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?