Displaying 20 results from an estimated 5000 matches similar to: "[BioC] Errors using biocLite on Apple OS X"
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
2012 Jan 18
1
png cairo device problems on Mac 10.6.8
Hi all,
I have been having problems generating png files on a Mac running OS X 10.6.8.
Here's a simple example
> png("foo.png", type = "cairo"); plot(1:10); dev.off();
null device
1
libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
The resultant file is of size 0 Kb.
Is this the proper place to report this issue? Or should
2008 Dec 01
1
[BioC] Rcurl 0.8-1 update for bioconductor 2.7
Hi Patrick,
Greetings from !(sunny) Pittsburgh.
What's the scoop on RCurl on windows (XP)?
I've tried to install RCurl_0.92-0.zip and RCurl_0.9-3.zip,
with both R 2.7.2 and R 2.8.0 from the RGUI (utils:::menuInstallLocal),
and get the error
"Windows binary packages in zipfiles are not supported".
which (according to google's one and only hit) comes from a perl script.
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 Aug 03
4
FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
Hi all,
What are current methods people use in R to identify
mis-spelled column names when selecting columns
from a data frame?
Alice Johnson recently tackled this issue
(see [BioC] posting below).
Due to a mis-spelled column name ("FileName"
instead of "Filename") which produced no warning,
Alice spent a fair amount of time tracking down
this bug. With my fumbling fingers
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
2006 Oct 12
1
getMethods() not finding all methods
Running R2.4.0 on Apple Mac OS X 10.4.8,
in Emacs ESS mode, and also R.app.
In an attempt to learn a bit more about
a particular method (geneNames in package affy)
I invoked
getMethods("geneNames")
which produced geneNames methods, but not the
one in affy (output below).
I had to know the signature (AffyBatch) in order
to find the method
> getMethod("geneNames",
2006 Jul 20
3
How do I modify an exported function in a locked environment?
Running R.app on Mac OS X 10.4
> version
_
platform powerpc-apple-darwin8.6.0
arch powerpc
os darwin8.6.0
system powerpc, darwin8.6.0
status
major 2
minor 3.1
year 2006
2006 Jul 20
3
How do I modify an exported function in a locked environment?
Running R.app on Mac OS X 10.4
> version
_
platform powerpc-apple-darwin8.6.0
arch powerpc
os darwin8.6.0
system powerpc, darwin8.6.0
status
major 2
minor 3.1
year 2006
2008 Jul 27
1
64-bit R on Mac OS X 10.5.4
Hi Matt
Your method is the easiest way for me to install the 64-bit R. I followed the directions on your web site and then did the following:
R --arch=x86_64
source("http://bioconductor.org/biocLite.R")
biocLite(type = "source",lib = "/Library/Frameworks/R.framework/Versions/2.8/Resources/RLib64")
I got many errors and warnings which I copied to the attached file.
2013 Mar 04
4
enabling reproducible research & R package management & install.package.version & BiocLite
Hi,
In support of reproducible research at my Institute, I seek an approach to re-creating the R environments in which an analysis has been conducted.
By which I mean, the exact version of R and the exact version of all packages used in a particular R session.
I am seeking comments/criticism of this as a goal, and of the following outline of an approach:
=== When all the steps to an workflow
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
2017 Nov 01
0
beta binomial distribution installation
Hello,
Thank you for your response. I need to install RankTail package since it contains the beta binomial distribution, CDF and inverse CDF in the usual form which I need to use. However rmutil package contain unusual forms for these functions. So it is easier for me to deal with the forms are contained in RankTail.
I tried to install bioconductor package, using the following commands but 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
2006 Oct 08
2
'weaver' package problem
Hi Seth,
The possibility of caching computations would be a great boon when
one is iteratively refining a paper; so I'm most grateful for your
work on this. Unfortunately I have a problem to report:
******************installing******************
> source("http://bioconductor.org/biocLite.R")
> biocLite("weaver")
Running getBioC version 0.1.8 with R version
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
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
2008 Jul 04
1
Problem in installing Biobase
Hi,
Recently I try to install Biobase component using the tutorials from
cran.r-project.org/doc/Rnews/Rnews_2006-5.pdf
I tried
u <- "http://bioconductor.org/biocLite.R"
> source(u)
> biocLite("pkgDepTools", dependencies=TRUE)
Running biocinstall version 2.0.8 with R version 2.5.1
Your version of R requires version 2.0 of Bioconductor.
Warning in
2008 Jul 17
2
Fw: how i can install Rgraphviz in R2.7.1
--- On Tue, 15/7/08, haani hanni <maaryam_khan@yahoo.com> wrote:
From: haani hanni <maaryam_khan@yahoo.com>
Subject: how i can install Rgraphviz in R2.7.1
To: "Nabble" <support@nabble.com>
Cc: r-help-request@r-project.org
Date: Tuesday, 15 July, 2008, 1:39 PM
hello
i am a new user of R.i have window XP Proffessional in my P.C.i wanted to make the graphs of my
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")