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 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel