[BioC] installing Bioconductor on Mac OS tiger
Kay Schneitz
schneitz at wzw.tum.de
Wed Aug 10 17:02:00 CEST 2005
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 Universität München
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
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