[BioC] bioc package installation problem

[Dan Tenenbaum]

On Tue, Apr 9, 2013 at 12:03 PM, carol white <wht_crl at yahoo.com> wrote:
> Hi,
> I can't install ShortRead package. Is it because biocLite doesn't install automatically the dependencies and I have to install them before ShortRead?
>
>
> Best,
>
> Carol
>
> --------------------------------------------------------------------------
>
> source("http://bioconductor.org/biocLite.R")
> BiocInstaller version 1.2.1, ?biocLite for help
>>  biocLite("ShortRead")
> BioC_mirror: 'http://www.bioconductor.org'
> Using R version 2.14, BiocInstaller version 1.2.1.
> Installing package(s) 'ShortRead'
> also installing the dependencies ‘RCurl’, ‘XML’, ‘rtracklayer’, ‘Rsamtools’
>
> trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.1.tar.gz'
> Content type 'application/x-gzip' length 870915 bytes (850 Kb)
> opened URL
> ==================================================
> downloaded 850 Kb
>
> trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz'
> Content type 'application/x-gzip' length 1578308 bytes (1.5 Mb)
> opened URL
> ==================================================
> downloaded 1.5 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
>
> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/ShortRead_1.12.4.tar.gz'
> Content type 'application/x-gzip' length 2104718 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 ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/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
> checking for sed... /bin/sed
> checking for pkg-config... /usr/bin/pkg-config
> checking for xml2-config... no
> Cannot find xml2-config


This means you need libcurl/libxml2 on your system. I'm not sure which linux
distribution you are running but on Ubuntu the command to install this
is:

sudo apt-get insgtall libxml2-dev libcurl-dev


Dan


> ERROR: configuration failed for package ‘XML’
> * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/XML’
> ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package ‘rtracklayer’
> * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/rtracklayer’
> ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’
> * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
> ERROR: dependency ‘Rsamtools’ is not available for package ‘ShortRead’
> * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/ShortRead’
>
> The downloaded packages are in
>     ‘/tmp/Rtmpn9i2Os/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
> 5: In install.packages(pkgs = pkgs, repos = repos, ...) :
>   installation of package ‘ShortRead’ had non-zero exit status
>         [[alternative HTML version deleted]]
>
>
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