Displaying 20 results from an estimated 1000 matches similar to: "Setting bioconductor repository in .Rprofile. Is there a permanent way?"
2010 Jul 08
2
package installation for Windows 7
Neither biocLite nor the GUI menus can install packages on my system.
Here is relevant output:
> version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
> source("http://bioconductor.org/biocLite.R")
BioC_mirror =
2013 Apr 25
2
installing package
Hi
I am trying to install a package (bioconductor) but every time I try to install it I get this message:
source("http://bioconductor.org/biocLite.R")
Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
'lib = "C:/Program Files/R/R-3.0.0/library"' is not writable
Error in
2012 Sep 05
2
Installing lumi and hdrcde
To whom it may concern.
As I would like to analyse some array data I was keen on downloading the
lumi package that depends obviously on hdrcde that is not available for r
2.12.1. I did not find instructions to solve or circumvent this problem.
Installing hdrcde by hand did not work either. It was not detected by
> (.packages(all.available=TRUE))
if installed in the R library.
Thanks
Hermann
2012 Mar 06
1
DESeq package install error
HI, I would like to update my DESeq package version on R-2-14 using
bioclite() and get this message, could somebody help please?
> biocLite("DESeq")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'DESeq'
Installing package(s) into ?/nfs/team82/nac/R-modules?
(as ?lib? is unspecified)
trying URL
2010 Nov 15
1
Cannot install packages in R 2.12.0 on Windows 7
Hi,
I am unable to install packages on my R 2.12.0 Windows 7 machine. Here are the relevant lines:
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
2011 Aug 16
1
Problems installing SJava
Hello, I am trying to install SJava but I haven't been able to complete it
successfully. I have tried to install it from bioconductor using the
followin code and got the following output:
> source("http://www.bioconductor.org/biocLite.R")
BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().
> biocLite("SJava")
Using R version 2.12.2, biocinstall
2010 Jun 09
1
Problem with library(SSPA)
Hello,
I have the fellowing problem and I am thankful for any advice!
Regards,
Samuel
################################################################
> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> biocLite("SSPA")
Using R version 2.11.0, biocinstall version 2.6.7.
Installing
2013 Jan 17
2
error installing KEGGSOAP
Hi, I am new to bioconductor, trying to install KEGGSOAP package, but got warnings() when installing and error message when trying to load the package, can anyone suggest what went wrong?
many thanks
John
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> biocLite("KEGGSOAP")
BioC_mirror:
2013 Mar 28
1
Error in setMethod("combine"... was - Error when installing globaltest package
Hi All,
I posted this on the bioconductor list and didn't get a response there, so I'm hoping someone here can help.
I don't know a heck of a lot about R, so I apologize if this seems like a trivial issue. This error comes up when trying to install the bioconductor globaltest package.
Any clues?
Thanks!
Rusty
-----Original Message-----
From: bioconductor-bounces at r-project.org
2012 Jul 19
3
Are R packages supposed to be "relocatable"? (avoiding BioConductor scripts...)
I've asked a question in the BioConductor list about package
management. My solution depends on your answer to the following
question.
Are installed R packages "relocatable"?
I mean relocatable in the same sense that files in a RedHat RPM file
might be "relocatable" after compiling
(http://www.rpm.org/max-rpm/ch-rpm-reloc.html). This allows one to
build a package as the
2012 May 15
1
KEGGSOAP installation error
Hello,
I'm trying to install KEGGSOAP with bioconductor but i'm facing this
problem:
/> biocLite("KEGGSOAP")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.4.
Installing package(s) 'KEGGSOAP'
trying URL
'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/KEGGSOAP_1.30.0.tar.gz'
Content type
2011 May 31
1
how to define PKG_CONFIG_PATH ?
Dear List,
as I'm trying to install R and Rgraphwiz on a Fedora Linux, I have a problem with the environement variable "PKG_CONFIG_PATH". The library "libgvc" is not getting recognized / found, although a recent version libgvc is on the system and can be seen via /usr/lib64. I've tried to edit the paths described in /etc/ldpaths but without any success. Any hints how
2012 Apr 13
1
Rprofile.site?
Hello:
I've been using "Rprofile.site" for several years to set the
repos environment variable as follows:
options(repos=c(CRAN='http://cran.cnr.berkeley.edu',
CRANextra='http://www.stats.ox.ac.uk/pub/RWin') )
However, R 2.15.0 is not recognizing this. Instead, I get the
following:
options('repos')
$repos
2006 Mar 16
2
Bioconductor package on linux machine
Hi together,
we received a question about the bioconductor package,
maybe anybody could help the guy and I will deliver the message over our
forum to him.
If this way is allowed ...
Regards Knut
Here the question:
Hello,
I have installed R on a linux machine. I have then installed the
biocLite.R package from bioconductor.
I wanted to install a few other packages - hgu133plus2cdf, rma .
I
2011 Nov 30
1
install "multtest" and "preprocessCore" packages in Bioconductor library
Hi Nguyen,
> Subject: [R] install "multtest" and "preprocessCore" packages in
> Bioconductor library
> Date: Wed, 30 Nov 2011 09:57:36 -0800
> From: UyenThao Nguyen <unguyen at tethysbio.com>
> To: r-help <r-help at r-project.org>
> CC: uth.nguyen at ucdavis.edu <uth.nguyen at ucdavis.edu>
>
> Hi All,
>
> I've tried to
2009 Aug 07
2
error installing bioconductor
Hi, I am new to R. I am downloaded the installer for R 2.9.1, and that
installed just fine.
Then I want to install Biocondcutor packages. According to bioconductor
website, I input the following commands.
> source("http://bioconductor.org/biocLite.R")
> bioLite()
Error: could not find function "bioLite"
What am I doing wrong here?
Thanks
--
View this message in
2008 Jun 19
1
Installation Error with Bioconductor on R
Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following:
source("http://bioconductor.org/biocLite.R")
biocLite()
When I do that, I get the following error:
Running biocinstall version 2.2.9 with R version 2.7.0
Your version of R
2013 Oct 23
3
Problema con Bioconductor y R 3.0.2
No se bien si hacer la pregunta aca, pero en la lista de correo de
bioconductor he tenido algunos problemas para hacer la consulta.
Por un error actualice R de la version 15.0.3 a la 3.0.2, y ahora no me
corren las librerias de bioconductor. Al intentar usar alguna me aparece
el mensaje :
Your Bioconductor is out-of-date, upgrade to version 2.13 by following
instructions at
2009 Jun 23
1
Cannot install pakages from Bioconductor besides the default installation
I am running the last R version on SuSE 11.1.
I installed the Bioconductor environment following the instructions on the web. As a consequence some
core packages from Bioconductors were installed.
I need to add some more packages. So I tried biomaRt as follows.
It does not get installed correctly.
Please see the following sequence.
Thank you in advance.
Maura
>
2011 Jun 10
3
CRAN package with dependencies on Bioconductor
Dear all,
for a CRAN-package that depends on another Bioconductor-package I find two
things annoying and would like to know whether there are some workarounds:
1) Is there some inevitable problem that install.packages does not install
uninstalled packages (on which the specified package depends) also from
Bioconductor (in the correct version)?
2) In my understanding (please correct me if