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

[Bogdan]

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