[BioC] failed to install biocondoctuor

[Steve Lianoglou]

Hi,

On Tue, Dec 3, 2013 at 5:47 AM, Wang Peter <wng.peter at gmail.com> wrote:
> i just reinstall the biocondoctuor in china.
> it is very slow, due to chinese restriction to foreign website

I never knew that was "a thing" ... seems rather unfortunate.

Are there bioc (or at least CRAN) mirrors *within* China? Perhaps that
might help.

> and i meet such error, i never met before

The errors below do seem rather strange. Seems to suggest that many
files were only partially downloaded.

I'd try another mirror first (even if you can't get one within China),
and then I'd try to download the package (and its dependencies) that
you are trying to install second to see if you can do it manually.

I'd also suggest you upgrade to R 3.0.2 first before continuing.

HTH,
-steve

>
>
> 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
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>
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-- 
Steve Lianoglou
Computational Biologist
Genentech