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Subject:	Rcpp installation fails on Cygwin: Rcpp::Timer not supported by your OS.
From:	Enrico Ferrero <enricoferrero86 AT gmail DOT com>
To:	edd AT debian DOT org
Cc:	marco atzeri <marco DOT atzeri AT gmail DOT com>, cygwin AT cygwin DOT com
X-MIME-Autoconverted:	from quoted-printable to 8bit by delorie.com id r6VHc5hc001133

Hi Dirk,

When trying to install your Rcpp R package from CRAN on Cygwin,
compilation aborts with the following error:
Timer.cpp:35:6: error: #error "Rcpp::Timer not supported by your OS."

A simple Google search brought up this bug on the Debian bug tracking
system: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=697032

The full log from the R console is below:
#################################
> install.packages("Rcpp")
Installing package into ‘/usr/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/Rcpp_0.10.4.tar.gz'
Content type 'application/gz' length 2397813 bytes (2.3 Mb)
opened URL
==================================================
downloaded 2.3 Mb

Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help

   Welcome to R!

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/lib/R/include -DNDEBUG -I../inst/include/       -ggdb -O2
-pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/debug/R-3.0.1-1
-fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/debug/R-3.0.1-1
 -c Date.cpp -o Date.o
g++ -I/usr/lib/R/include -DNDEBUG -I../inst/include/       -ggdb -O2
-pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/debug/R-3.0.1-1
-fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/debug/R-3.0.1-1
 -c Module.cpp -o Module.o
gcc -I/usr/lib/R/include -DNDEBUG -I../inst/include/       -ggdb -O2
-pipe -std=gnu99
-fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/debug/R-3.0.1-1
-fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/debug/R-3.0.1-1
 -c Rcpp_init.c -o Rcpp_init.o
g++ -I/usr/lib/R/include -DNDEBUG -I../inst/include/       -ggdb -O2
-pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/debug/R-3.0.1-1
-fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/debug/R-3.0.1-1
 -c Timer.cpp -o Timer.o
Timer.cpp:35:6: error: #error "Rcpp::Timer not supported by your OS."
Timer.cpp:94:6: error: #error "Rcpp::Benchmark::Timer not supported by your OS."
/usr/lib/R/etc/Makeconf:132: recipe for target `Timer.o' failed
make: *** [Timer.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/usr/lib/R/site-library/Rcpp’

The downloaded source packages are in
        ‘/tmp/RtmpHnCW28/downloaded_packages’
Warning message:
In install.packages("Rcpp") :
  installation of package ‘Rcpp’ had non-zero exit status

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: i686-pc-cygwin (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.10.3
#################################

Is there anything I can do to get it to work?

Thank you.
Best,

-- 
Enrico Ferrero
PhD Student
Steve Russell Lab - Department of Genetics
FlyChip - Cambridge Systems Biology Centre
University of Cambridge

e DOT ferrero AT gen DOT cam DOT ac DOT uk
http://flypress.gen.cam.ac.uk/

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