2 quick questions 1) So I recent decided to stick with the subversion R2.10 and to recompile weekly and use BioC2.5. (linux-ubuntu) Sometimes, as I guess maybe expected, I get errors in various libraries .... Not sure is that is a "Good idea" or what others do.. Dumb question, is there a different mailing list where these errors should be reported or are those reported here ... given they are on the development version.... 2) PS I have an irritating problem with tcltk... does anyone with ubuntu know if the tcl8.5 and tcl8.5-dev libraries are all that should are required to fix this? pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages $ /home/pleo/R_latest/bin/R CMD INSTALL --clean tcltk2_1.0-8.tar.gz * installing to library ?/home/pleo/R_latest/library? * installing *source* package ?tcltk2? ... ** R ** inst ** preparing package for lazy loading Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error : package 'tcltk' could not be loaded ERROR: lazy loading failed for package ?tcltk2? * removing ?/home/pleo/R_latest/library/tcltk2? pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages$ R version 2.10.0 Under development (unstable) (2009-05-24 r48603) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.1.0 lattice_0.17-25 MASS_7.3-0 loaded via a namespace (and not attached): [1] grid_2.10.0 RCurl_0.95-1 tools_2.10.0 XML_2.3-0

Dear Paul, Regarding you 2nd question, I believe you should also install tk8.5 and tk8.5- dev in addition to the tcl packages. Hope this fixes your problem. Laurent On Monday 25 May 2009 08:21:14 am Paul Leo wrote: > 2 quick questions > > 1) > So I recent decided to stick with the subversion R2.10 and to recompile > weekly and use BioC2.5. (linux-ubuntu) Sometimes, as I guess maybe > expected, I get errors in various libraries .... Not sure is that is a > "Good idea" or what others do.. > > Dumb question, is there a different mailing list where these errors > should be reported or are those reported here ... given they are on the > development version.... > > 2) > PS I have an irritating problem with tcltk... > does anyone with ubuntu know if the tcl8.5 and tcl8.5-dev libraries are > all that should are required to fix this? > > pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages > $ /home/pleo/R_latest/bin/R CMD INSTALL --clean tcltk2_1.0-8.tar.gz > * installing to library ?/home/pleo/R_latest/library? > * installing *source* package ?tcltk2? ... > ** R > ** inst > ** preparing package for lazy loading > Error in firstlib(which.lib.loc, package) : > Tcl/Tk support is not available on this system > Error : package 'tcltk' could not be loaded > ERROR: lazy loading failed for package ?tcltk2? > * removing ?/home/pleo/R_latest/library/tcltk2? > pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages$ > > > > > > R version 2.10.0 Under development (unstable) (2009-05-24 r48603) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] biomaRt_2.1.0 lattice_0.17-25 MASS_7.3-0 > > loaded via a namespace (and not attached): > [1] grid_2.10.0 RCurl_0.95-1 tools_2.10.0 XML_2.3-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

Paul, To address your first issue, the choice of (stable) release quality vs. (unstable) development quality software depends on circumstance. The former tends to be recommended for end users who would like to use established portions of the software or need to be able to audit their analyses. The latter tends to be recommended for end users who would like to use parts of the software that is undergoing active development or developers who are working on software components of their own for the next release. In general, you should contact the package maintainer if you find any issues with their packages in BioC 2.5 (devel). Just make sure you follow the standard reporting procedure: 1) ensure you are using the latest version of their package and its dependencies, 2) provide a reproducible example, and 3) supply a printout of the sessionInfo(). If you are using the relatively new sequence analysis infrastructure (IRanges/Biostrings/BSgenome/ShortRead/etc.) and believe there is an issue of debate over what has been implemented and what you consider to be best practices, you can post your issue to the Bioc-sig-seq mailing list. A number of BioC developers are striving to make Bioconductor as prominent in the sequence analyses space as it is in the microarray analyses space and the more user feedback we get, the stronger our offering can be. Patrick Quoting Paul Leo <p.leo at="" uq.edu.au="">: > 2 quick questions > > 1) > So I recent decided to stick with the subversion R2.10 and to recompile > weekly and use BioC2.5. (linux-ubuntu) Sometimes, as I guess maybe > expected, I get errors in various libraries .... Not sure is that is a > "Good idea" or what others do.. > > Dumb question, is there a different mailing list where these errors > should be reported or are those reported here ... given they are on the > development version.... > > 2) > PS I have an irritating problem with tcltk... > does anyone with ubuntu know if the tcl8.5 and tcl8.5-dev libraries are > all that should are required to fix this? > > pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages > $ /home/pleo/R_latest/bin/R CMD INSTALL --clean tcltk2_1.0-8.tar.gz > * installing to library ?/home/pleo/R_latest/library? > * installing *source* package ?tcltk2? ... > ** R > ** inst > ** preparing package for lazy loading > Error in firstlib(which.lib.loc, package) : > Tcl/Tk support is not available on this system > Error : package 'tcltk' could not be loaded > ERROR: lazy loading failed for package ?tcltk2? > * removing ?/home/pleo/R_latest/library/tcltk2? > pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages$ > > > > > > R version 2.10.0 Under development (unstable) (2009-05-24 r48603) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] biomaRt_2.1.0 lattice_0.17-25 MASS_7.3-0 > > loaded via a namespace (and not attached): > [1] grid_2.10.0 RCurl_0.95-1 tools_2.10.0 XML_2.3-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Paul, Paul Leo wrote: > 2 quick questions > > 1) > So I recent decided to stick with the subversion R2.10 and to recompile > weekly and use BioC2.5. (linux-ubuntu) Sometimes, as I guess maybe > expected, I get errors in various libraries .... Not sure is that is a > "Good idea" or what others do.. > > Dumb question, is there a different mailing list where these errors > should be reported or are those reported here ... given they are on the > development version.... > > 2) > PS I have an irritating problem with tcltk... > does anyone with ubuntu know if the tcl8.5 and tcl8.5-dev libraries are > all that should are required to fix this? > > pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages > $ /home/pleo/R_latest/bin/R CMD INSTALL --clean tcltk2_1.0-8.tar.gz Note that it's almost always a bad idea to install packages this way. For Bioconductor packages, we highly recommend you use biocLite() as explained here: http://bioconductor.org/docs/install/ This method will handle the dependencies for you -- and BioC packages tend to have a lot! (Note that biocLite() also works for installing CRAN packages.) Otherwise I confirm what Laurent Gatto said before: you need tk-dev on Ubuntu. After you've installed it, you need to reinstall R (configure + make). Don't forget to include the recommended packages (I think tcltk is one of them) before you do 'configure + make'. There is no need to install tcltk2_1.0-8.tar.gz separately. When you are done, start R and check capabilities(). Then library(tcltk)... Cheers, H. > * installing to library ?/home/pleo/R_latest/library? > * installing *source* package ?tcltk2? ... > ** R > ** inst > ** preparing package for lazy loading > Error in firstlib(which.lib.loc, package) : > Tcl/Tk support is not available on this system > Error : package 'tcltk' could not be loaded > ERROR: lazy loading failed for package ?tcltk2? > * removing ?/home/pleo/R_latest/library/tcltk2? > pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages$ > > > > > > R version 2.10.0 Under development (unstable) (2009-05-24 r48603) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] biomaRt_2.1.0 lattice_0.17-25 MASS_7.3-0 > > loaded via a namespace (and not attached): > [1] grid_2.10.0 RCurl_0.95-1 tools_2.10.0 XML_2.3-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319