刘鹏飞 | 13 Oct 06:59 2013
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Re: Install DESeq2 on windows R 3.0.1/2

Hi£¬
Thanks Steve. I am not familiar with R and did not keep the sessionInfo()
as the error appeared. And I think now the problem is solved by using
Rtools to install package locfit from sources.

>Can you explain what you mean by "automatically install"? Are you installing
using the biocLite function, or?
Yes, by using the following on R 3.0.1
source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")

> I search the CRAN (http://ftp.ctex.org/mirrors/CRAN/), but the lattest
> version was built on R 2.15.
>I'm curious where you are able to find that information from the website?
I did not find that information from the website. The error occur in
Chinese so I translated into English: locfit was bulit before R 3.0.0. So I
serarch the CRAN for the lattest version of windows binary and get
locfit_1.5-9.1.zip,
after remove the install locfit package, I reinstall the
the locfit_1.5-9.1.zip from R by the install from zip file way. After I
check the descrption of the locfit package in the R/library/locfit and find
the information that it is built on R 2.15.3 (Built: R 2.15.3;
i386-w64-mingw32; 2013-10-07 04:27:30 UTC; windows
). which means the lattest version is built before R 3.0.0, the same as the
error suggested.

>Again -- what do you mean by "automatically installation" of R 3.0.2?
source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")
error : DESeq2 is not available now for R 3.0.2

Now I solve the problem by following steps
1, copy the DESeq2 file in the library of R 3.0.1 to the library R 3.0.2
(several packages need to be modified because the lattest version of them
built on R 3.0.2, so in R 3.0.1 I need to change all of them, but in R
3.0.2 I just need to reinstall locfit)

2, Install Rtools R 3.0.x and using the following command to install locfit
from source in cmd:
Rcmd INSTALL ¡°C:/Users/microbe/Downloads/locfit_1.5-9.1.tar.gz¡± -l
¡°D:\R-3.0.2\library¡±
and the description of licfit now is:
Built: R 3.0.2; i386-w64-mingw32; 2013-10-10 10:50:00 UTC; windows

now after load  DESeq2
>sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] DESeq2_1.0.19           RcppArmadillo_0.3.920.1 Rcpp_0.10.5
[4] lattice_0.20-23         Biobase_2.21.7          GenomicRanges_1.12.5
[7] IRanges_1.19.38         BiocGenerics_0.7.5

loaded via a namespace (and not attached):
 [1] annotate_1.39.0       AnnotationDbi_1.23.27 DBI_0.2-7
 [4] genefilter_1.43.0     grid_3.0.2            locfit_1.5-9.1
 [7] RColorBrewer_1.0-5    RSQLite_0.11.4        splines_3.0.2
[10] stats4_3.0.2          survival_2.37-4       XML_3.98-1.1
[13] xtable_1.7-1

seems all OK, am I right?

2013/10/11 Steve Lianoglou <lianoglou.steve@...>

> Hi,
>
> On Thu, Oct 10, 2013 at 6:30 PM, ÁõÅô·É <liupfskygre@...m> wrote:
> > Hi
> >    I have a problem on installation of DESeq2 on windows. I use R 3.0.1.
> > After automatically install, I loaded  DESeq2, the error message:
> > the package locfit is built before 3.0.0, you should reinstall it.
>
> Can you explain what you mean by "automatically install"? Are you
> installing using the biocLite function, or?
>
> > I search the CRAN (http://ftp.ctex.org/mirrors/CRAN/), but the lattest
> > version was built on R 2.15.
>
> I'm curious where you are able to find that information from the website?
>
> > How could I solve this problems?
> >
> > BTW, automatically installation on R 3.0.2 was not available,
>
> Again -- what do you mean by "automatically installation" of R 3.0.2?
>
> > I copy the
> > DESeq2 file in the library of R 3.0.1, the same problem appers.
>
> Ca you paste the output of sessionInfo() after this warning is triggered?
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>

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