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
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 <mtmor...@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 <mtmor...@fhcrc.org
>> <mailto: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
>> <mailto:Bioc-devel@r-project.**org<Bioc-devel@r-project.org>>
>> mailing list
>>
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>>
>>
>> <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
>
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