On Fri, Dec 28, 2012 at 11:31 AM, 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 >>
Sorry, I steered you wrong earlier. As I mentioned elsewhere on this list: RConverters.h has been removed from R-devel in recent days. Biobase 2.19.2 no longer refers to this file. You can check it out from svn https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase/ (login: readonly/readonly) Or install it with biocLite("Biobase") after 10:30AM Seattle time on Friday. Thanks, Dan >> 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