[Bioc-devel] Add OrgDb class to slot, warning during build
Dan Tenenbaum
dtenenba at fhcrc.org
Fri Dec 28 20:31:46 CET 2012
On Fri, Dec 28, 2012 at 11:01 AM, Jesper Gådin <jesper.gadin at gmail.com> wrote:
> After some fighting I have now the bleeding edge of R and the bioconductor
> packages, and my own package was installed without any errors. Perfect!
>
> Even if I finally got everything to work I get this error worth mentioning:
>
>>biocLite("Biobase", type="source")
>
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.9.6), R version 3.0.0.
> Installing package(s) 'Biobase'
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/src/contrib/Biobase_2.19.1.tar.gz
> '
> Content type 'application/x-gzip' length 1845259 bytes (1.8 Mb)
> opened URL
> ==================================================
> downloaded 1.8 Mb
>
> * installing *source* package ‘Biobase’ ...
> ** libs
> gcc -std=gnu99 -I/home/<somepath>/r-devel/include -DNDEBUG
> -I/usr/local/include -fpic -g -O2 -c Rinit.c -o Rinit.o
> Rinit.c:3:31: fatal error: R_ext/RConverters.h: No such file or directory
> compilation terminated.
> make: *** [Rinit.o] Error 1
> ERROR: compilation failed for package ‘Biobase’
> * removing ‘/home/<somepath>/r-devel/library/Biobase’
> * restoring previous ‘/home/<somepath>/r-devel/library/Biobase’
>
Hmm, this does seem somehow broken, Does the file
$R_HOME/include/R_ext/RConverters.h
exist?
Are you using the same version of R interactively as you are on the
command line (rdev)? If not, does this work when you do?
Dan
> Instead I can install Biobase source by,
> #"rdev" is my alias for r-devel
>> rdev CMD INSTALL Biobase -l $R_DEV_LIB
>
> This is somehow weird...
>
> /Jesper
>
>> sessionInfo()
> R Under development (unstable) (2012-12-28 r61466)
> 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_1.3.1
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.21.9 Biobase_2.19.1 BiocGenerics_0.5.6
> [4] biomaRt_2.15.0 Biostrings_2.27.8 bitops_1.0-5
> [7] BSgenome_1.27.1 DBI_0.2-5 GenomicFeatures_1.11.5
> [10] GenomicRanges_1.11.20 IRanges_1.17.23 parallel_3.0.0
> [13] RCurl_1.95-3 Rsamtools_1.11.14 RSQLite_0.11.2
> [16] rtracklayer_1.19.6 stats4_3.0.0 tools_3.0.0
> [19] XML_3.95-0.1 zlibbioc_1.5.0
>
>
>
> On Mon, Dec 24, 2012 at 2:18 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>
>> On 12/23/2012 05:07 PM, Jesper Gådin wrote:
>>
>>> 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)
>>>
>>
>> You'll need to use R-devel aka R-3.0; this will likely mean 'starting from
>> scratch' with installing bioc packages, so they'll all then be up-to-date
>> and most (all?) of these warnings will go away. Right now, you have a mix
>> of 'devel' and release Bioc packages (note the even (release) and odd
>> (devel) 'y' part of the x.y.z version numbers in your Bioc packages), which
>> is a recipe for disaster. Some of the warnings might persist, but that's
>> life in the devel lanes -- there is some code re-organization going on at
>> the moment, and things may be in a temporary state of flux.
>>
>> Martin
>>
>> 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 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]]
>>>
>>>
>>>
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>>> >
>>>
>>>
>>>
>>> --
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
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>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793 <tel:%28206%29%20667-2793>
>>>
>>>
>>>
>>
>> --
>> 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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