[BioC] Problem installing genefilter (Ubuntu 12.04; Bioconductor v2.12)

[James W. MacDonald]

Hi Olivier,

On 7/31/2013 11:54 AM, Olivier [guest] wrote:
> I'm having problems installing genefilter. Grateful if you could help. Thanks.
>> biocLite('genefilter')
> ... (ommitted lines for clarity)
> * 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

This is your hint ^^^^^^^^^^^

If you google ubuntu xml2-config, you will see that you need to do

apt-get install libxml2-dev

Best,

Jim


> ERROR: configuration failed for package ‘XML’
> * removing ‘/home/olivier/R/x86_64-pc-linux-gnu-library/3.0/XML’
> ERROR: dependency ‘XML’ is not available for package ‘annotate’
> * removing ‘/home/olivier/R/x86_64-pc-linux-gnu-library/3.0/annotate’
> ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
> * removing ‘/home/olivier/R/x86_64-pc-linux-gnu-library/3.0/genefilter’
>
> The downloaded source packages are in
> 	‘/tmp/Rtmpylk0c1/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 ‘genefilter’ had non-zero exit status
>
>   -- output of sessionInfo():
>
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8
>   [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.10.3 ALL_1.4.14           Biobase_2.20.1       BiocGenerics_0.6.0
> [5] limma_3.16.7
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099