Displaying 20 results from an estimated 1100 matches similar to: "installing dependencies: binary vs source"
2010 Nov 10
1
installed.packages Error: subscript out of bounds
Hi,
Today we've seen the following problem with the R-2.12 that we use
for our Windows builds:
> installed.packages()
Error: subscript out of bounds
After some investigation we discovered that the cause of this failure
was that 1 of the 890 packages currently installed on the machine
(Windows Server 2003 R2) had its DESCRIPTION file empty:
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 =
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 Nov 18
1
Why SAM has totally diffent results in R2.1.1 and R2.4.0
Hi,
I am using SAM (from siggenes_1.2.11 package) method to select genes from
a microarray data set. After installing the latest R2.4.0 on my computer, to
my surprise the results are totally different from that calculated using
R2.1.1. Even the example code doesn't work the same way under these two
versions of R. Does anybody know what is going on? Thanks for any
suggestions.
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
2010 Oct 11
1
'R CMD build' not cleaning the src/ folder on Windows
Hi,
'R CMD build' (with R 2.12.0 RC) fails to clean the src/ folder
on Windows:
D:\biocbld\bbs-2.7-bioc>ls meat/BUS/src
BUS.cpp BUS.h
D:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\BUS
* checking for file 'meat\BUS/DESCRIPTION' ... OK
* preparing 'BUS':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package
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
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
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
2010 Jul 13
6
permutation-based FDR
Hola a todos,
Tengo un pequeño problemilla...
Tengo unas 9000 variables que he contrastado con 1 en concreto con el test
de wilcoxon. He calculado el p-valor, y queria corregirlo con el
permutation-based FDR. He encontrado una funcion con R comp.fdr()que hace
esta corrección, pero te pide que le pongas las variables con las
observaciones y te hace el test (según he entendido). Yo solo quiero
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
2006 Jun 29
2
Biobass, SAGx, and Jonckheere-Terpstra test
Hi list,
I tried to load the package SAGx and failed because it complains it's
looking for the Biobass which is not there. Then I looked up the package
list and Biobass is not found.
I'm trying to run the Jonckheere-Terpstra test and from what I see in
the R archive, SAGx is the only place it's been implemented.
> library(SAGx)
Loading required package: multtest
Loading required
2010 Jun 10
1
R-based version of R CMD build broken on Windows
Hi,
The R-based version of R CMD build doesn't work for me on Windows:
E:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\Biobase
* checking for file 'meat\Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
Warning in shell(sprintf("%s > %s
2004 Jan 20
1
Re: Need help on how to list functions from a loaded package...
To All
How does one get a list of functions from a loaded package so that one can
then get the appropriate help for each of the functions. Currently my
method is
based on a lot of trial-and-error.
Here's an example of what I mean...
>From this forum I learn that an interesting package called "multtest" exists
on Bioconductor.
I then use R Console's "Packages" --
2002 Mar 06
3
Problem in .First.lib
Hello!
I downloaded a package "multtest" (from bioconductor.org) in R, and
installed it by 'R CMD <package>' (after unzipping and taring).
The problem is when I say 'library(multtest)' in R, the following error is
generated:
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
2006 Feb 01
1
R CMD check barfs at 'suggested' package
I have been running R CMD check for the first time on of our own
packages, which otherwise builds, installs and runs just fine. The
package depends on package akima and suggests package multtest;
suggesting multtest is indicated because a) it loads a lot of other
Bioconductor packages, very slowly, and b) it is only needed for one
specific subroutine, which executes require(multtest)
2005 Oct 10
1
bug loading libraries with winXP and 2.2.0 but not 2.1.1 (PR#8200)
Full_Name: Ken Kompass
Version: 2.2.0
OS: winXP pro (2002 version, SP2)
Submission from: (NULL) (128.252.149.244)
Using R2.2.0 I get this error msg when loading certain bioconductor libraries
(depending on whether the library contains file named "all.rda" in R folder of
library) :
> library(multtest)
Error in open.connection(con, "rb") : unable to open connection
In
2006 Feb 01
1
Rd files with unknown sections
Hi,
With recent versions of R-devel, "R CMD check" complains about
some "Rd files with unknown sections".
hpages at gladstone:~> R CMD check multtest_1.9.4.tar.gz
...
...
* checking Rd files ... WARNING
Rd files with unknown sections:
/home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/boot.resample.Rd:
notes
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