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

[Alvaro Cuadros Inostroza]

Hello,

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.
	
> 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 ]

-- 
Alvaro