Entering edit mode
Hi,
On Thu, Feb 14, 2013 at 3:39 PM, Maintainer <maintainer at="" 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/contri
b/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/contri
b/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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