Dear Forum
my machine runs Ubuntu 9.04. I am trying to install Biomart, what I realize
is that something is missing and it can't install XML, RCurl but I don't
know what more to do, I looked in previous posts but I did not find
infoprmation that helped.
Thanks
Andreia
biocLite("biomaRt")
Running biocinstall version 2.3.14 with R version 2.8.1
Your version of R requires version 2.3 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using
'/home/user/R/x86_64-pc-linux-gnu-library/2.8'
also installing the dependencies XML, RCurl
trying URL 'http://cran.fhcrc.org/src/contrib/XML_2.6-0.tar.gz'
Content type 'application/x-gzip' length 680366 bytes (664 Kb)
opened URL
==================================================
downloaded 664 Kb
trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.3-0.tar.gz'
Content type 'application/x-gzip' length 799689 bytes (780 Kb)
opened URL
==================================================
downloaded 780 Kb
trying URL '
http://bioconductor.org/packages/2.3/bioc/src/contrib/biomaRt_1.16.0.tar.gz'
Content type 'application/x-gzip' length 278561 bytes (272 Kb)
opened URL
==================================================
downloaded 272 Kb
* Installing *source* package 'XML' ...
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 ANSI C... 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
ERROR: configuration failed for package 'XML'
** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/XML'
* Installing *source* package 'RCurl' ...
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package 'RCurl'
** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/RCurl'
* Installing *source* package 'biomaRt' ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths())) :
there is no package called 'RCurl'
Calls: <Anonymous> ... code2LazyLoadDB -> loadNamespace -> namespaceImport
-> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'biomaRt'
** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/biomaRt'
The downloaded packages are in
/tmp/RtmpzdpweV/downloaded_packages
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
installation of package 'XML' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
installation of package 'RCurl' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
installation of package 'biomaRt' had non-zero exit status
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