[BioC] failed to install biocondoctuor

[Dan Tenenbaum]

You don't say which mirrors you are using. What is the output of:

library(BiocInstaller)
biocinstallRepos()

?

Try using the mirror that Tengfei Yin set up in China:

http://mirrors.ustc.edu.cn/bioc/

You should also pick a CRAN mirror in China, from this list:

http://cran.r-project.org/mirrors.html

Dan


----- Original Message -----
> From: "Wang Peter" <wng.peter at gmail.com>
> To: bioconductor at r-project.org
> Sent: Tuesday, December 3, 2013 5:47:32 AM
> Subject: [BioC] failed to install biocondoctuor
> 
> i just reinstall the biocondoctuor in china.
> it is very slow, due to chinese restriction to foreign website
> 
> and i meet such error, i never met before
> 
> 
> package �annotate� successfully unpacked and MD5 sums checked
> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> "Type"))
> :
>   cannot open the connection
> In addition: Warning messages:
> 1: packages �base�, �boot�, �class�, �compiler�, �datasets�,
> �foreign�,
> �graphics�, �grDevices�, �grid�, �MASS�, �methods�, �nlme�,
> �parallel�,
> �spatial�, �splines�, �stats�, �stats4�, �tcltk�, �tools�, �utils�
> are not
> available (for R version 2.15.2)
> 2: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 262334 != reported length 4200978
> 3: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 57623 != reported length 2346708
> 4: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 436576 != reported length 889011
> 5: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 1481998 != reported length 2048190
> 6: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 589241 != reported length 724724
> 7: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 123147 != reported length 3506196
> 8: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
> file
> 9: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> "Type")) :
>   cannot open compressed file 'AnnotationDbi/DESCRIPTION', probable
>   reason
> 'No such file or directory'
> > sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: i386-w64-mingw32/i386 (32-bit)
> locale:
> [1] LC_COLLATE=Chinese_People's Republic of China.936
> [2] LC_CTYPE=Chinese_People's Republic of China.936
> [3] LC_MONETARY=Chinese_People's Republic of China.936
> [4] LC_NUMERIC=C
> [5] LC_TIME=Chinese_People's Republic of China.936
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] BiocInstaller_1.8.3
> loaded via a namespace (and not attached):
> [1] tools_2.15.2
> 
> --
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute for Plant Research
> Cornell University
> Tower Road, Ithaca, NY 14853-1801
> Office phone: 1-607-254-1267(day)
> Official email:sg839 at cornell.edu
> Facebook:http://www.facebook.com/profile.php?id=100001986532253
> 
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> 
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