Oops. Yes, I should be using devel all the time. Thanks much, I had already started spelunking in Biostrings, this will save me time. On Fri, Jun 29, 2012 at 1:42 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Looks like you are mixing and matching release and devel packages > (AnnotationDbi_1.19.15 is a devel package). > This can lead to unpredictable results. > You can either maintain two separate R installations for release and > devel, or maintain one but use the technique described here: > > http://bioconductor.org/developers/useDevel/ > > Dan > > > On Fri, Jun 29, 2012 at 1:24 PM, Tim Triche, Jr. <tim.triche@gmail.com> > wrote: > > Installing package(s) 'GenomicFeatures' > > trying URL ' > > > http://www.bioconductor.org/packages/2.10/bioc/src/contrib/GenomicFe atures_1.8.2.tar.gz > > ' > > Content type 'application/x-gzip' length 1745766 bytes (1.7 Mb) > > opened URL > > ================================================== > > downloaded 1.7 Mb > > > > * installing *source* package ‘GenomicFeatures’ ... > > ** R > > ** inst > > ** preparing package for lazy loading > > Error : object ‘readDNAStringSet’ is not exported by > 'namespace:Biostrings' > > ERROR: lazy loading failed for package ‘GenomicFeatures’ > > * removing ‘/usr/lib64/R/library/GenomicFeatures’ > > * restoring previous ‘/usr/lib64/R/library/GenomicFeatures’ > > > > The downloaded source packages are in > > ‘/tmp/Rtmp3aHGQx/downloaded_packages’ > > Updating HTML index of packages in '.Library' > > Making packages.html ... done > > > > sessionInfo(): > > > > R> sessionInfo() > > R version 2.15.0 (2012-03-30) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > > LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 > > LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices datasets utils methods base > > > > other attached packages: > > [1] AnnotationDbi_1.19.15 GenomicRanges_1.9.28 IRanges_1.15.15 > > matrixStats_0.5.0 MASS_7.3-19 methylumi_2.3.4 > > ggplot2_0.9.1 > > [8] reshape2_1.2.1 scales_0.2.1 Biobase_2.17.6 > > BiocGenerics_0.3.0 BiocInstaller_1.4.7 dataframe_2.5 > > devtools_0.7 > > [15] gtools_2.7.0 > > > > loaded via a namespace (and not attached): > > [1] annotate_1.35.2 biomaRt_2.13.1 Biostrings_2.24.1 > > colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 > > grid_2.15.0 httr_0.1.1 > > [10] labeling_0.1 lattice_0.20-6 memoise_0.1 munsell_0.3 > > plyr_1.7.1 proto_0.3-9.2 R.methodsS3_1.4.2 > > RColorBrewer_1.0-5 RCurl_1.91-1 > > [19] RSQLite_0.11.1 stats4_2.15.0 stringr_0.6 > tools_2.15.0 > > XML_3.9-4 xtable_1.7-0 zlibbioc_1.3.0 > > > > > > -- > > *A model is a lie that helps you see the truth.* > > * > > * > > Howard Skipper< > http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

Followup: useDevel() fixed the problem. Thanks! On Fri, Jun 29, 2012 at 1:42 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Looks like you are mixing and matching release and devel packages > (AnnotationDbi_1.19.15 is a devel package). > This can lead to unpredictable results. > You can either maintain two separate R installations for release and > devel, or maintain one but use the technique described here: > > http://bioconductor.org/developers/useDevel/ > > Dan > > > On Fri, Jun 29, 2012 at 1:24 PM, Tim Triche, Jr. <tim.triche@gmail.com> > wrote: > > Installing package(s) 'GenomicFeatures' > > trying URL ' > > > http://www.bioconductor.org/packages/2.10/bioc/src/contrib/GenomicFe atures_1.8.2.tar.gz > > ' > > Content type 'application/x-gzip' length 1745766 bytes (1.7 Mb) > > opened URL > > ================================================== > > downloaded 1.7 Mb > > > > * installing *source* package ‘GenomicFeatures’ ... > > ** R > > ** inst > > ** preparing package for lazy loading > > Error : object ‘readDNAStringSet’ is not exported by > 'namespace:Biostrings' > > ERROR: lazy loading failed for package ‘GenomicFeatures’ > > * removing ‘/usr/lib64/R/library/GenomicFeatures’ > > * restoring previous ‘/usr/lib64/R/library/GenomicFeatures’ > > > > The downloaded source packages are in > > ‘/tmp/Rtmp3aHGQx/downloaded_packages’ > > Updating HTML index of packages in '.Library' > > Making packages.html ... done > > > > sessionInfo(): > > > > R> sessionInfo() > > R version 2.15.0 (2012-03-30) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > > LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 > > LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices datasets utils methods base > > > > other attached packages: > > [1] AnnotationDbi_1.19.15 GenomicRanges_1.9.28 IRanges_1.15.15 > > matrixStats_0.5.0 MASS_7.3-19 methylumi_2.3.4 > > ggplot2_0.9.1 > > [8] reshape2_1.2.1 scales_0.2.1 Biobase_2.17.6 > > BiocGenerics_0.3.0 BiocInstaller_1.4.7 dataframe_2.5 > > devtools_0.7 > > [15] gtools_2.7.0 > > > > loaded via a namespace (and not attached): > > [1] annotate_1.35.2 biomaRt_2.13.1 Biostrings_2.24.1 > > colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 > > grid_2.15.0 httr_0.1.1 > > [10] labeling_0.1 lattice_0.20-6 memoise_0.1 munsell_0.3 > > plyr_1.7.1 proto_0.3-9.2 R.methodsS3_1.4.2 > > RColorBrewer_1.0-5 RCurl_1.91-1 > > [19] RSQLite_0.11.1 stats4_2.15.0 stringr_0.6 > tools_2.15.0 > > XML_3.9-4 xtable_1.7-0 zlibbioc_1.3.0 > > > > > > -- > > *A model is a lie that helps you see the truth.* > > * > > * > > Howard Skipper< > http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]