[BioC] [resolved] xps compilation error on Debian squeeze/testing

[cstrato]

Dear Bogdan,

I forgot to mention that root_v5.24.00 works only with the development 
version of xps, thus if you download the official version of xps you 
need to use root_v5.22.00.

One more issue:
Since you had to "#include <stdlib.h>" in so many files I suspect that 
you may be missing an essential development package, may be for make? 
However, since I am no expert, maybe a Debian expert has a hint what 
might be the problem.

Best regards
Christian

Bogdan wrote:
> Hi,
>
> after the installation of BioConductor, running
>
>   
>> biocLite("xps")
>>     
>
> produces compilation error (see full log at the end of email):
>
> g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSUtils.cxx
> XPSUtils.cxx: In function ‘void READ_WSTRING(std::ifstream&, char*&,
> Bool_t)’:
> XPSUtils.cxx:4611: error: ‘wcstombs’ was not declared in this scope
> make: *** [XPSUtils.o] Error 1
> ERROR: compilation failed for package ‘xps’
> * Removing ‘/home/bogdan/R/i486-pc-linux-gnu-library/2.9/xps’
>
> I'm running Debian testing (squeeze) on i386, and have gcc-4.3
> installed.
>
> Resolving:
> - adding #include <stdlib.h> to XPSUtils.cxx caused "'atoi' was not
> declared in XPSSchemes.cxx"
> - adding #include <stdlib.h> to XPSSchemes.cxx caused "XPSData.cxx:2029:
> error: ‘wcstombs’ was not declared in this scope"
> - adding #include <stdlib.h> to XPSData.cxx caused "XPSSelector.cxx:502:
> error: call of overloaded ‘abs(Int_t&)’ is ambiguous"
> - adding #include <stdlib.h> to XPSSelector.cxx caused
> "XPSPreProcessing.cxx:5693: error: call of overloaded ‘abs(Int_t&)’ is
> ambiguous"
> - same include in XPSPreProcessing caused "XPSFilter.cxx:739: error:
> ‘atof’ was not declared in this scope"
> - finally, adding that same include to XPSFilter.cxx allowed successful
> compilation, installation, and loading of xps package; I haven't yet
> tested any further, though.
>
> My 'solution' looks ugly, and might have introduced errors into XPS. Any
> other suggestions on proper installation are welcome (please CC me on
> reply, I am not subscribed to this list).
>
>
> Regards,
> Bogdan
>
>
> ===
> full log of xps installation follows
> ===
>
>
>   
>> biocLite("xps")                                                              
>>     
> Using R version 2.9.1, biocinstall version
> 2.4.12.                             
> Installing Bioconductor version 2.4
> packages:                                  
> [1]
> "xps"                                                                      
> Please
> wait...                                                                 
>
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using
> '/home/bogdan/R/i486-pc-linux-gnu-library/2.9'      
> trying URL
> 'http://bioconductor.org/packages/2.4/bioc/src/contrib/xps_1.4.8.tar.gz'    
> Content type 'application/x-gzip' length 5021629 bytes (4.8
> Mb)                        
> opened
> URL                                                                             
> ==================================================                                     
> downloaded 4.8
> Mb                                                                      
>
> * Installing *source* package ‘xps’ ...
> checking for gcc... gcc -std=gnu99     
> checking for C compiler default output file name... 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 -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -std=gnu99 -E
> checking for gcc... (cached) gcc -std=gnu99
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc -std=gnu99 accepts -g... (cached) yes
> checking for gcc -std=gnu99 option to accept ANSI C... (cached) none
> needed
> checking for root-config... yes
> found ROOT version 5.18/00b in directory /usr
> ** libs
> ** arch -
> g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c TMLMath.cxx
> TMLMath.cxx:1109:1: warning: "xmax" redefined
> TMLMath.cxx:1060:1: warning: this is the location of the previous
> definition
> g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c TStat.cxx
> g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c StatUtils.cxx
> g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSBase.cxx
> g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSUtils.cxx
> XPSUtils.cxx: In function ‘void READ_WSTRING(std::ifstream&, char*&,
> Bool_t)’:
> XPSUtils.cxx:4611: error: ‘wcstombs’ was not declared in this scope
> make: *** [XPSUtils.o] Error 1
> ERROR: compilation failed for package ‘xps’
> * Removing ‘/home/bogdan/R/i486-pc-linux-gnu-library/2.9/xps’
>
> The downloaded packages are in
>         ‘/tmp/RtmpbYQURP/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'xps' had non-zero exit status
>
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