Question: genefilter installation error
0
gravatar for Subinoy Biswas
4.7 years ago by
Subinoy Biswas10 wrote:
Please help me I am getting error while installing genefilter package ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (AnnotationDbi) ERROR: dependency ?XML? is not available for package ?annotate? * removing ?/home/subinoy/R/x86_64-pc-linux-gnu-library/3.1/annotate? ERROR: dependency ?annotate? is not available for package ?genefilter? * removing ?/home/subinoy/R/x86_64-pc-linux-gnu- library/3.1/genefilter? The downloaded source packages are in ?/tmp/RtmpFu8HQT/downloaded_packages? Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?XML? had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?annotate? had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?genefilter? had non-zero exit status 4: installed directory not writable, cannot update packages 'codetools', 'MASS', 'spatial' > library(genefilter) Error in library(genefilter) : there is no package called ?genefilter? [[alternative HTML version deleted]]
genefilter • 4.9k views
ADD COMMENTlink modified 4.7 years ago by Cherif Ben Hamda150 • written 4.7 years ago by Subinoy Biswas10
1

Hi,

this solved the issue on my Ubuntu 14:

sudo apt-get install r-cran-xml

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

 

Romeo Kienzler

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by romeo.kienzler10
Answer: genefilter installation error
0
gravatar for Martin Morgan
4.7 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
On 08/22/2014 01:21 PM, Subinoy Biswas wrote: > Please help me I am getting error while installing genefilter package > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ** testing if installed package can be loaded > * DONE (AnnotationDbi) > ERROR: dependency ?XML? is not available for package ?annotate? The problem is here, the package XML is not installed, probably it failed to install earlier in the installation process. On Linux XML has a system dependency; on my system it is satisfied with sudo apt-get install libxml2-dev Martin > * removing ?/home/subinoy/R/x86_64-pc-linux-gnu- library/3.1/annotate? > ERROR: dependency ?annotate? is not available for package ?genefilter? > * removing ?/home/subinoy/R/x86_64-pc-linux-gnu- library/3.1/genefilter? > > The downloaded source packages are in > ?/tmp/RtmpFu8HQT/downloaded_packages? > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?XML? had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?annotate? had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?genefilter? had non-zero exit status > 4: installed directory not writable, cannot update packages 'codetools', > 'MASS', 'spatial' >> library(genefilter) > > Error in library(genefilter) : there is no package called ?genefilter? > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 4.7 years ago by Martin Morgan ♦♦ 23k
Answer: genefilter installation error
0
gravatar for Cherif Ben Hamda
4.7 years ago by
Tunisia
Cherif Ben Hamda150 wrote:
Hi Subinoy, Tap this line in consol sudo apt-get install libcurl4-openssl-dev libxml2-dev And this in R install.packages("RCurl") install.packages("XML") After that : source("http://bioconductor.org/biocLite.R") biocLite("genefilter") Tell me if it works Best Cherif Le 24 ao?t 2014 06:33, "Subinoy Biswas" <suny.bio at="" gmail.com=""> a ?crit : > Please help me I am getting error while installing genefilter package > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ** testing if installed package can be loaded > * DONE (AnnotationDbi) > ERROR: dependency ?XML? is not available for package ?annotate? > * removing ?/home/subinoy/R/x86_64-pc-linux-gnu- library/3.1/annotate? > ERROR: dependency ?annotate? is not available for package ?genefilter? > * removing ?/home/subinoy/R/x86_64-pc-linux-gnu- library/3.1/genefilter? > > The downloaded source packages are in > ?/tmp/RtmpFu8HQT/downloaded_packages? > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?XML? had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?annotate? had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?genefilter? had non-zero exit status > 4: installed directory not writable, cannot update packages 'codetools', > 'MASS', 'spatial' > > library(genefilter) > > Error in library(genefilter) : there is no package called ?genefilter? > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 [[alternative HTML version deleted]]
ADD COMMENTlink written 4.7 years ago by Cherif Ben Hamda150
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