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 <mtmorgan@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@fhcrc.org
>> <mailto:mtmorgan@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
>>         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
>

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