Hi Patrick, Thanks for your reply. I have install the latest Biostrings (2.15.21), rtracklayer (1.7.4), ShortRead (1.5.15), IRanges (1.5.46), BSgenome (1.15.4) and Biostrings (2.15.21) packages and I sill received the same error message when I tried to install Rsamtools. I have also tried it with the packages directly from the SVN account (rtracklayer 1.7.9,....) but there is still too many error that appeared.
If you have any other ideas (platform, version, 64 bit ...), please let me know? Thanks Arnaud. > sessionInfo() R version 2.11.0 Under development (unstable) (2009-10-20 r50178) i386-apple-darwin10.0.0 locale: [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.7.4 RCurl_1.2-1 bitops_1.0-4.1 ShortRead_1.5.15 [5] lattice_0.17-26 BSgenome_1.15.4 Biostrings_2.15.21 IRanges_1.5.46 loaded via a namespace (and not attached): [1] Biobase_2.5.8 grid_2.11.0 hwriter_1.1 tools_2.11.0 XML_2.6-0 On 10-02-17 12:26 PM, "Patrick Aboyoun" <[email protected]> wrote: Arnaud, There have been some changes in how Biostrings, rtracklayer, (and maybe ShortRead?) are working with connections. If you grab the latest update for these three packages, this problem should be solved. Patrick On 2/17/10 7:45 AM, Droit Arnaud wrote: > Dear all, > > I have read about Rsamtools being in dev repositories and I would like to try > it. > My working environment is Snow Leopard 64 bit and R version 2.11 (see the > SessionInfo at the end). When I try to install it, I have the following error > message : > > Attaching package: 'IRanges' > The following object(s) are masked from package:base : > > Map, > cbind, > mapply, > order, > pmax, > pmax.int, > pmin, > pmin.int, > rbind, > rep.int, > table > > Error in importIntoEnv(impenv, impnames, ns, impvars) : > objects ''.__C__file', '.__C__connection'' are not exported by > 'namespace:Biostrings' > ERROR: lazy loading failed for package 'Rsamtools' > > * removing '/Library/Frameworks/R.framework/Resources/library/Rsamtools' > > Does anyone have some idea about this problem ? > > Thanks > > Arnaud. > > >> sessionInfo() >> > R version 2.11.0 Under development (unstable) (2009-10-20 r50178) > i386-apple-darwin10.0.0 > > locale: > [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.3.41 lattice_0.17-26 BSgenome_1.15.4 > Biostrings_2.15.21 > [5] IRanges_1.5.46 > > loaded via a namespace (and not attached): > [1] Biobase_2.5.8 grid_2.11.0 hwriter_1.1 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
