Hi Dirk -- That worked. I committed it as well.<div> Thanks!</div><div> -- François</div><div><br><div class="gmail_quote">On Mon, Feb 8, 2010 at 13:38, Dirk Eddelbuettel <span dir="ltr"><<a href="mailto:edd@debian.org">edd@debian.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5"><br>
On 8 February 2010 at 13:24, François Michonneau wrote:<br>
| Hi Dirk,<br>
|<br>
| With a fresh svn checkout, I can't build the package on my machine.<br>
| I get the following error message.<br>
|<br>
| Cheers,<br>
| -- François<br>
|<br>
| francois@francois-laptop:~/Desktop/phylobase$ R CMD build pkg/<br>
| * checking for file 'pkg/DESCRIPTION' ... OK<br>
| * preparing 'pkg':<br>
| * checking DESCRIPTION meta-information ... OK<br>
| * cleaning src<br>
| * running cleanup<br>
| * installing the package to re-build vignettes<br>
| * installing *source* package ‘phylobase’ ...<br>
| ** libs<br>
| g++ -I/usr/share/R/include -fpic -g -O2 -c NCLInterface.cpp -o<br>
| NCLInterface.o<br>
| g++ -I/usr/share/R/include -fpic -g -O2 -c ReadWithNCL.cpp -o<br>
| ReadWithNCL.o<br>
| ReadWithNCL.cpp:27:18: error: Rcpp.h: No such file or directory<br>
| ReadWithNCL.cpp:44: error: ‘RcppExport’ does not name a type<br>
| ReadWithNCL.cpp:121: error: ‘RcppExport’ does not name a type<br>
| ReadWithNCL.cpp:169: error: ‘RcppExport’ does not name a type<br>
| make: *** [ReadWithNCL.o] Error 1<br>
| ERROR: compilation failed for package ‘phylobase’<br>
| * removing ‘/tmp/Rinst2338445123/phylobase’<br>
| ERROR<br>
| Installation failed.<br>
| Removing '/tmp/Rinst2338445123'<br>
<br>
</div></div>src/Makevars got hosed. Do you have one? Try dropping this one in:<br>
<br>
--- cut -----------------------------------------------------------------------<br>
RCPP_FLAGS=`${R_HOME}/bin/Rscript -e "Rcpp:::CxxFlags()"`<br>
RCPP_LIBS=`${R_HOME}/bin/Rscript -e "Rcpp:::LdFlags()"`<br>
#<br>
PKG_CPPFLAGS=-I. ${RCPP_FLAGS} -DHAVE_INTTYPES_H<br>
PKG_LIBS=${RCPP_LIBS}<br>
--- cut -----------------------------------------------------------------------<br>
<br>
That file was accidentally deleted in cleanup, (on line three or so); check<br>
if that is fixed in the script cleanup. I had a 'file out of date' error and<br>
commit and may not have checked a clean version.<br>
<br>
I'll try a fresh svn checkout myself later.<br>
<font color="#888888"><br>
Dirk<br>
</font><div><div></div><div class="h5"><br>
<br>
|<br>
|<br>
| On Mon, Feb 8, 2010 at 12:40, Dirk Eddelbuettel <<a href="mailto:edd@debian.org">edd@debian.org</a>> wrote:<br>
| ><br>
| > On 2 February 2010 at 10:44, Dirk Eddelbuettel wrote:<br>
| > | [ Resending with 7-bit clean headers without Francois's cedille ]<br>
| > |<br>
| > | On 1 February 2010 at 12:41, Dirk Eddelbuettel wrote:<br>
| > | | On 1 February 2010 at 13:22, François Michonneau wrote:<br>
| > | | | Hi all,<br>
| > | | |<br>
| > | | | It looks that we're still having some troubles building the package on R-forge.<br>
| > | | |<br>
| > | | | Now, we get the following error message for the linux builds:<br>
| > | | | g++ -shared -L/usr/local/lib64 -o phylobase.so NCLInterface.o<br>
| > | | | ReadWithNCL.o ancestors.o descendants.o phyloXX.o reorderBinary.o<br>
| > | | | reorderRobust.o -L/home/rforge/lib/R/2.10/Rcpp/lib -lRcpp<br>
| > | | | -Wl,-rpath,/home/rforge/lib/R/2.10/Rcpp/lib -Llib/ncl -lncl<br>
| > | | | -L/srv/R/R-patched/build.10-01-29/lib -lR<br>
| > | | | /usr/bin/ld: lib/ncl/libncl.a(nxsassumptionsblock.o): relocation<br>
| > | | | R_X86_64_32 against `.rodata.str1.1' can not be used when making a<br>
| > | | | shared object; recompile with -fPIC<br>
| > | | | lib/ncl/libncl.a: could not read symbols: Bad value<br>
| > | | | collect2: ld returned 1 exit status<br>
| > | |<br>
| > | | Good catch. I never need that on 32bit where it works automatically so I<br>
| > | | forgot. This basically means that out plan of using<br>
| > | |<br>
| > | | configure --enable-static --disable-shared<br>
| > | |<br>
| > | | doesn't work as configure no longer seems to add -fPIC. That stinks.<br>
| > | |<br>
| > | | I think the simplest solution is to tell configure to stuff itself, and to<br>
| > | | use the same Makefile we already use for Windows, maybe with an explicit<br>
| > | | -fPIC thrown in for good measure.<br>
| > |<br>
| > | Didn't work. I wasn't thinking hard enough.<br>
| > |<br>
| > | For OS X, three builds are attempted for three architectures. That cannot<br>
| > | work with a single configure.<br>
| > |<br>
| > | Maybe we need to throw our arms up in the air and just import the sources<br>
| > | files from pkg/src/ncl/ncl into pkg/src/ and treat them as part of the<br>
| > | package.<br>
| ><br>
| > After discussing this some more with Francois, I have now made this change<br>
| > and committed it as a 'request for comment' type commit. So now we no longer<br>
| > have a seperate source directory for ncl but simply comingle the ncl sources<br>
| > with the phylobase sources.<br>
| ><br>
| > Advantage: R knows how to build<br>
| ><br>
| > Disadvantage: comingled :-/<br>
| ><br>
| > It works for me on Linux, and I submitted it to the automated win-builder (by<br>
| > locally altering DESCRIPTION to make me Maintainer:, and I also like to<br>
| > change the version). The result is in:<br>
| ><br>
| > From: Uwe.Ligges@R-Project.org<br>
| > To: <a href="mailto:edd@debian.org">edd@debian.org</a><br>
| > Cc: Uwe.Ligges@R-Project.org<br>
| > Subject: Package phylobase_0.5.2.tar.gz has been checked and built<br>
| > Date: Mon, 08 Feb 2010 18:20:59 +0100<br>
| ><br>
| > Dear package maintainer,<br>
| ><br>
| > this notification has been generated automatically.<br>
| > Your package phylobase_0.5.2.tar.gz has been built (if working) and checked for Windows.<br>
| > Please check the log files and (if working) the binary package at:<br>
| > <a href="http://win-builder.r-project.org/oIyt0KC6A03C" target="_blank">http://win-builder.r-project.org/oIyt0KC6A03C</a><br>
| > The files will be removed after roughly 72 hours.<br>
| > Installation time in seconds: 124<br>
| > Check time in seconds: 113<br>
| > Check result: WARNING<br>
| > R version 2.10.1 (2009-12-14) (32-bit)<br>
| ><br>
| > All the best,<br>
| > Uwe Ligges<br>
| > (CRAN maintainer of binary packages for Windows)<br>
| ><br>
| > So if anyone with OS X could try this, preferably over multiarch etc, it<br>
| > would be great. Maybe we can _finally_ put this to bed in a few days.<br>
| ><br>
| > Dirk<br>
| ><br>
| ><br>
| > --<br>
| > Registration is open for the 2nd International conference R / Finance 2010<br>
| > See <a href="http://www.RinFinance.com" target="_blank">http://www.RinFinance.com</a> for details, and see you in Chicago in April!<br>
| ><br>
<br>
</div></div>--<br>
<div><div></div><div class="h5"> Registration is open for the 2nd International conference R / Finance 2010<br>
See <a href="http://www.RinFinance.com" target="_blank">http://www.RinFinance.com</a> for details, and see you in Chicago in April!<br>
</div></div></blockquote></div><br></div>