[Bioc-devel] BiocGenerics attach when GenomicFeatures imported

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
<mailto: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, Herv? Pag?s <hpages at fredhutch.org
<mailto:hpages at fredhutch.org>> wrote:

    Hi Marcin,

    On 10/19/2015 05:11 AM, Marcin Cie?lik 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?:
        ....

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