installation warnings and other related questions
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Weiwei Shi ★ 1.2k
@weiwei-shi-1407
Last seen 10.2 years ago
Dear Listers: I am trying to use Bioconductor doing some microarray analysis. When I installed it via following commands in R, I got the following warnings: source("http://www.bioconductor.org/biocLite.R") biocLite() cannot open: HTTP status was '404 Not Found' Warning: unable to access index for repository http://www.bioconductor.org/packages/data/experiment/stable/bin/window s/contrib/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/windows/contr ib/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/windows/contri b/2.1 dependency 'golubEsets' is not available The configuration of my R and machine is > R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 1.1 year 2005 month 06 day 20 language R In my opinion, it is due to the HTTP connection error since I tried to put those links in IE and they got HTTP 404 errors. I am really interested, for example, using golubEsets so I installed it from here: http://www.bioconductor.org/data/experimental/html/golubEsets.html However, I am interested in knowing what about the other warnings... As important as above, are there any good online materials covering using bioC and R in analyzing microarray/bioinformatics data, esp. via data mining approaches? Thank you very much! Best, Weiwei -- Weiwei Shi, Ph.D "Did you always know?" "No, I did not. But I believed..." ---Matrix III
Microarray Microarray • 898 views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
Hi Weiwei, On 24 Oct 2005, helprhelp at gmail.com wrote: > Dear Listers: I am trying to use Bioconductor doing some microarray > analysis. When I installed it via following commands in R, I got the > following warnings: source("http://www.bioconductor.org/biocLite.R") > biocLite() > > cannot open: HTTP status was '404 Not Found' Warning: unable to > access index for repository > http://www.bioconductor.org/packages/data/experiment/stable/bin/wind ows/contrib/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/windows/con trib/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/windows/cont rib/2.1 > dependency 'golubEsets' is not available > > The configuration of my R and machine is >> R.version > _ > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major 2 > minor 1.1 > year 2005 > month 06 > day 20 > language R Thanks for the report. Something needs fixing and we will get on it :-) I recommend that you install the latest released version of R (2.2.0) and then repeat the biocLite routine. This will allow you to install the latest released versions of Bioconductor packages which are sure to have bug fixes and other improvements. + seth
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
On 24 Oct 2005, sfalcon at fhcrc.org wrote: > Thanks for the report. Something needs fixing and we will get on it > :-) I believe this is now fixed. So you should be able to again use biocLite with R 2.1.x. But I still strongly recommend that you upgrade to R 2.2.0. Best, + seth
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Hi, There: (Thanks for Seth's help; after upgrading, it is fine now though the golobEsets has to be manually installed). could anyone answer my second question from the original post? " As important as above, are there any good online materials covering using bioC and R in analyzing microarray/bioinformatics data, esp. via data mining approaches? " Thank you very much! Best, Weiwei On 10/24/05, Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: > On 24 Oct 2005, sfalcon at fhcrc.org wrote: > > Thanks for the report. Something needs fixing and we will get on it > > :-) > > I believe this is now fixed. So you should be able to again use > biocLite with R 2.1.x. But I still strongly recommend that you > upgrade to R 2.2.0. > > Best, > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Weiwei Shi, Ph.D "Did you always know?" "No, I did not. But I believed..." ---Matrix III
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> Hi, There: > (Thanks for Seth's help; after upgrading, it is fine now though the > golobEsets has to be manually installed). > > could anyone answer my second question from the original post? > " > As important as above, are there any good online materials covering > using bioC and R in analyzing microarray/bioinformatics data, esp. via > data mining approaches? > " Wei-Wei, Most of the packages, if not all the packages, come with a 'Vignette'. http://www.bioconductor.org/docs/vignettes.html If the list of Vignette is a little intimidating, especially when new to R, you may want to have a feel for can be done by looking at one of the workshop material http://www.bioconductor.org/workshops/ (the one in Bressanone, Italy, had all the material online I think). When it comes to data mining/exploratory data analysis with R, there are several books covering different aspects of the topic. You can also pick some of the online documentation, like for example http://www.cran.r-project.org/doc/contrib/usingR.pdf Hoping this helps, L. > Thank you very much! > > Best, > > Weiwei > > On 10/24/05, Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: >> On 24 Oct 2005, sfalcon at fhcrc.org wrote: >> > Thanks for the report. Something needs fixing and we will get on it >> > :-) >> >> I believe this is now fixed. So you should be able to again use >> biocLite with R 2.1.x. But I still strongly recommend that you >> upgrade to R 2.2.0. >> >> Best, >> >> + seth >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > > -- > Weiwei Shi, Ph.D > > "Did you always know?" > "No, I did not. But I believed..." > ---Matrix III > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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