There were no GEOquery function after installing

Question

[Ginsea Chen]

Hi

I have some questions when I try to use GEOquery to obtain GEO database. 

First, I installed GEOquery through follow steps:

> source('http://bioconductor.org/biocLite.R')
Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help
> biocLite('GEOquery')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
  3.1.0.
Installing package(s) 'GEOquery'
also installing the dependencies ‘XML’, ‘RCurl’

trying URL 'http://mirrors.xmu.edu.cn/CRAN/src/contrib/XML_3.98-1.1.tar.gz'
Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb

trying URL 'http://mirrors.xmu.edu.cn/CRAN/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://bioconductor.org/packages/2.14/bioc/src/contrib/GEOquery_2.30.0.tar.gz'
Content type 'application/x-gzip' length 13636235 bytes (13.0 Mb)
opened URL
==================================================
downloaded 13.0 Mb

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... rm: cannot remove `a.out.dSYM': Is a directory
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
ERROR: configuration failed for package ‘XML’
* removing ‘/home/ginsea/R-3.1.0/library/XML’
* 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/ginsea/R-3.1.0/library/RCurl’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘GEOquery’
* removing ‘/home/ginsea/R-3.1.0/library/GEOquery’

The downloaded source packages are in
    ‘/tmp/RtmpfM5wSK/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘GEOquery’ had non-zero exit status

then I tried to use GEOquery through inputting:

> library(GEOquery)

but R told me "Error in library(GEOquery) : there is no package called ‘GEOquery' "

library("GEOquery") has the same question.

So I don't sure what should I do?

 

 

Answer 1

[Neilfws]

Your basic problem is that GEOquery did not install correctly:

  installation of package ‘GEOquery’ had non-zero exit status

The reason for that is that the dependencies "XML" and "RCurl" also failed to install properly:

  installation of package ‘XML’ had non-zero exit status
  installation of package ‘RCurl’ had non-zero exit status

Working our way back through the warnings and errors, we can see that the installation did not find two tools on your system: curl-config and xml2-config. This is because extra packages are required on your system.

I am assuming that you are using some kind of Linux. You need the libxml2 and libcurl4 development packages. On an Ubuntu-based Linux, this is quite simple:

sudo apt-get install libxml2-dev
sudo apt-get install libcurl4-openssl-dev

You can check that everything worked using "which curl-config" and "which xml2-config", then try 'biocLite("GEOquery")' again.

[Ginsea Chen]

Dear Neilfws

The question have been solved, Thanks for your help.

Best regards

Ginsea Chen