[Bioc-devel] Add OrgDb class to slot, warning during build
On Fri, Dec 28, 2012 at 12:29 PM, Jesper G?din <jesper.gadin at 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 <dtenenba at fhcrc.org> wrote:
On Fri, Dec 28, 2012 at 11:01 AM, Jesper G?din <jesper.gadin at 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 <mtmorgan at fhcrc.org> wrote:
On 12/23/2012 05:07 PM, Jesper G?din 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 at fhcrc.org
<mailto:mtmorgan at fhcrc.org>> wrote:
Hi Jesper --
On 12/22/2012 05:09 PM, Jesper G?din 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
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