install and re-load your package, BiocGenerics now gets attached?
I would be surprised if that was the case.

Almost, BiocGenerics is loaded via namespace when I load my package. When I
call a function (att from my package) that calls genes() the BiocGeneris
are attached.

1. By use the genes function I mean calling the genes function by a
function from the package I am developing. In the example package this is:

att <- function() {
    # this works fine no impicit "attach"
    txdb <- makeTxDbFromGFF(system.file("extdata", "test.gtf",
package="attch"))
    # this cause an implicit attach
    gen <- genes(txdb)
}

2. file contents:

DESCRIPTION
Package: attch
Title: What the Package Does (one line, title case)
Version: 0.0.0.9000
Authors at R: person("First", "Last", email = "first.last at example.com", role =
c("aut", "cre"))
Description: What the package does (one paragraph).
Depends:
 R (>= 3.2.0)
Imports:
 IRanges,
 GenomeInfoDb,
 GenomicRanges,
 GenomicFeatures,
 Biostrings,
 rtracklayer
License: What license is it under?
LazyData: true

NAMESPACE
# Generated by roxygen2 (4.1.1): do not edit by hand
export(att)
import(GenomicFeatures)

3. None of the reasons you listed as causing an implicit attach seems to
apply here.

Thanks,
Marcin



On Mon, Oct 19, 2015 at 5:56 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Marcin,
>
> On 10/19/2015 05:11 AM, Marcin Cieślik wrote:
>
>> Dear Bioc Developers,
>>
>> I am developing a package that depends on GenomicFeatures which I am
>> adding
>> to my package using Imports: and import(GenomicFeatures). However, when I
>> use the "genes" function the "BiocGenerics" package gets attached (I am
>> not
>> adding BiocGenerics to my Depends:).
>>
>
> Not sure exactly what you mean by "use the genes() function". Do you
> mean when you add an internal call to genes() in one of the functions
> of your package? Are you saying that before you add that call, when you
> install and load your package BiocGenerics doesn't get attached (only
> loaded via a namespace), but after you add the call to genes() and
> re-install and re-load your package, BiocGenerics now gets attached?
> I would be surprised if that was the case.
>
> However, if by "use the genes() function" you mean use the genes()
> function in an example or in the vignette then running the example or
> the code in the vignette will necessarily attach GenomicFeatures and
> consequently BiocGenerics (which GenomicFeatures depends on via the
> Depends field).
>
> Please clarify in which context you "use the genes() function". Also
> please show your DESCRIPTION file.
>
>
>> Am I missing something? Why would a package be non-explicitly attached?
>>
>
> There could be several reasons for that:
>
> - your package could depend (via the Depends field) on a package that
>   depends itself (via the Depends field again) directly or indirectly
>   on BiocGenerics
>
> - one of the functions in your package could use an explicit call
>   to library() or require() to attach a package that depends directly
>   or indirectly (via the Depends field) on BiocGenerics
>
> - not sure what happens exactly if your package contains a dataset
>   that is a serialized instance of a class defined in a package
>   that depends directly or indirectly (via the Depends field) on
>   BiocGenerics, but that could be another reason or at least something
>   to investigate
>
> Hard to know exactly what's going on in your case without more
> information.
>
> Thanks,
> H.
>
>
>> Yours,
>> Marcin
>>
>> A tiny hopefully reproducible example:
>>
>> download package:
>> https://drive.google.com/open?id=0B_OomVx_ca5wcEVmR3JVMWp5YTA
>> R CMD INSTALL /mctp/users/mcieslik/attch_0.0.0.9000.tar.gz
>> from R:
>> library(attch)
>> att()
>> Attaching package: ‘BiocGenerics’
>>
>> The following objects are masked from ‘package:parallel’:
>> ....
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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