Thanks !
Am away from office the following 10 days, but will follow your advice when
back, and hopefully everything will then work as intended.
Jesper
On Thu, Jan 3, 2013 at 7:17 AM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:
> On Fri, Dec 28, 2012 at 11:31 AM, Dan Tenenbaum <dtene...@fhcrc.org>
> wrote:
> > On Fri, Dec 28, 2012 at 11:01 AM, Jesper Gådin <jesper.ga...@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 <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
> >>>> 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]]
> >>
> >>
> >> _______________________________________________
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
>
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