Displaying 20 results from an estimated 1000 matches similar to: "Bioconductor installation on 64 bit R problem"
2006 Apr 27
1
proposed modifications to deprecated
Hi,
Over the past six months we have had a few problems with deprecation
and Seth Falcon and I want to propose a few additions to the mechanism
that will help deal with cases other than the deprecation of functions.
In the last release one of the arguments to La.svd was deprecated, but
the warning message was very unclear and suggested that in fact La.svd
was deprecated.
Adding a
2006 Aug 29
2
Bioconductor installation errors
Hello,
I follow the Bioconductor instruction (http://www.bioconductor.org/download
<http://www.bioconductor.org/download> ) to install Biocoductor, there have
some errors:
/usr/lib/R/bin/SHLIB: line 115: make: command not found
chmod: cannot access `/usr/local/lib/R/site-library/affyio/libs/*': No such
file or directory
ERROR: compilation failed for package 'affyio'
**
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
2010 Sep 02
3
Metadata update
Hi there.
Anybody knows how can I send metadata updates to a running mountpoint in
Icecast?
Thanks
--
__________________________________________________________
| , , |
| / \ |
| ((__-^^-,-^^-__)) Octavio Rossell Tabet |
| `-_---' `---_-' octavio at
2010 Sep 02
4
Metadata update
This is exactly what I want.
I have a continuous stream to a live mountpoint that needs to be
metadata updates. Is this http request you mention any documentation to
study?
El 02/09/10 08:43, Johann Soukup escribi?:
> Hi Octavio,
>
> I guess you are talking about live mount points.
>
> We use a http request through the admin/metadata application of the
> Icecast admin
2007 Sep 13
1
trouble with installing Biobase package
Hi Everybody,
I am having a problem with loading Biobase package. I typed
2 lines below at R prompt
> source ("http://boconductor.org/biocLite.R")
> biocLite (lib="/usr/local/lib/R/library")
which attempted to install a bunch of packages with varying
degree of success. Out of 29, 13 failed. Biobase is one of
them. As a matter of fact, when I looked at logs, most
2006 Nov 11
1
Install bioconductor
Hello useRs,
I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0.
I have some error messages during installation, in particular for the
package "affy" :
"Error: package 'affy' required by 'makecdfenv' could not be found"
I have tryed to install 'makecdfenv' with the command :
getBioC("makecdfenv")
But I have this message
2005 Sep 08
1
Install packages to non-default lib on Windows
We are trying to setup a Windows server that will allow any of our
users to build a binary R package given a source package.
The idea is to have a central R installation and allow users to
install packages to their own package library for the purposes of
binary package building.
It seems, however, that write access to $R_HOME is required as part of
the install step even when -l is used to
2008 Nov 15
1
unable to view vignette in R
Hello All R-Gurus:
ISSUE:
Cannot view R vignettes due in Ubuntu Linux (a debian variant).
note: this issue has been posted to this list before with no responses given
see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html
DETAILS:
I am trying to view an R vignette.
Here is the situation: I issue the openvignette(), then select the
vignette I wish to view...and the system returns:
2003 Sep 11
1
potentially nasty interaction between R 1.8.0 and tetex
I've been having problems building vignettes in bioconductor packages
with R-devel. Turns out that Rdevel/share/texmf/hyperref.cfg wants
Blue and Red predefined, when only blue and red are defined (as of
rsync Rdevel, Sept 10th). This is on a Debian unstable system (Sept
9th version). Might not apply to all other tetex systems. Seems to
have bitten the bioconductor build system, though.
2008 Sep 05
1
Problem installing Biobase on Solaris
Hi everyone
This is my first post to the list. I had experience installing and using
Bioconductor on Linux and Windows systems but I am encountering problems
installing Biobase on Solaris running on Sparc. The package compilation
works fine, with only a warning
warning: implicit declaration of function `__builtin_isnan'
the help files are generated but in the end it fails with an error
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 =
2012 Nov 26
1
A problem subsetting a data frame
Hi all,
I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows
> testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4"))
>> Error in
2006 Oct 11
1
Possible bug in accessing methods documentation?
Hi,
Reading help("Documentation"), I'm led to believe that a help call
like:
?myFun(x, sqrt(wt))
Will search for help on the appropriate method in the case that myFun
is generic. This isn't working for me. Here is an example using the
Biobase package:
## If Biobase is not installed
source("http://bioconductor.org/biocLite.R")
biocLite("Biobase")
2006 Oct 11
1
Possible bug in accessing methods documentation? (PR#9291)
On 10/11/2006 2:48 PM, Seth Falcon wrote:
> Hi,
>
> Reading help("Documentation"), I'm led to believe that a help call
> like:
>
> ?myFun(x, sqrt(wt))
>
> Will search for help on the appropriate method in the case that myFun
> is generic. This isn't working for me. Here is an example using the
> Biobase package:
>
> ## If Biobase is
2003 Sep 05
2
S4 Method Collisions with "[" (PR#4075)
Full_Name: Colin A. Smith
Version: 1.8.0
OS: Mac OS X 10.2.6
Submission from: (NULL) (216.102.90.18)
Both Biobase and my package annaffy use S4 classes to define methods for "[".
Both packages use the save image method of installation. (See annaffy 1.0.3 in
BioC CVS.)
Depending on how both packages are loaded, the Biobase definitions seem to be
getting masked out:
>
2003 Oct 27
1
initialization of S4 classes/methods
I'm seeing weird issues in methods initialization, i.e. loading
marrayClasses loads Biobase, and when explicitly done, as in
library(Biobase)
library(marrayClasses)
is fine, but when Biobase is loaded via a require statement in
marrayClasses' .First.Lib, I end up with:
Warning message: In the method signature for function "coerce", class
"exprSet" has no
2003 Sep 18
2
R-1.7.1 package installation problem
Hi there,
I am a bioinformatician working in DFCI. I am new to R. Yesterday I installed
the R-1.7.1 to my Linux (since I am not able to find R-1.8 on the webpage). But
I have some package installation problems ...
1. install.packages2() function isn't available. If I type at R prompt:
>install.packages2("Biobase")
Error: couldn't find function
2010 Oct 24
1
R-devel CMD build fails when vignette present
If I try to build a package with a vignette
R CMD build Biobase
I see
* checking for file 'Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* creating vignettes ... OK
* cleaning src
Error in setwd(pkgname) : cannot change working directory
Execution halted
This is
2002 Jun 10
2
library() with v. 1.5.0 for Mac OS X Carbon
I am having trouble with the library function of R Version 1.5.0 for Mac
OS X Carbon when I try to load libraries that did not come with the R
installation. For example, I put the Biobase library from
bioconductor.org in the 'library' folder. R cannot find it, even though
it can find the pre-installed libraries:
> library() # this lists standard libraries such as 'boot',