Hi there, I noticed a weired issue after installing Bioconductor. My configuration: Bioconductor 1.6, biocLite; R version 2.1.1, R Cocoa GUI version 1.12, Mac OS 10.4 with latest system updates installed, Powerbook G4. I installed the custom version of R including the fortran compiler stuff. Problem: Datamanager only shows an empty table, datasets are not displayed anymore. This only occurs after restart of R (upon installing bioconductor, datamanager works --> restart --> Problems. I could confirm this issue after several installs/delete everything (R and bioconductor), reinstall cycles. Any help or pointers? I included a printout of the workspace at the end of this message Many thanks in advance, Kay R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0 R ist freie Software und kommt OHNE JEGLICHE GARANTIE. Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten. Tippen Sie 'license()' or 'licence()' f"ur Details dazu. R ist ein Gemeinschaftsprojekt mit vielen Beitragenden. Tippen Sie 'contributors()' f"ur mehr Information und 'citation()', um zu erfahren, wie R oder R packages in Publikationen zitiert werden k"onnen. Tippen Sie 'demo()' f"ur einige Demos, 'help()' f"ur on-line Hilfe, oder 'help.start()' f"ur eine HTML Browserschnittstelle zur Hilfe. Tippen Sie 'q()', um R zu verlassen. [Vorher gesicherter Workspace wiederhergestellt] > source("http://www.bioconductor.org/biocLite.R") Warnmeldungen: 1: datasets have been moved from package 'base' to package 'datasets' in: data(package = .packages(all.available = TRUE)) 2: datasets have been moved from package 'stats' to package 'datasets' in: data(package = .packages(all.available = TRUE)) > biocLite() Running bioCLite version 0.1 with R version 2.1.1 Running biocinstall version 1.2 with R version 2.1.1 Warnmeldung: "Offnen fehlgeschlagen: HTTP Status war '404 Not Found' Warnung: unable to access index for repository http:// www.bioconductor.org/packages/data/annotation/stable/bin/macosx/2.1 Warnmeldung: "Offnen fehlgeschlagen: HTTP Status war '404 Not Found' Warnung: unable to access index for repository http:// www.bioconductor.org/packages/data/experiment/stable/bin/macosx/2.1 Warnmeldung: "Offnen fehlgeschlagen: HTTP Status war '404 Not Found' Warnung: unable to access index for repository http:// www.bioconductor.org/packages/omegahat/stable/bin/macosx/2.1 Warnmeldung: "Offnen fehlgeschlagen: HTTP Status war '404 Not Found' Warnung: unable to access index for repository http:// www.bioconductor.org/packages/lindsey/stable/bin/macosx/2.1 also installing the dependencies 'GO', 'KEGG' versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/GO_1.8.2.tgz' Content type 'application/x-gzip' length 12585063 bytes URL ge"offnet ================================================== downloaded 12290Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/KEGG_1.8.1.tgz' Content type 'application/x-gzip' length 192310 bytes URL ge"offnet ================================================== downloaded 187Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/affy_1.6.7.tgz' Content type 'application/x-gzip' length 1325356 bytes URL ge"offnet ================================================== downloaded 1294Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/affydata_1.4.1.tgz' Content type 'application/x-gzip' length 9896558 bytes URL ge"offnet ================================================== downloaded 9664Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/affyPLM_1.3.3.tgz' Content type 'application/x-gzip' length 3907660 bytes URL ge"offnet ================================================== downloaded 3816Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/annaffy_1.0.18.tgz' Content type 'application/x-gzip' length 221396 bytes URL ge"offnet ================================================== downloaded 216Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/annotate_1.5.16.tgz' Content type 'application/x-gzip' length 1620645 bytes URL ge"offnet ================================================== downloaded 1582Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/Biobase_1.5.12.tgz' Content type 'application/x-gzip' length 511275 bytes URL ge"offnet ================================================== downloaded 499Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/Biostrings_1.1.1.tgz' Content type 'application/x-gzip' length 154494 bytes URL ge"offnet ================================================== downloaded 150Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/DynDoc_1.5.5.tgz' Content type 'application/x-gzip' length 42537 bytes URL ge"offnet ================================================== downloaded 41Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/gcrma_1.1.4.tgz' Content type 'application/x-gzip' length 84185 bytes URL ge"offnet ================================================== downloaded 82Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/genefilter_1.6.3.tgz' Content type 'application/x-gzip' length 257726 bytes URL ge"offnet ================================================== downloaded 251Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/geneplotter_1.6.1.tgz' Content type 'application/x-gzip' length 1462701 bytes URL ge"offnet ================================================== downloaded 1428Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/hgu95av2_1.8.4.tgz' Content type 'application/x-gzip' length 5898099 bytes URL ge"offnet ================================================== downloaded 5759Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/limma_2.0.4.tgz' Content type 'application/x-gzip' length 937889 bytes URL ge"offnet ================================================== downloaded 915Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/marray_1.6.3.tgz' Content type 'application/x-gzip' length 4230853 bytes URL ge"offnet ================================================== downloaded 4131Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/matchprobes_1.0.22.tgz' Content type 'application/x-gzip' length 7284196 bytes URL ge"offnet ================================================== downloaded 7113Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/multtest_1.7.3.tgz' Content type 'application/x-gzip' length 1422985 bytes URL ge"offnet ================================================== downloaded 1389Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/reposTools_1.5.19.tgz' Content type 'application/x-gzip' length 467893 bytes URL ge"offnet ================================================== downloaded 456Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/ROC_1.1.1.tgz' Content type 'application/x-gzip' length 102431 bytes URL ge"offnet ================================================== downloaded 100Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/vsn_1.6.3.tgz' Content type 'application/x-gzip' length 1514500 bytes URL ge"offnet ================================================== downloaded 1479Kb versuche URL 'http://www.bioconductor.org/packages/bioc/stable/bin/ macosx/2.1/xtable_1.2-5.tgz' Content type 'application/x-gzip' length 24720 bytes URL ge"offnet ================================================== downloaded 24Kb The downloaded packages are in /tmp/RtmpLMeuVn/downloaded_packages Warnmeldung: cannot create HTML package index in: make.packages.html() > ##RESTART of R, then trying to use Datamanager from R.GUI: displays empty window and the following error messages: Fehler in rbind(...) : Anzahl der Spalten der Matrizen muss "ubereinstimmen (siehe Argument 2) Zus"atzlich: Warnmeldungen: 1: datasets have been moved from package 'base' to package 'datasets' in: data(package = .packages(all.available = TRUE)) 2: datasets have been moved from package 'stats' to package 'datasets' in: data(package = .packages(all.available = TRUE)) Fehler in rbind(...) : Anzahl der Spalten der Matrizen muss "ubereinstimmen (siehe Argument 2) Zus"atzlich: Warnmeldungen: 1: datasets have been moved from package 'base' to package 'datasets' in: data(package = .packages(all.available = TRUE)) 2: datasets have been moved from package 'stats' to package 'datasets' in: data(package = .packages(all.available = TRUE)) > ========================================= Prof. Dr. Kay Schneitz Entwicklungsbiologie der Pflanzen Wissenschaftszentrum Weihenstephan Technische Universit?t M?nchen Am Hochanger 4 D-85354 Freising/Germany Tel: +49 (0)8161 715438 Fax: +49 (0)8161 713337 Email: schneitz at wzw.tum.de URL: plantdev.bio.wzw.tum.de AIM: ovulek Jabber: ovulek at jabber.org