Search
Question: hugene10st.db not available?
0
gravatar for Mark Robinson
7.7 years ago by
Mark Robinson1.1k
Mark Robinson1.1k wrote:
Hi all. I'm trying to install the hugene10st.db package. I was unsuccessful with the standard approach of: ------------------ > source("http://bioconductor.org/biocLite.R") > biocLite("hugene10st.db") Using R version 2.9.1, biocinstall version 2.4.12. Installing Bioconductor version 2.4 packages: [1] "hugene10st.db" Please wait... Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib /2.9 Warning message: In getDependencies(pkgs, dependencies, available, lib) : package 'hugene10st.db' is not available > biocLite("mogene10st.db") Using R version 2.9.1, biocinstall version 2.4.12. Installing Bioconductor version 2.4 packages: [1] "mogene10st.db" Please wait... Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib /2.9 Warning message: In getDependencies(pkgs, dependencies, available, lib) : package 'mogene10st.db' is not available > biocLite("limma") Using R version 2.9.1, biocinstall version 2.4.12. Installing Bioconductor version 2.4 packages: [1] "limma" Please wait... Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib /2.9 trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/contri b/2.9/limma_2.18.2.tgz' Content type 'application/x-gzip' length 1121233 bytes (1.1 Mb) opened URL ================================================== downloaded 1.1 Mb ------------------ ... although you can see that works for other BioC packages, so its not simply a connection issue. Correspondingly, the hyperlinks to the various version of the package do not work for me: http://www.bioconductor.org/packages/2.4/data/annotation/html/hugene10 st.db.html (The same appears true of the 2.5 links). Am I doing something silly here? Cheers, Mark
ADD COMMENTlink modified 7.7 years ago by Marc Carlson7.2k • written 7.7 years ago by Mark Robinson1.1k
0
gravatar for Marc Carlson
7.7 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Mark, In the latest versions of Bioconductor, that package has been replaced by TWO packages (depending on which revision you want to used): hugene10stprobeset.db <http: www.bioconductor.org="" packages="" 2.4="" data="" annotation="" html="" hugene1="" 0stprobeset.db.html=""> and hugene10sttranscriptcluster.db <http: www.bioconductor.org="" packages="" 2.4="" data="" annotation="" html="" hugene1="" 0sttranscriptcluster.db.html=""> You can simply go to the links above, decide which version you need, and then use biocLite() as usual to get the package you want. Marc Mark Robinson wrote: > Hi all. > > I'm trying to install the hugene10st.db package. > > I was unsuccessful with the standard approach of: > > ------------------ > >> source("http://bioconductor.org/biocLite.R") >> biocLite("hugene10st.db") >> > Using R version 2.9.1, biocinstall version 2.4.12. > Installing Bioconductor version 2.4 packages: > [1] "hugene10st.db" > Please wait... > > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contr ib/2.9 > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package 'hugene10st.db' is not available > >> biocLite("mogene10st.db") >> > Using R version 2.9.1, biocinstall version 2.4.12. > Installing Bioconductor version 2.4 packages: > [1] "mogene10st.db" > Please wait... > > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contr ib/2.9 > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package 'mogene10st.db' is not available > >> biocLite("limma") >> > Using R version 2.9.1, biocinstall version 2.4.12. > Installing Bioconductor version 2.4 packages: > [1] "limma" > Please wait... > > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contr ib/2.9 > trying URL > 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/cont rib/2.9/limma_2.18.2.tgz' > Content type 'application/x-gzip' length 1121233 bytes (1.1 Mb) > opened URL > ================================================== > downloaded 1.1 Mb > ------------------ > > ... although you can see that works for other BioC packages, so its not > simply a connection issue. Correspondingly, the hyperlinks to the various > version of the package do not work for me: > > http://www.bioconductor.org/packages/2.4/data/annotation/html/hugene 10st.db.html > > (The same appears true of the 2.5 links). > > Am I doing something silly here? > > Cheers, > Mark > > _______________________________________________ > 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 > >
ADD COMMENTlink written 7.7 years ago by Marc Carlson7.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 131 users visited in the last hour