[BioC] Installing Gostat
James W. MacDonald
jmacdon at uw.edu
Wed Oct 16 16:24:49 CEST 2013
On Wednesday, October 16, 2013 7:06:08 AM, R [guest] wrote:
>
> Installing GOstats gives the following error, any ideas what it could be?
>
>
>
>> biocLite("GOstats")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
> Installing package(s) 'GOstats'
> also installing the dependencies ‘GSEABase’, ‘genefilter’, ‘XML’, ‘Category’, ‘annotate’
>
> trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GSEABase_1.24.0.tar.gz'
> Content type 'application/x-gzip' length 233828 bytes (228 Kb)
> opened URL
> ==================================================
> downloaded 228 Kb
>
> trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/genefilter_1.44.0.tar.gz'
> Content type 'application/x-gzip' length 1145312 bytes (1.1 Mb)
> opened URL
> ==================================================
> downloaded 1.1 Mb
>
> trying URL 'http://cran.rstudio.com/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://bioconductor.org/packages/2.13/bioc/src/contrib/Category_2.28.0.tar.gz'
> Content type 'application/x-gzip' length 598049 bytes (584 Kb)
> opened URL
> ==================================================
> downloaded 584 Kb
>
> trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/annotate_1.40.0.tar.gz'
> Content type 'application/x-gzip' length 1834767 bytes (1.7 Mb)
> opened URL
> ==================================================
> downloaded 1.7 Mb
>
> trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GOstats_2.28.0.tar.gz'
> Content type 'application/x-gzip' length 2828202 bytes (2.7 Mb)
> opened URL
> ==================================================
> downloaded 2.7 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
^^^^^^^^^^^ That line is your hint. A quick google search will bring up
tons of similar questions, and the answer, which is that you need to
install the libxml2 and libxml2-dev packages.
How you do that is dependent on your distro, but assuming a Debian
variant, you would do something like
sudo apt-get install libxml2 libxml2-dev
Or maybe you just ask your sysadmin to install it for you, depending on
your situation.
Best,
Jim
> ERROR: configuration failed for package ‘XML’
> * removing ‘/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/XML’
> ERROR: dependency ‘XML’ is not available for package ‘annotate’
> * removing ‘/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/annotate’
> ERROR: dependencies ‘annotate’, ‘XML’ are not available for package ‘GSEABase’
> * removing ‘/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/GSEABase’
> ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
> * removing ‘/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/genefilter’
> ERROR: dependencies ‘GSEABase’, ‘genefilter’, ‘annotate’ are not available for package ‘Category’
> * removing ‘/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/Category’
> ERROR: dependencies ‘Category’, ‘annotate’ are not available for package ‘GOstats’
> * removing ‘/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/GOstats’
>
> The downloaded source packages are in
> ‘/tmp/Rtmppuncin/downloaded_packages’
> 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 ‘annotate’ had non-zero exit status
> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package ‘GSEABase’ had non-zero exit status
> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package ‘genefilter’ had non-zero exit status
> 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package ‘Category’ had non-zero exit status
> 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package ‘GOstats’ had non-zero exit status
> 7: installed directory not writable, cannot update packages 'lattice', 'spatial'
>
> -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.12.0 edgeR_3.4.0 limma_3.18.0
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
More information about the Bioconductor
mailing list