[Bioc-devel] mzR compilation error gcc 4.70 arch linux (and a patch)

[Steffen Neumann]

Hi Alvaro,

On Tue, 2012-05-15 at 07:34 +0000, Alvaro Cuadros Inostroza wrote:
> I got the following compilation error while installing the package
> 'mzR' (devel version 1.3.6) in arch linux (fully updated) (my package,
> TargetSearch, depends on mzR). Here is the relevant part.

Thanks for the notice and the patch. I applied it to the devel version,
it compiles and check fine on my gcc-4.6 and mzR-1.3.7 
should be out soon. Please report if there's anything missing.

Yours,
Steffen



> 	
> > biocLite("mzR")
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.5.7.
> Installing package(s) 'mzR'
> 
> [...]
> 
> g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include"   -fpic  -g -O2  -c boost/thread/src/pthread/once.cpp -o boost/thread/src/pthread/once.o
> In file included from ./boost/thread/detail/platform.hpp:17:0,
>                  from ./boost/thread/once.hpp:12,
>                  from boost/thread/src/pthread/once.cpp:7:
> ./boost/config/requires_threads.hpp:29:4: error: #error "Threading support unavaliable: it has been explicitly disabled with BOOST_DISABLE_THREADS"
> In file included from ./boost/thread/once.hpp:12:0,
>                  from boost/thread/src/pthread/once.cpp:7:
> ./boost/thread/detail/platform.hpp:67:9: error: #error "Sorry, no boost threads are available for this platform."
> 
> [...]
> 
> The full error log is here [1].
> 
> I also got the same error with the release version of mzR (1.2.1). With an older gcc I do *not* get this error.
> 
> Since it seemed a problem with the boost libraries, I searched the web and found a bug report [2] in which they explain it's a configuration error due to a change in gcc 4.70 (or something like that). Also, in that page a fix and patch is provided (see link at the bottom) which I adapted and pasted here [3] for mzR. It works for both release and devel versions. At least it fixed the compilation error for me. Maybe it needs more testing...
> 
> [1] http://pastebin.com/T2tSEWPM
> [2] https://svn.boost.org/trac/boost/ticket/6165
> [3] http://pastebin.com/gYBAr2Td
> 
> [alvaro at home ~]$ gcc --version
> gcc (GCC) 4.7.0 20120505 (prerelease)
> Copyright (C) 2012 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
> 
> 
> > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] BiocInstaller_1.5.7
> 
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
> 
> Best regards.
> [ CC: to the mainteners ]
> 

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
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