On Fri, Dec 28, 2012 at 12:29 PM, Jesper Gådin <jesper.ga...@gmail.com> wrote:
> Hi Dan,
>
> Actually my $R_HOME is empty. But even if I would set $R_HOME to r-devel
> directory the include/R_ext/ does not contain RConverters.h (only the files
> specified below are present)
>
R_HOME is set by R. So you find out its value from within R, for example:
Sys.getenv("R_HOME")
Try this from your various R installations.
It appears that R was not installed correctly. The file RConverters.h
should be present. How did you install R? Might want to try again.
Dan
> /R_ext$ ls
> Applic.h
> Arith.h
> BLAS.h
> Boolean.h
> Callbacks.h
> Complex.h
> Constants.h
> Error.h
> GetX11Image.h
> GraphicsDevice.h
> GraphicsEngine.h
> Lapack.h
> Linpack.h
> MathThreads.h
> Memory.h
> QuartzDevice.h
> Parse.h
> Print.h
> PrtUtil.h
> R-ftp-http.h
> RS.h
> Random.h
> Rdynload.h
> Riconv.h
> RStartup.h
> Utils.h
> eventloop.h
> libextern.h
> rlocale.h
> stats_package.h
> stats_stubs.h
> Visibility.h
>
> Yes I was using the same version of "rdev" interactively as from command
> line.
>
> Notice, that I wasnt allowed to install Biobase from the command line at a
> start, but with these commands after eachother then it worked:
> (1)rdev CMD INSTALL Biobase -l $R_DEV_LIB #error
> (2)R CMD INSTALL Biobase #No error
> (3)R CMD INSTALL Biobase -l $R_DEV_LIB #error
> (4)rdev CMD INSTALL Biobase -l $R_DEV_LIB #no error, same command as in (1)
>
> Also notice that I have the RConverters.h located in
> ~/bin/R-2.15.1/include/R_ext/RConverters.h
> /usr/local/lib64/R/include/R_ext/RConverters.h
> /usr/share/R/include/R_ext/RConverters.h
>
> Hope this helps :)
>
> /Jesper
>
>
> On Fri, Dec 28, 2012 at 8:31 PM, 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
>> >
>> > 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]]
>> >
>> >
>> > _______________________________________________
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>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
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