On 03/05/2015 01:21 AM, Zaynab Mousavian wrote:> Hi all,
>
> I have tried to install GO.db package in R, but the following error is
please ask questions about Bioconductor packages on the Bioconductor support
forum https://support.bioconductor.org. Please also review answers to your
question on Biostars first.
You are using an old version of R / Bioconductor but a new version of RSQLite.
Use either a current version of R / Bioconductor or an old version of RSQLite,
as explained here https://support.bioconductor.org/p/63555.
If you are having trouble installing a current version of R on linux, indicate
your OS and how you are currently installing R. Be sure to follow the relevant
directions from, e.g., http://cran.r-project.org/. Perhaps the R-SIG-Debian
archives and mailing list have additional hints
https://stat.ethz.ch/pipermail/r-sig-debian/.
Martin
> given to me:
>
> biocLite(c("GO.db"))
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
> Installing package(s) 'GO.db'
> trying URL
>
'http://bioconductor.org/packages/2.13/data/annotation/src/contrib/GO.db_2.10.1.tar.gz'
> Content type 'application/x-gzip' length 26094175 bytes (24.9 Mb)
> opened URL=================================================> downloaded
24.9 Mb
> * installing *source* package ?GO.db? ...** R** inst** preparing
> package for lazy loading** help*** installing help indices** building
> package indices** testing if installed package can be loaded
> Error : .onLoad failed in loadNamespace() for 'GO.db', details:
> call: match.arg(synchronous, c("off", "normal",
"full"))
> error: 'arg' must be NULL or a character vector
> Error: loading failed
> Execution halted
> ERROR: loading failed* removing
> ?/home/zmousavian/R/x86_64-pc-linux-gnu-library/3.0/GO.db?
>
> The downloaded source packages are in
> ?/tmp/RtmpBDs1Tq/downloaded_packages?
> Warning messages:1: In install.packages(pkgs = pkgs, lib = lib, repos
> = repos, ...) :
> installation of package ?GO.db? had non-zero exit status2: installed
> directory not writable, cannot update packages
'colorspace','lattice',
> 'mgcv', 'survival'
>
>
> Can anyone help me to install it?
>
> Regards
>
>
>
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