[Bioc-devel] Add OrgDb class to slot, warning during build
Dan Tenenbaum
dtenenba at fhcrc.org
Thu Jan 3 08:17:43 CET 2013
On Fri, Dec 28, 2012 at 11:31 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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
>>
Sorry, I steered you wrong earlier.
As I mentioned elsewhere on this list:
RConverters.h has been removed from R-devel in recent days.
Biobase 2.19.2 no longer refers to this file. You can check it out from svn
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase/
(login: readonly/readonly)
Or install it with biocLite("Biobase") after 10:30AM Seattle time on Friday.
Thanks,
Dan
>> 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]]
>>>>
>>>>
>>>>
>>>> ______________________________**___________________
>>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.**org<Bioc-devel at r-project.org>>
>>>> mailing list
>>>> https://stat.ethz.ch/mailman/_**_listinfo/bioc-devel<https://stat.ethz.ch/mailman/__listinfo/bioc-devel>
>>>>
>>>> <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 <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
>>>
>>
>> [[alternative HTML version deleted]]
>>
>>
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