Solved. Thanks a lot!


On Wed, Jul 31, 2013 at 8:06 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> 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
>
>

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