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 <mtmor...@fhcrc.org> wrote:
> Hi Jesper --
>
>
> On 12/22/2012 05:09 PM, Jesper Gådin 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
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>> ______________________________**_________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/**listinfo/bioc-devel<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>
>>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
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