[BioC] problems installing lumi

Pan Du dupan.mail at gmail.com
Thu Sep 6 16:59:51 CEST 2012


Hi Hermann

Based on your screen printout, I believe your R installation has problem.
After R installation, try biocLite first.
  source('http://bioconductor.org/biocLite.R')
  biocLite()
Then install R
  biocLite('lumi')
If some required package cannot  be installed. Try to install them
manually. For example:
  install.package('hdrcde')
Or you can download from CRAN website and install locally.
After install missing dependent packages, try biocLite('lumi') again.


Pan

On Thu, Sep 6, 2012 at 3:00 AM,  <bioconductor-request at r-project.org> wrote:

> ------------------------------
> Date: Thu, 6 Sep 2012 10:02:14 +0200
> From: Hermann Norpois <hnorpois at googlemail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] problems installing lumi
> Message-ID:
>         <CAKyZeBtm+ysKj12eYCHFn=7cHPHxwJO_tDuVzKiJSWExyN_z1w at mail.gmail.com>
> Content-Type: text/plain
>
> Dear list,
>
> I had and still have trouble installing lumi. After an R update and the
> installation of the hdrcde package it still does not work with the lumi
> package via biocLite("lumi"). This is the answer (R version 2.15): And I
> was not able to install the packages with dependencies neither.
>
> I would be happy for some help.
> Thanks
> Hermann Norpois
>
> * installing *source* package ‘XML’ ...
> ** Paket ‘XML’ erfolgreich entpackt und MD5 Summen überprüft
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> No ability to remove finalizers on externalptr objects in this verison of R
> checking for sed... /bin/sed
> checking for pkg-config... /usr/bin/pkg-config
> checking for xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package ‘XML’
> * removing ‘/usr/local/lib/R/site-library/XML’
> * installing *source* package ‘RCurl’ ...
> ** Paket ‘RCurl’ erfolgreich entpackt und MD5 Summen überprüft
> checking for curl-config... no
> Cannot find curl-config
> ERROR: configuration failed for package ‘RCurl’
> * removing ‘/usr/local/lib/R/site-library/RCurl’
> ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package
> ‘rtracklayer’
> * removing ‘/usr/local/lib/R/site-library/rtracklayer’
> ERROR: dependency ‘XML’ is not available for package ‘annotate’
> * removing ‘/usr/local/lib/R/site-library/annotate’
> ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
> * removing ‘/usr/local/lib/R/site-library/genefilter’
> ERROR: dependencies ‘annotate’, ‘genefilter’ are not available for package
> ‘methylumi’
> * removing ‘/usr/local/lib/R/site-library/methylumi’
> ERROR: dependencies ‘methylumi’, ‘rtracklayer’, ‘annotate’ are not
> available for package ‘lumi’
> * removing ‘/usr/local/lib/R/site-library/lumi’
>
>         [[alternative HTML version deleted]]
>
>
>
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