HI Dan,

I finally got a chance to try your instructions.  Just wanted to let you
know everything installed properly and I am now working with Rsamtools and
other Bioconductor packages. Thank you very much.  Cheers, Theresa

On Thu, Feb 14, 2013 at 5:45 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> Hi,
>
>
> On Thu, Feb 14, 2013 at 3:39 PM, Maintainer <maintainer@bioconductor.org>
> wrote:
> >
> > I am encountering a problem with trying to install Rsamtools from the
> latest release of Bioconductor. I am using R version 2.14 but the latest
> release of Bioconductor is for R version 2.15.  I am new to R and
> Bioconductor so I am wondering if these installation errors are due to the
> wrong version of R.   Unfortunately, I tried updating R (in Ubuntu 12.04)
> but my version of R still remains 2.14.
> >
>
> Follow the instructions at http://cran.r-project.org/bin/linux/ubuntu/
> to update your Ubuntu repositories so they point to the latest version
> of R.
>
> > I will continue try to update to R (ver 2.15) but can someone tell me if
> there is another potential problem based on the errors in my session output.
>
> Yes,  you need to
> sudo apt-get insgtall libxml2-dev libcurl-dev
>
> Dan
>
>
>
> Thanks.
> >
> >  -- output of sessionInfo():
> >
> >> source("http://bioconductor.org/biocLite.R")
> >> biocLite("Rsamtools")
> > BioC_mirror: 'http://www.bioconductor.org'
> > Using R version 2.14, BiocInstaller version 1.2.1.
> > Installing package(s) 'Rsamtools'
> > Installing package(s) into ‘/usr/local/lib/R/site-library’
> > (as ‘lib’ is unspecified)
> > also installing the dependencies ‘RCurl’, ‘XML’, ‘rtracklayer’
> >
> > trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-3.tar.gz'
> > Content type 'application/x-gzip' length 868491 bytes (848 Kb)
> > opened URL
> > ==================================================
> > downloaded 848 Kb
> >
> > trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.95-0.1.tar.gz'
> > Content type 'application/x-gzip' length 1724282 bytes (1.6 Mb)
> > opened URL
> > ==================================================
> > downloaded 1.6 Mb
> >
> > trying URL '
> http://www.bioconductor.org/packages/2.9/bioc/src/contrib/rtracklayer_1.14.4.tar.gz
> '
> > Content type 'application/x-gzip' length 1606020 bytes (1.5 Mb)
> > opened URL
> > ==================================================
> > downloaded 1.5 Mb
> >
> > trying URL '
> http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Rsamtools_1.6.3.tar.gz
> '
> > Content type 'application/x-gzip' length 2088820 bytes (2.0 Mb)
> > opened URL
> > ==================================================
> > downloaded 2.0 Mb
> >
> > * installing *source* package ‘RCurl’ ...
> > ** package ‘RCurl’ successfully unpacked and MD5 sums checked
> > checking for curl-config... no
> > Cannot find curl-config
> > ERROR: configuration failed for package ‘RCurl’
> > * removing ‘/usr/local/lib/R/site-library/RCurl’
> > * installing *source* package ‘XML’ ...
> > ** package ‘XML’ successfully unpacked and MD5 sums checked
> > 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’
> > ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package
> ‘rtracklayer’
> > * removing ‘/usr/local/lib/R/site-library/rtracklayer’
> > ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’
> > * removing ‘/usr/local/lib/R/site-library/Rsamtools’
> >
> > The downloaded packages are in
> >         ‘/tmp/RtmpGSb3No/downloaded_packages’
> > Warning messages:
> > 1: In install.packages(pkgs = pkgs, repos = repos, ...) :
> >   installation of package ‘RCurl’ had non-zero exit status
> > 2: In install.packages(pkgs = pkgs, repos = repos, ...) :
> >   installation of package ‘XML’ had non-zero exit status
> > 3: In install.packages(pkgs = pkgs, repos = repos, ...) :
> >   installation of package ‘rtracklayer’ had non-zero exit status
> > 4: In install.packages(pkgs = pkgs, repos = repos, ...) :
> >   installation of package ‘Rsamtools’ had non-zero exit status
> >>
> >
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
> >
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