Question: There were no GEOquery function after installing
0
gravatar for Ginsea Chen
4.5 years ago by
Ginsea Chen120
Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
Ginsea Chen120 wrote:

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?

 

 

R software error • 4.3k views
ADD COMMENTlink modified 4.5 years ago by Neilfws48k • written 4.5 years ago by Ginsea Chen120
4
gravatar for Neilfws
4.5 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 4.5 years ago by Neilfws48k

Dear Neilfws

The question have been solved, Thanks for your help.

Best regards

Ginsea Chen

ADD REPLYlink written 4.5 years ago by Ginsea Chen120
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