[Bioc-devel] Add OrgDb class to slot, warning during build
Martin Morgan
mtmorgan at fhcrc.org
Tue Jan 1 23:11:55 CET 2013
On 12/28/2012 11:01 AM, Jesper Gådin 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!
For what it's worth I do
mkdir src/
cd src
svn checkout https://svn.r-project.org/R/trunk/ R-devel
R-devel/tools/rsync-recommended
cd ../
mkdir -p bin/R-devel
cd bin/R-devel
~/src/R-devel/configure && make -j
This is my interpretation of RShowDoc("R-admin"). Should not be any need to
specify type="source" on linux.
Martin
>
> 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’
>
> 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
> <mailto: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>
> <mailto: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.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793 <tel:%28206%29%20667-2793>
> <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 <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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