On 12/28/2012 11:01 AM, Jesper Gådin 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!
For what it's worth I do
mkdir src/
cd src
svn checkout https://svn.r-project.org/R/trunk/ R-devel
R-devel/tools/rsync-recommended
cd ../
mkdir -p bin/R-devel
cd bin/R-devel
~/src/R-devel/configure && make -j
This is my interpretation of RShowDoc("R-admin"). Should not be any need to
specify type="source" on linux.
Martin
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 <mtmor...@fhcrc.org
<mailto: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>
<mailto: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
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