Hi Dan,
Actually my $R_HOME is empty. But even if I would set $R_HOME to r-devel
directory the include/R_ext/ does not contain RConverters.h (only the files
specified below are present)
/R_ext$ 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]]
> >
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
