When I go to Packages & Data, select Package Installer, then choose BioConductor (binaries), then click on Get List. The list is blank. Here is the output from the R console when I do this: trying URL 'http://www.bioconductor.org/bin/macosx/2.1/PACKAGES' Content type 'text/plain; charset=ISO-8859-1' length 15 bytes opened URL ================================================== downloaded 15 bytes Here is the Session Info: > sessionInfo() R version 2.1.0, 2005-05-12, powerpc-apple-darwin7.9.0 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" > When I select BioConductor (sources), I get a full list, but I am unable to install them, Output of R console when I try this option: > Packages are shown, but when I select one and chose install selected, nothing happens. I have also tried: source("http://www.bioconductor.org/getBioC.R") this will download the getBioC functionality into your R session. To install Bioconductor packages, use the function "getBioC" as follows. To download and install the default packages, type: getBioC() I get this output on the console: > getBioC() Running getBioC version 0.2 with R version 2.1.0 http://www.bioconductor.org/scripts/2.1/biocinstall.R Running biocinstall version 0.9 with R version 2.1.0 Warning message: cannot open: HTTP status was '404 Not Found' Warning: unable to access index for repository http:// www.bioconductor.org/packages/bioc/stable/bin/macosx/2.1 Warning message: cannot open: HTTP status was '404 Not Found' Warning: unable to access index for repository http:// www.bioconductor.org/packages/bioc/stable/bin/macosx/2.1 Warning message: cannot open: HTTP status was '404 Not Found' Warning: unable to access index for repository http:// www.bioconductor.org/packages/data/annotation/stable/bin/macosx/2.1 Warning message: cannot open: HTTP status was '404 Not Found' Warning: unable to access index for repository http:// www.bioconductor.org/packages/data/experiment/stable/bin/macosx/2.1 Warning message: cannot open: HTTP status was '404 Not Found' Warning: unable to access index for repository http:// www.bioconductor.org/packages/omegahat/stable/bin/macosx/2.1 Warning message: cannot open: HTTP status was '404 Not Found' Warning: unable to access index for repository http:// www.bioconductor.org/packages/lindsey/stable/bin/macosx/2.1 dependencies ?affy? are not availabledependencies ?affydata? are not availabledependencies ?affyPLM? are not availabledependencies ?annaffy? are not availabledependencies ?annotate? are not availabledependencies ?Biobase? are not availabledependencies ?Biostrings? are not availabledependencies ?DynDoc? are not availabledependencies ?edd? are not availabledependencies ?gcrma? are not availabledependencies ?genefilter? are not availabledependencies ?geneplotter? are not availabledependencies ?hgu95av2? are not availabledependencies ?makecdfenv? are not availabledependencies ?marray? are not availabledependencies ?matchprobes? are not availabledependencies ?multtest? are not availabledependencies ?reposTools? are not availabledependencies ?ROC? are not availabledependencies ?siggenes? are not availabledependencies ?tkWidgets? are not availabledependencies ?vsn? are not availabledependencies ?widgetTools? are not available dependency ?NA? is not available trying URL 'http://cran.fhcrc.org/bin/macosx/2.1/limma_1.9.3.tgz' Content type 'application/x-gzip' length 937214 bytes opened URL ================================================== downloaded 915Kb trying URL 'http://cran.fhcrc.org/bin/macosx/2.1/pamr_1.25.tgz' Content type 'application/x-gzip' length 1272079 bytes opened URL ================================================== downloaded 1242Kb trying URL 'http://cran.fhcrc.org/bin/macosx/2.1/sma_0.5.14.tgz' Content type 'application/x-gzip' length 3178148 bytes opened URL ================================================== downloaded 3103Kb trying URL 'http://cran.fhcrc.org/bin/macosx/2.1/statmod_1.1.0.tgz' Content type 'application/x-gzip' length 79240 bytes opened URL ================================================== downloaded 77Kb trying URL 'http://cran.fhcrc.org/bin/macosx/2.1/xtable_1.2-5.tgz' Content type 'application/x-gzip' length 24732 bytes opened URL ================================================== downloaded 24Kb The downloaded packages are in /tmp/RtmpyzP9yx/downloaded_packages > Packages are being installed at System Level (in R Framework) which is the default setting. Any clues as to what is happening? Chris Kirchberg 2848 Roslyn St., Unit 6 Denver, CO 80238 phone: 1.303.399.1768 mobile: 1.303.618.5545 cjkirchberg@gmail.com

Hi Chris, Chris Kirchberg <cjkirchberg@gmail.com> writes: > When I go to Packages & Data, select Package Installer, then choose > BioConductor (binaries), then click on Get List. > The list is blank. > > Any clues as to what is happening? We do not yet have OS X binary packages available for the Bioconductor 1.6 release. So that is why you are seeing the 404 error messages. We will do our best to have OS X binary packages available by the end of the week. Sorry for the inconvenience. + seth