[BioC] Failing to install genefilter-1.12.0

[Herve Pages]

Benilton Carvalho wrote:
> Hi Herve,
> 
> thanks for your feedback.
> 
> I do have libstdc++ and libstd++-devel (3.4.6-3) available... and
> c++config.h is installed on my system.

Can you compile those 2 lines with g++?

  #include <bits/c++config.h>
  int main() {}

(put them in file test.cpp and try to compile with 'g++ -Wall test.cpp')

If you can't then this means that g++ can't find your c++config.h file.
Make sure that:
  - /usr/include/c++/3.4.6/ is a standard system include directory: look at
    the value of the "--with-gxx-include-dir" configuration option in the
    ouput of 'g++ -v'
  - c++config.h is in /usr/include/c++/3.4.6/bits

Cheers,
H.


> 
> Any chance it is something else?
> 
> thanks,
> b
> 
> 
> On Mar 19, 2007, at 2:43 PM, Herve Pages wrote:
> 
>> Hi Benilton,
>>
>> Make sure that you have the libstdc++ _and_ the libstdc++-devel RPMs
>> installed on your Red Hat system.
>> On my SuSE 10.2 system, the exact names for those RPMs are
>>   libstdc++41
>>   libstdc++41-devel
>> The c++config.h file is included in the libstdc++41-devel RPM.
>>
>> Cheers,
>> H.
>>
>> Benilton Carvalho wrote:
>>> Hi everyone,
>>>
>>> I just built from the source R-2.4.1, so it's a "brand new"
>>> installation.
>>>
>>> Then:
>>>
>>> source("http://www.bioconductor.org/bioLite.R")
>>> biocLite(c("simpleaffy", "affyPLM", "RColorBrewer"))
>>>
>>> everything goes almost OK: I can't get genefilter to install
>>> (therefore I
>>> don't have simpleaffy)
>>>
>>> It's a long output that I get, but it starts with:
>>>
>>> In file included from
>>> /usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../include/c++/3.4.6/vector:67,
>>>
>>>                   from half_range_mode.cpp:4:
>>> /usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../include/c++/3.4.6/bits/stl_algobase.h:64:28:
>>>
>>> bits/c++config.h: No such file or directory
>>> In file included from
>>> /usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../include/c++/3.4.6/vector:68,
>>>
>>>                   from half_range_mode.cpp:4:
>>> /usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../include/c++/3.4.6/bits/allocator.h:80:
>>>
>>> error: expected template-name before '<' token
>>> /usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../include/c++/3.4.6/bits/allocator.h:80:
>>>
>>> error: expected `{' before '<' token
>>> /usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../include/c++/3.4.6/bits/allocator.h:80:
>>>
>>> error: expected unqualified-id before '<' token
>>>
>>>
>>> Have anyone observed something like this?
>>>
>>> thanks,
>>>
>>> b.
>>>
>>> -- 
>>>
>>>> sessionInfo()
>>> R version 2.4.1 (2006-12-18)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>> LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COLLATE=en_US.iso885915;LC_MONETARY=en_US.iso885915;LC_MESSAGES=en_US.iso885915;LC_PAPER=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C
>>>
>>>
>>> attached base packages:
>>> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets" 
>>> "methods"
>>> [7] "base"
>>>
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