[Bioc-devel] Add OrgDb class to slot, warning during build

Thanks!

That helped the problem with the OrgDb warning. Unfortunately when I installed
the devel AnnotationDbi and BiocGenerics, I got around 40 other warnings during
the R CMD INSTALL , looking like this:

** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
   A specification for S3 class ?AsIs? in package ?IRanges? seems equivalent to
one from package ?BiocGenerics? and is not turning on duplicate class
definitions for this class
Warning: multiple methods tables found for ?sort?
Warning: multiple methods tables found for ?rank?
Warning: multiple methods tables found for ?as.data.frame?
Warning: multiple methods tables found for ?unlist?
Warning: multiple methods tables found for ?match?
Warning: replacing previous import ?.__C__AsIs? when loading ?IRanges?
Warning: replacing previous import ?as.data.frame? when loading ?IRanges?
Warning: replacing previous import ?match? when loading ?IRanges?
Warning: replacing previous import ?rank? when loading ?IRanges?
...
...

Can it be helped? And am very curious also to why all these warnings?

Jesper

NEW SESSIONINFO

 > sessionInfo()

R version 2.15.1 (2012-06-22)

Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] basicASE_1.3

loaded via a namespace (and not attached):
  [1] AnnotationDbi_1.21.9  Biobase_2.16.0        BiocGenerics_0.5.6
  [4] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-5
  [7] BSgenome_1.24.0       DBI_0.2-5             GenomicFeatures_1.8.3
[10] GenomicRanges_1.8.13  IRanges_1.14.4        parallel_2.15.1
[13] RCurl_1.95-3          Rsamtools_1.8.6       RSQLite_0.11.2
[16] rtracklayer_1.16.3    stats4_2.15.1         tools_2.15.1
[19] XML_3.95-0.1          zlibbioc_1.2.0

 >

On Sun, Dec 23, 2012 at 8:06 AM, Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>> wrote:

    Hi Jesper --


    On 12/22/2012 05:09 PM, Jesper G?din wrote:

        Hello all,

        #I have been attempting to create a slot in my own class foo that is
        supposed to contain an OrgDb object from the AnnotationDbi-package.
        Actually it works, but during my build I get this warning:

        ** R
        ** inst
        ** preparing package for lazy loading
        Warning: Class "OrgDb" is defined (with package slot ?AnnotationDbi?) but
        no metadata object found to revise superClass information---not exported?
        Making a copy in package fooPackage

        #Below the parts of the code that may be relevant to solve the problem.
        #My AllClasses file contain these lines:
        setClassUnion("OrgDbOrNULL", c("OrgDb","NULL"))
        setClass("foo",representation(

                      OrgDb="OrgDbOrNULL",
                      TxDbUCSC="TranscriptDbOrNULL"

                      )
        )

        #My NAMESPACE file contain these lines:
        importClassesFrom(__AnnotationDbi, AnnotationDb)
        importClassesFrom(__GenomicFeatures, TranscriptDb)

        #My DESCRIPTION file contain these lines:
        Depends: R (>= 2.15.1), AnnotationDbi
        Imports: methods, BiocGenerics, IRanges, GenomicRanges, GenomicFeatures,
        Rsamtools, AnnotationDbi


        #To add the TranscriptDb works perfectly(no warnings during build), but not
        the AnnotationDb. I have looked at the source code for AnnotationDb and
        realized it has reference classes. This might be causing the warning during
        build, of the reason that I cannot import the OrgDb class in NAMESPACE, and
        that because it is not exported from AnnotationDbi. Thought putting it in
        the Depends field in the DESCRIPTION would help, but it did not,
        unfortunately. All kinds of help is appreciated.


    Thanks for reporting this. I have updated AnnotationDbi to export the OrgDb
    class. This is in AnnotationDbi 1.21.9, in the 'devel' version of
    Bioconductor (available when using the devel version of R). Version 1.21.9
    will be available with biocLite after about 10am PST Monday.

    You will also need to add

       importClassesFrom(__AnnotationDbi, AnnotationDb, OrgDb)

    to your NAMESAPCE.

    Best,

    Martin


        Sincerely,
        Jesper


            sessionInfo()

        R version 2.15.1 (2012-06-22)
        Platform: x86_64-unknown-linux-gnu (64-bit)

        locale:
           [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
           [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
           [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
           [7] LC_PAPER=C                 LC_NAME=C
           [9] LC_ADDRESS=C               LC_TELEPHONE=C
        [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

        attached base packages:
        [1] stats     graphics  grDevices utils     datasets  methods   base

        other attached packages:
        [1] basicASE_1.3         AnnotationDbi_1.18.4 Biobase_2.16.0
        [4] BiocGenerics_0.2.0

        loaded via a namespace (and not attached):
           [1] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-5
           [4] BSgenome_1.24.0       DBI_0.2-5             GenomicFeatures_1.8.3
           [7] GenomicRanges_1.8.13  IRanges_1.14.4        RCurl_1.95-3
        [10] Rsamtools_1.8.6       RSQLite_0.11.2        rtracklayer_1.16.3
        [13] stats4_2.15.1         tools_2.15.1          XML_3.95-0.1
        [16] zlibbioc_1.2.0

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