Search
Question: unable to install package
0
gravatar for Guest User
4.0 years ago by
Guest User12k
Guest User12k wrote:
how to install bioconductor packages ? I'm unable to install any package from bioconductor. im using this in Win 7 home basic. please help me. -- output of sessionInfo(): > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Warning message: installed directory not writable, cannot update packages 'foreign', 'lattice', 'Matrix', 'mgcv' > biocLite(affy) Error in match(x, table, nomatch = 0L) : object 'affy' not found -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 9 months ago by amsindra0 • written 4.0 years ago by Guest User12k
0
gravatar for Dan Tenenbaum
4.0 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
----- Original Message ----- > From: "ashok raja balla [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, ashokrajaballa at live.com > Cc: "affy Maintainer" <rafa at="" jhu.edu=""> > Sent: Wednesday, November 6, 2013 6:43:32 PM > Subject: [BioC] unable to install package > > > how to install bioconductor packages ? > I'm unable to install any package from bioconductor. > im using this in Win 7 home basic. please help me. > > -- output of sessionInfo(): > > > biocLite() > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version > 3.0.2. > Warning message: > installed directory not writable, cannot update packages 'foreign', > 'lattice', > 'Matrix', 'mgcv' This is just a warning and you can ignore it. > > biocLite(affy) > Error in match(x, table, nomatch = 0L) : object 'affy' not found > The correct command is: biocLite("affy") Note the quotation marks. Dan > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 4.0 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for Martin Morgan
4.0 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
On 11/06/2013 06:43 PM, ashok raja balla [guest] wrote: > > how to install bioconductor packages ? > I'm unable to install any package from bioconductor. > im using this in Win 7 home basic. please help me. > > -- output of sessionInfo(): > >> biocLite() > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. > Warning message: > installed directory not writable, cannot update packages 'foreign', 'lattice', > 'Matrix', 'mgcv' >> biocLite(affy) try quoting the package name you would like to install biocLite("affy") This is how it is shown on the package landing page, e.g., http://bioconductor.org/packages/release/bioc/html/affy.html Martin > Error in match(x, table, nomatch = 0L) : object 'affy' not found > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 4.0 years ago by Martin Morgan ♦♦ 20k
0
gravatar for sebastian.mynott
2.7 years ago by
United Kingdom
sebastian.mynott0 wrote:

I am having a similar issue but I am logged in as Administrator (the only user on my computer). The result is that when I try to install a package like this:

source("http://bioconductor.org/biocLite.R")

Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help

biocLite("ShortRead") BioC_mirror: http://bioconductor.org

When the package(s) downloads, I get this:

The downloaded binary packages are in /var/folders/nb/09qklh116w558w77gcpn7zhm0000gp/T//RtmpX1P4OU/downloaded_packages

Warning message: installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival' 

A check of the library gives me this:

library(Shortread)

Error in library(Shortread) : there is no package called ‘Shortread’

I am using Bioconductor 3.0 in R 3.1.2 GUI 1.65 Mavericks build running in RStudio 0.98.1102.

Any suggestions would be most welcome!

Seb

ADD COMMENTlink written 2.7 years ago by sebastian.mynott0

R is case sensitive -- library(ShortRead). It's not a good idea to run software as administrator.

ADD REPLYlink written 2.7 years ago by Martin Morgan ♦♦ 20k
0
gravatar for amsindra
9 months ago by
amsindra0
amsindra0 wrote:

1.Go to terminal

2.Run R as a root user :sudo R

3.source("http://www.bioconductor.org/biocLite.R")

4,biocLite()

5.update option:(write ) a

so it will update automatically

ADD COMMENTlink written 9 months ago by amsindra0
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: 140 users visited in the last hour