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@gene.com> > Hi, > > On Thu, Oct 10, 2013 at 6:30 PM, ÁõÅô·É <liupfskygre@gmail.com> 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 > -- Pengfei Liu, PhD Candidate Lab of Microbial Ecology College of Resources and Environmental Sciences China Agricultural University No.2 Yuanmingyuanxilu, Beijing, 100193 P.R. China Tel: +86-10-62731358 Fax: +86-10-62731016 E-mail: liupfskygre@gmail.com If you are afraid of tomorrow, how can you enjoy today! Keep hungry, Keep foolish! Moving forward! [[alternative HTML version deleted]]