[BioC] Installing packages

[Dan Tenenbaum]

Rohmatul Fajriyah wrote:

> Dear All,
>
> I recently tried to use the Biconductor Cloud AMI (RStudio).
>
> I installed some packages and it was ok.
> Then I installed the "gsl", "Rcmdr" and "MBCB"packages and it was not ok.
>
> For the "Rcmdr" and "MBCB", the message was:
> Warning in fun(libname, pkgname) : couldn't connect to display ":0"
>

Rcmdr will not work under Rstudio Server. They use different GUI paradigms.

>
> For the "gsl", the message was:
>
> Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> * installing *source* package ‘gsl’ ...
> ** package ‘gsl’ successfully unpacked and MD5 sums checked
> checking for gsl-config... no
> configure: error: gsl-config not found, is GSL installed?
> ERROR: configuration failed for package ‘gsl’
> * removing ‘/home/ubuntu/R/library/gsl’
> Warning in install.packages :
>   installation of package ‘gsl’ had non-zero exit status
>
> Here for the sessionInfo()
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> Â [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C Â  Â  Â  Â  LC_TIME=C Â  Â  Â  Â  Â  Â LC_COLLATE=C Â  Â  Â  Â
> Â [5] LC_MONETARY=C Â  Â  Â  Â LC_MESSAGES=C Â  Â  Â  Â LC_PAPER=C Â  Â  Â  Â  Â  LC_NAME=C Â  Â  Â  Â  Â Â
> Â [9] LC_ADDRESS=C Â  Â  Â  Â  LC_TELEPHONE=C Â  Â  Â  LC_MEASUREMENT=C Â  Â  LC_IDENTIFICATION=CÂ
>
> attached base packages:
> [1] tcltk     stats     graphics  grDevices utils     datasets  methods   base    Â
>
> other attached packages:
> Â [1] NormalGamma_0.1.0 Â  histogram_0.0-23 Â  Â optimx_2012.04.01 Â  numDeriv_2012.9-1 Â
> Â [5] car_2.0-15 Â  Â  Â  Â  Â nnet_7.3-4 Â  Â  Â  Â  Â MASS_7.3-21 Â  Â  Â  Â  ffpe_1.2.0 Â  Â  Â  Â Â
> Â [9] TTR_0.21-1 Â  Â  Â  Â  Â xts_0.8-8 Â  Â  Â  Â  Â  zoo_1.7-7 Â  Â  Â  Â  Â  lumi_2.10.0 Â  Â  Â  Â
> [13] nleqslv_1.9.4 Â  Â  Â  affy_1.36.0 Â  Â  Â  Â  Biobase_2.18.0 Â  Â  Â BiocGenerics_0.4.0Â
> [17] MBCB_1.12.0 Â  Â  Â  Â  tcltk2_1.2-3 Â  Â  Â  Â BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
> Â [1] AnnotationDbi_1.20.0 Â DBI_0.2-5 Â  Â  Â  Â  Â  Â  IRanges_1.16.2 Â  Â  Â Â
> Â [4] KernSmooth_2.23-8 Â  Â  Matrix_1.0-9 Â  Â  Â  Â  Â RSQLite_0.11.2 Â  Â  Â Â
> Â [7] XML_3.95-0.1 Â  Â  Â  Â  Â affyio_1.26.0 Â  Â  Â  Â  annotate_1.36.0 Â  Â  Â
> [10] colorspace_1.1-1 Â  Â  Â grid_2.15.1 Â  Â  Â  Â  Â  lattice_0.20-10 Â  Â  Â
> [13] methylumi_2.4.0 Â  Â  Â  mgcv_1.7-21 Â  Â  Â  Â  Â  nlme_3.1-104 Â  Â  Â  Â Â
> [16] parallel_2.15.1 Â  Â  Â  preprocessCore_1.20.0 sfsmisc_1.0-23 Â  Â  Â Â
> [19] stats4_2.15.1 Â  Â  Â  Â  tools_2.15.1 Â  Â  Â  Â  Â xtable_1.7-0 Â  Â  Â  Â Â
> [22] zlibbioc_1.4.0Â
>

I have now installed gsl on the BioC 2.11 AMI, so if you start a new
instance, this package should be installed.

Dan


> Any help, is really appreciated, Â please ...
>
> Thank you very much.
>
> With kind regards,
> R Fajriyah
> (as far as I am concerned, I am not a member of this group yet)


>
>     [[alternative HTML version deleted]]
>