Rcpp installation fails on Cygwin: Rcpp::Timer not supported by your OS.

Rcpp installation fails on Cygwin: Rcpp::Timer not supported by your OS.

[Enrico Ferrero]

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.ferrero@gen.cam.ac.uk
http://flypress.gen.cam.ac.uk/

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Re: Rcpp installation fails on Cygwin: Rcpp::Timer not supported by your OS.

[Yaakov (Cygwin/X)]

On 2013-07-31 12:37, Enrico Ferrero wrote:
> 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."

Such an error means that the code needs to be patched to select (or add) 
a code block specific to that platform.  A patch for Cygwin can be found 
in Ports git:

http://cygwin-ports.git.sourceforge.net/git/gitweb.cgi?p=cygwin-ports/R-Rcpp;a=tree

Specifically for Cygwin, based on my limited understanding of Rcpp, it 
would appear that libRcpp.dll (the library, not the Rcpp.dll module) 
should be moved to $PATH, and a symlink .dll.a put in its place, for the 
benefit of other modules which would use this library.  The cygport(5) 
found in the aforementioned repo handles that for you.


Yaakov


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Re: Rcpp installation fails on Cygwin: Rcpp::Timer not supported by your OS.

[Enrico Ferrero]

Thanks Yaakov,
That looks exactly like what I need. May I ask how would I go about
patching and installing it on my system?
Cheers,

On 31 July 2013 19:42, Yaakov (Cygwin/X)
<yselkowitz@users.sourceforge.net> wrote:
> On 2013-07-31 12:37, Enrico Ferrero wrote:
>>
>> 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."
>
>
> Such an error means that the code needs to be patched to select (or add) a
> code block specific to that platform.  A patch for Cygwin can be found in
> Ports git:
>
> http://cygwin-ports.git.sourceforge.net/git/gitweb.cgi?p=cygwin-ports/R-Rcpp;a=tree
>
> Specifically for Cygwin, based on my limited understanding of Rcpp, it would
> appear that libRcpp.dll (the library, not the Rcpp.dll module) should be
> moved to $PATH, and a symlink .dll.a put in its place, for the benefit of
> other modules which would use this library.  The cygport(5) found in the
> aforementioned repo handles that for you.
>
>
> Yaakov
>
>
> --
> Problem reports:       http://cygwin.com/problems.html
> FAQ:                   http://cygwin.com/faq/
> Documentation:         http://cygwin.com/docs.html
> Unsubscribe info:      http://cygwin.com/ml/#unsubscribe-simple
>



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

e.ferrero@gen.cam.ac.uk
http://flypress.gen.cam.ac.uk/

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Re: Rcpp installation fails on Cygwin: Rcpp::Timer not supported by your OS.

[Yaakov (Cygwin/X)]

On 2013-08-01 02:46, Enrico Ferrero wrote:
> Thanks Yaakov,
> That looks exactly like what I need. May I ask how would I go about
> patching and installing it on my system?

1) Manually:

wget http://cran.r-project.org/src/contrib/Rcpp_0.10.4.tar.gz
wget -O 0.10.4-cygwin.patch 
'http://cygwin-ports.git.sourceforge.net/git/gitweb.cgi?p=cygwin-ports/R-Rcpp;a=blob_plain;f=0.10.4-cygwin.patch;hb=HEAD'
tar axf Rcpp_0.10.4.tar.gz
pushd Rcpp
patch -p2 < ../0.10.4-cygwin.patch
popd
R CMD INSTALL ./Rcpp
mv /usr/lib/R/site-library/Rcpp/lib/libRcpp.dll /usr/bin/
ln -s /usr/bin/libRcpp.dll /usr/lib/R/site-library/Rcpp/lib/libRcpp.dll.a

2) Install cygport and git (and their prereqs), then:

git clone git://cygwin-ports.git.sourceforge.net/gitroot/cygwin-ports/R-Rcpp
cd R-Rcpp
cygport R-Rcpp.cygport fetch prep build install package
tar axf R-Rcpp-0.10.4-1/dist/R-Rcpp/R-Rcpp-0.10.4-1.tar.bz2 -C /
git clean -dfq


Yaakov


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