On 07/25/2011 05:13 AM, Martin Morgan wrote:
On 07/25/2011 02:28 AM, Jane Merlevede wrote:
Hello,
As you advise me, I installed R version 2.14 but I can't use the DEXSeq
library: package "‘DEXSeq’ is not available (for R Under
development)"... Do you know why?
It's a Bioconductor package, installed the Bioconductor way,
http://bioconductor.org/install/
that is,
source("http://bioconductor.org/biocLite.R";)
biocLite("DEXSeq")
library(DEXSeq)
Glad the installation went ok, and I think DEXSeq will install correctly
for you.
Usually the 'devel' branch of R is quite stable, but actually just at
the moment there is some instability and you might experience problems
when trying to install or load some package combinations. One error
message is
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "[", for signature
"signature"
Error: loading failed
and unfortunately the only really accessible solution, if you encounter
this at a crucial stage of your analysis, is to wait a few days and
update your R.
Actually, a solution is to build R from a snapshot several days ago,
before 2011-07-21 from
ftp://ftp.stat.math.ethz.ch/Software/R
Martin
Martin
Thanks,
Jane
>R.2.14
R Under development (unstable) (2011-07-24 r56492)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
R est un logiciel libre livré sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de détails.
R est un projet collaboratif avec de nombreux contributeurs.
Tapez 'contributors()' pour plus d'information et
'citation()' pour la façon de le citer dans les publications.
Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.
> install.packages("DEXSeq")
--- SVP sélectionner un miroir CRAN pour cette session ---
CRAN mirror
1: Argentina (La Plata) 2: Argentina (Mendoza)
3: Australia (Canberra) 4: Australia (Melbourne)
5: Austria 6: Belgium
7: Brazil (PR) 8: Brazil (RJ)
9: Brazil (SP 1) 10: Brazil (SP 2)
11: Canada (BC) 12: Canada (NS)
13: Canada (ON) 14: Canada (QC 1)
15: Canada (QC 2) 16: Chile
17: China (Beijing 1) 18: China (Beijing 2)
19: China (Hefei) 20: China (Hong Kong)
21: China (Xiamen) 22: Colombia (Bogota)
23: Colombia (Cali) 24: Denmark
25: France (Toulouse) 26: France (Lyon 1)
27: France (Lyon 2) 28: Germany (Berlin)
29: Germany (Goettingen) 30: Germany (Muenchen)
31: Germany (Wiesbaden) 32: Greece
33: Indonesia 34: Iran
35: Ireland 36: Italy (Milano)
37: Italy (Padua) 38: Italy (Palermo)
39: Japan (Hyogo) 40: Japan (Tsukuba)
41: Korea 42: Mexico (Mexico City)
43: Mexico (Texcoco) 44: Netherlands (Amsterdam)
45: Netherlands (Utrecht) 46: New Zealand
47: Norway 48: Philippines
49: Poland (Gdansk) 50: Poland (Oswiecim)
51: Poland (Wroclaw) 52: Russia
53: Singapore 54: Slovakia 1
55: Slovakia 2 56: South Africa
57: Spain (Madrid) 58: Sweden
59: Switzerland 60: Taiwan (Taichung)
61: Taiwan (Taipei 1) 62: Taiwan (Taipei 2)
63: Thailand 64: UK (Bristol)
65: UK (London) 66: UK (St Andrews)
67: USA (AZ) 68: USA (CA 1)
69: USA (CA 2) 70: USA (IA)
71: USA (MA) 72: USA (MI)
73: USA (MO) 74: USA (OH)
75: USA (OR) 76: USA (PA 1)
77: USA (PA 2) 78: USA (TX 1)
79: USA (TX 2) 80: USA (WA 1)
81: USA (WA 2)
Sélection : 26
Message d'avis :
In getDependencies(pkgs, dependencies, available, lib) :
package ‘DEXSeq’ is not available (for R Under development)
>
2011/7/24 Martin Morgan <mtmor...@fhcrc.org <mailto:mtmor...@fhcrc.org>>
On 07/22/2011 07:40 AM, Jane Merlevede wrote:
Hello,
I have used DESeq for gene differential expression analysis and
I would like
to use DEXSeq now for exon differential expression analysis.
The point is that the library DEXSeq seems to be available only
in R version
2.14.0 (unstable). I am working on Linux (CentOS), with R
version 2.13.0. I
have not found this R version 2.14.0 for Linux... Finally, I
cannot use
DEXSeq.
I would like to know if DEXSeq will be soon available in R
version 2.13.0.
Or is the only solution to work with Windows?
As Sean mentions, this requires R-devel. It is not that difficult to
build R from source on Linux, see sections 1 and 2 of
http://cran.fhcrc.org/doc/__manuals/R-admin.html
<http://cran.fhcrc.org/doc/manuals/R-admin.html>
The source code is available here
http://cran.fhcrc.org/sources.__html
<http://cran.fhcrc.org/sources.html>
you are looking for R-devel.tar.gz
Martin
Thank you for your help,
Jane Merlevède
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