Displaying 20 results from an estimated 500 matches similar to: "Installation Error with Bioconductor on R"
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 =
2007 Nov 02
0
loading installes package including all needed subpackages
Hallo,
I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command?
Thanks, Corinna
Here is the result of the command library():
Pakete in Library
2006 Aug 11
1
[BioC] problem loading affycoretools (more details)
Hi again,
I have been playing around with the order of loading packages, and as far
as I can tell, there's nothing specific with affycoretools that's causing
my Rgui to crash (i.e., shuts down and the Microsoft 'please send error
report' box pops up). Instead, it has something to do with the order & type
of packages that are loaded that add items to the menu bar by
2007 Oct 30
6
trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64
I have recently upgraded to Ubuntu Gutsy and, for the first time, am
using a 64-bit installation. After failing miserably to install R from
source, not a problem for me in the past with a 32-bit install, I went
the route of using the Debian Etch build. This went smoothly, but I am
unable to update my numerous R and BioConductor packages, getting
non-zero exit status errors on each package. Is
2003 Oct 30
0
Release of Bioconductor 1.3
The Bioconductor core group would like to announce the 1.3 release of
the Bioconductor software. There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to check them out. Release 1.3 is intended to be operated
with R version 1.8.X, which can be obtained at CRAN
(http://cran.r-project.org/)
-- WHAT FEATURES DOES THIS RELEASE PROVIDE?
2003 Oct 30
0
Release of Bioconductor 1.3
The Bioconductor core group would like to announce the 1.3 release of
the Bioconductor software. There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to check them out. Release 1.3 is intended to be operated
with R version 1.8.X, which can be obtained at CRAN
(http://cran.r-project.org/)
-- WHAT FEATURES DOES THIS RELEASE PROVIDE?
2005 Oct 18
2
Installing Bioconductor on R
hi all,
Am new to R. I am having problems installing Bioconductor package in
R on fedora core 4 running on AMD64 bit machine.
this is the error message I get :
gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o
chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o
idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o
2008 Dec 01
2
[BioC] BioC 2.3 standard installation
I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R
on Ubuntu 8.1. I had no errors before!
> install.packages("XML")
Warning in install.packages("XML") :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL
2003 Aug 07
5
gregmisc
Hi
How do I install "gregmisc" packages?
I did-
% sudo R
> install.packages("gregmisc")
.
.
> barplot2()
but,
Error: couldn't find function "barplot2"
--
atuya
Mac OSX 10.2.6
R 1.7.1
2004 May 17
0
Bioconductor 1.4 released
Greetings!
The Bioconductor core group would like to announce the 5th release of
Bioconductor, version 1.4. There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to upgrade existing tools and check out the new packages.
Release 1.4 is intended to be operated with R version 1.9.x, which can
be obtained at CRAN
2010 Feb 08
1
objects masked from packages
dear all,
I have a problem with a masked object in a package we created here.
we make a package for a workflow of internal analysis of microarray data.
to create the package we used:
> install.packages(pkgs="affyAnalysis", repos=NULL)
> R CMD INSTALL affyAnalysis
Erzeuge Verzeichnisse ...
Erzeuge DESCRIPTION ...
Erzeuge NAMESPACE ...
Erzeuge Read-and-delete-me ...
Kopiere
2007 Mar 23
1
can't load just saved R object "ReadItem: unknown type 65"
I have run into a problem loading a just saved R object using R-devel. I
have been saving and loading this particular type of R object for a long
while and never ran into this problem. I save, then immediately reload
(to test save) and get "ReadItem: unnknown type 65".
This error is reproducible after logout from server and restart of emacs
and R.
Below is my output and
2007 Mar 23
1
can't load just saved R object "ReadItem: unknown type 65"
I have run into a problem loading a just saved R object using R-devel. I
have been saving and loading this particular type of R object for a long
while and never ran into this problem. I save, then immediately reload
(to test save) and get "ReadItem: unnknown type 65".
This error is reproducible after logout from server and restart of emacs
and R.
Below is my output and
2003 May 29
0
Bioconductor 1.2 Released
The Bioconductor development team announces release 1.2 of the
Bioconductor packages for the analysis of genomic data. Bioconductor
is an open source bioinformatics software project based on the R language.
Version 1.2 features:
=====================
* All packages from the 1.1 release are included. All current bug
fixes have been applied, and most have been upgraded and
provide enhanced
2007 Feb 15
2
Problems with 'delay'/'delayedAssign' when installing data package
I downloaded:
http://www.bioconductor.org/data/metaData/hgu95av2_1.7.0.tar.gz
described as:
Package: hgu95av2
Title: A data package containing annotation data for hgu95av2
Version: 1.7.0
Created: Wed Jan 12 16:57:23 2005
Author: Lin,Chenwei
Description: Annotation data file for hgu95av2 assembled using data
from public data repositories
Maintainer:
2007 Mar 23
0
can't load just saved R object using R-devel "ReadItem: unknown type 65"
I am unable to load a just saved R object. Get message "ReadItem:
unknown type 65" I am using R-devel and the problem is reproducible
after logout and restarting R.
Output and sessionInfo() below.
Mark
> setwd("~/Genomics/Experiments.Genomic/BB01/acb.shell")
> local(save(affy.object.preprocessed, file
="affy.object.preprocessed.R" ))
>
2004 May 14
2
rma and gcrma do not work in R 1.9.0
I run R 1.9.0 on windows 2000, and have the following libraries installed:
affydata_1.3.1
affy_1.4.23
Biobase_1.4.10
DynDoc_1.3.14
gcrma_1.0.6
hgu133acdf_1.4.3
hgu95av2cdf_1.4.3
hgu95av2probe_1.0
matchprobes_1.0.7
moe430acdf_1.4.3
multcomp_0.4-6
mvtnorm_0.6-6
rae230acdf_1.4.3
reposTools_1.3.29
rgu34acdf_1.4.3
tkWidgets_1.5.1
widgetTools_1.2.7
1. The rma function (in affy library) always crashes.
2007 Feb 28
1
problem with help.start and ?somefunction
Hi all,
I am going to be teaching a workshop next week using R and Bioconductor in one of our university's computer labs. They have recently installed R 2.4.1 for me, and I'm checking all my scripts. I just noticed that using the ?somefunction call to access the documentation for that function is not working. On my own PC, the ? call output changed between R 2.3 and 2.4; before it would
2011 Jun 13
2
cause 'memory not mapped'
Dear R-help
Hi,
I'm Won.
I try to do microarray normalization by R.
I use justRMA function within affy package, got error about segment fault.
I don't know why it happen.
I attached error below.
Please help me.
Thank you.
Cheers,
Won
=======================
OS : Redhat linux
Cpu : intel xeon X5570
Memory : 26Gb
&
OS : Ubuntu
Cpu : intel q6600
Memory : 8Gb
2006 Aug 31
1
problem with postscript output of R-devel on Windows
I have developed a problem with the postscript output of plot on Windows. My code still works properly with R 2.3 but, with R 2.4, the white text on red background does not show up. It does, however, show up when output is sent to the screen. Below is my code and sessionInfo.
R version 2.4.0 Under development (unstable) (2006-08-29 r39012)
i386-pc-mingw32
locale:
LC_COLLATE=English_United