<div dir="ltr"><div>Hi Dominick, <br><br>Yitping is
compiling (successfully) with macports, but there seem to be an issue when actually calling the code. <br>I see in the log that mkoctfile uses clang, while R calls
llvm-g++, could that be the origin of the problem? <br><br></div><div>Yitping, could you please try the following:<br><br></div><div>install.packages('RcppOctave', repos='<a href="http://web.cbio.uct.ac.za/~renaud/CRAN">http://web.cbio.uct.ac.za/~renaud/CRAN</a>', INSTALL_opts = '--no-docs --no-help')<br>
</div><div>library(RcppOctave)<br></div><div>OctaveConfig()<br></div><div>getLoadedDLLs()<br></div><div>o_runif(1)<br></div><div class="gmail_extra">
<br><br></div><div class="gmail_extra">Thank you<br></div><div class="gmail_extra"><br><div class="gmail_quote">On 21 November 2013 11:36, Renaud Gaujoux <span dir="ltr"><<a href="mailto:renaud@mancala.cbio.uct.ac.za" target="_blank">renaud@mancala.cbio.uct.ac.za</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr"><div><div>Thanks for the details Yitping, forwarding now to the list.<br></div>Please remember to Cc the list in your replies, so that there is a record for future public reference.<br></div><div><div>
<div><div><div><br>
<div class="gmail_extra"><div class="gmail_quote">On 20 November 2013 22:20, Yitping Kok <span dir="ltr"><<a href="mailto:yitping@mpe.mpg.de" target="_blank">yitping@mpe.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="word-wrap:break-word"><div>Hi Renaud,</div><div><br></div><div>Thanks for your prompt reply. I tried the install_github() method you suggested but to no success either. The error is similar to what I had earlier, which source codes downloaded from RcppOctave cran webpage. Below are the log and error messages in case it is helpful.</div>
<div><br></div><div>I have also included the output of sessionInfo() and Sys.info(). My Octave installation was done through MacPorts (<span style="font-size:12px;color:rgb(195,55,32)"><b>octave</b></span><span style="font-size:12px">-devel @3.6.4_9+atlas+docs+gcc48</span>). </div>
<div><br></div><div>Thanks in advance.</div><div><br></div><div>Yitping</div><div><br></div><div><div><div style="margin:0px;font-size:12px">> library(devtools)</div><div style="margin:0px;font-size:12px">> install_github('RcppOctave', 'renozao', ref = 'develop')</div>
</div><div style="margin:0px;font-size:12px"><b>Installing github repo(s) RcppOctave/develop from renozao</b></div><div style="margin:0px;font-size:12px"><b>Downloading RcppOctave.zip from <a href="https://github.com/renozao/RcppOctave/archive/develop.zip" target="_blank">https://github.com/renozao/RcppOctave/archive/develop.zip</a></b></div>
<div style="margin:0px;font-size:12px"><b>Installing package from /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip</b></div><div style="margin:0px;font-size:12px"><b>Installing RcppOctave</b></div>
<div style="margin:0px;font-size:12px"><b>'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL \</b></div><div style="margin:0px;font-size:12px"><b> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop' \</b></div>
<div style="margin:0px;font-size:12px"><b> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library' \</b></div><div style="margin:0px;font-size:12px"><b> --with-keep.source --install-tests </b></div>
<div style="margin:0px;font-size:12px;min-height:14px"><br></div><div style="margin:0px;font-size:12px">* installing *source* package 'RcppOctave' ...</div><div style="margin:0px;font-size:12px">checking for gcc... gcc</div>
<div style="margin:0px;font-size:12px">checking whether the C compiler works... yes</div><div style="margin:0px;font-size:12px">checking for C compiler default output file name... a.out</div><div style="margin:0px;font-size:12px">
checking for suffix of executables... </div><div style="margin:0px;font-size:12px">checking whether we are cross compiling... no</div><div style="margin:0px;font-size:12px">checking for suffix of object files... o</div><div style="margin:0px;font-size:12px">
checking whether we are using the GNU C compiler... yes</div><div style="margin:0px;font-size:12px">checking whether gcc accepts -g... yes</div><div style="margin:0px;font-size:12px">checking for gcc option to accept ISO C89... none needed</div>
<div style="margin:0px;font-size:12px">checking for g++... g++</div><div style="margin:0px;font-size:12px">checking whether we are using the GNU C++ compiler... yes</div><div style="margin:0px;font-size:12px">checking whether g++ accepts -g... yes</div>
<div style="margin:0px;font-size:12px">Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R</div><div style="margin:0px;font-size:12px">Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include</div>
<div style="margin:0px;font-size:12px">checking whether R is a shared library... yes</div><div style="margin:0px;font-size:12px">checking type of Operating System... Darwin</div><div style="margin:0px;font-size:12px">checking whether OS is Mac OS (Darwin)... yes</div>
<div style="margin:0px;font-size:12px">Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"</div><div style="margin:0px;font-size:12px">Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include</div>
<div style="margin:0px;font-size:12px">checking for octave-config... /opt/local/bin/octave-config</div><div style="margin:0px;font-size:12px">checking for mkoctfile... /opt/local/bin/mkoctfile</div><div style="margin:0px;font-size:12px">
checking Octave include flags... -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include</div><div style="margin:0px;font-size:12px">checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib</div>
<div style="margin:0px;font-size:12px">checking Octave libraries... -loctinterp -loctave -lcruft</div><div style="margin:0px;font-size:12px">checking Octave version... 3.6.4</div><div style="margin:0px;font-size:12px">checking whether to infer output names for Octave function (>= 3.4.3)... yes</div>
<div style="margin:0px;font-size:12px">Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft</div><div style="margin:0px;font-size:12px">Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1</div>
<div style="margin:0px;font-size:12px">checking RcppOctave Octave module directory... /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules</div><div style="margin:0px;font-size:12px">configure: creating ./config.status</div>
<div style="margin:0px;font-size:12px">config.status: creating src/Makevars</div><div style="margin:0px;font-size:12px">configure: creating ./config.status</div><div style="margin:0px;font-size:12px">config.status: creating src/Makevars</div>
<div style="margin:0px;font-size:12px">config.status: creating src/modules/Makefile</div><div style="margin:0px;font-size:12px">** libs</div><div style="margin:0px;font-size:12px">"/opt/local/bin/mkoctfile" -v <a href="http://utils.cc" target="_blank">utils.cc</a></div>
<div style="margin:0px;font-size:12px">/usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 <a href="http://utils.cc" target="_blank">utils.cc</a> -o utils.o</div>
<div style="margin:0px;font-size:12px">/usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64</div>
<div style="margin:0px;font-size:12px">"/opt/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" <a href="http://Rrng.cc" target="_blank">Rrng.cc</a></div>
<div style="margin:0px;font-size:12px">/usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include <a href="http://Rrng.cc" target="_blank">Rrng.cc</a> -o Rrng.o</div>
<div style="margin:0px;font-size:12px">/usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64</div>
<div style="margin:0px;font-size:12px"># Copying Octave modules to directory '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'</div><div style="margin:0px;font-size:12px">llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -fPIC -I/opt/local/include -c conversion.cpp -o conversion.o</div>
<div style="margin:0px;font-size:12px">llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -fPIC -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o</div>
<div style="margin:0px;font-size:12px">llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation</div>
<div style="margin:0px;font-size:12px">installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs</div><div style="margin:0px;font-size:12px">** R</div><div style="margin:0px;font-size:12px">
** demo</div><div style="margin:0px;font-size:12px">** inst</div><div style="margin:0px;font-size:12px">** tests</div><div style="margin:0px;font-size:12px">** preparing package for lazy loading</div><div style="margin:0px;font-size:12px">
** help</div><div style="margin:0px;font-size:12px">Error : /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41: .onLoad failed in loadNamespace() for 'RcppOctave', details:</div>
<div style="margin:0px;font-size:12px"> call: dyn.load(file, DLLpath = DLLpath, ...)</div><div style="margin:0px;font-size:12px"> error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':</div>
<div style="margin:0px;font-size:12px"> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value</div><div style="margin:0px;font-size:12px">
Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so</div><div style="margin:0px;font-size:12px"> Expected in: flat namespace</div><div style="margin:0px;font-size:12px">
in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so</div><div style="margin:0px;font-size:12px">ERROR: installing Rd objects failed for package 'RcppOctave'</div><div style="margin:0px;font-size:12px">
* removing '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><div style="margin:0px;font-size:12px">R version 3.0.2 (2013-09-25)</div>
<div style="margin:0px;font-size:12px">Platform: x86_64-apple-darwin10.8.0 (64-bit)</div><div style="margin:0px;font-size:12px;min-height:14px"><br></div><div style="margin:0px;font-size:12px">locale:</div><div style="margin:0px;font-size:12px">
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8</div><div style="margin:0px;font-size:12px;min-height:14px"><br></div><div style="margin:0px;font-size:12px">attached base packages:</div><div style="margin:0px;font-size:12px">
[1] stats graphics grDevices utils datasets methods base</div></div><div style="margin:0px;font-size:12px"><br></div><div style="margin:0px;font-size:12px"><br></div><div style="margin:0px;font-size:12px"><div style="margin:0px">
sysname </div><div style="margin:0px"> "Darwin" </div><div style="margin:0px"> release </div>
<div style="margin:0px"> "13.0.0" </div><div style="margin:0px"> version </div>
<div style="margin:0px">"Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64" </div><div style="margin:0px"> nodename </div>
<div style="margin:0px"> "dooku.local" </div><div style="margin:0px"> machine </div>
<div style="margin:0px"> "x86_64" </div><div style="margin:0px"> login </div>
<div style="margin:0px"> "yitping" </div><div style="margin:0px"> user </div>
<div style="margin:0px"> "yitping" </div><div style="margin:0px"> effective_user </div>
<span><font color="#888888"><div style="margin:0px"> “yitping"</div><div style="margin:0px"><br></div><div style="margin:0px">
<br></div><div style="margin:0px"><br></div></font></span></div><div><div><div style="margin:0px;font-size:12px"><br></div><div style="margin:0px;font-size:12px"><br></div><div><br></div><br><div><div>On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux <<a href="mailto:renaud@mancala.cbio.uct.ac.za" target="_blank">renaud@mancala.cbio.uct.ac.za</a>> wrote:</div>
<br><blockquote type="cite"><div dir="ltr"><div><div><div><div><div><div>Hi Yitping,<br><br></div>thank you for your interest in the RcppOctave package, which will hopefully provide what you need... once you get it working :D<br>
</div>It will be great to get your feedback on how things work from a Mac-Octave user point of view.<br>
</div><br>The package should compile fine with the settings described in the README file.<br></div>Can you please send more details on your R (output of sessionInfo() and Sys.info) and Octave installation.<br></div>Did you fetch the latest version of the source package from github? <br>
<br></div><div>In R, try:<br><br></div>library(devtools)<br><div><div><div>install_github('RcppOctave', 'renozao', ref = 'develop')<br><br><br></div><div>Renaud<br></div></div>
</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 20 November 2013 19:25, Yitping Kok <span dir="ltr"><<a href="mailto:yitping@mpe.mpg.de" target="_blank">yitping@mpe.mpg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Hi RcppOctave users,<div><br></div><div>I have just found out about this R packages and I am very excited about it. I am an Octave user and would like to use more R. Therefore I think this package will be perfect for me.</div>
<div><br></div><div>I also understand that the package still has some installation issues with Mac OS. However I tried to install the package on a Mac platform anyway for the sake of trying and this is what I got.</div><div>
<br></div><div>- I have Octave 3.6.4 installed.</div><div>- I managed to compile the shared library, RcppOctave.so.</div><div>- But I cannot proceed (to generating the documentation part) because the library cannot be loaded. This is the error message I got.</div>
<div><br></div><div><div style="margin:0px;font-size:12px"><b>Error in dyn.load("RcppOctave.so") : </b></div><div style="margin:0px;font-size:12px"><b> unable to load shared object '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':</b></div>
<div style="margin:0px;font-size:12px"><b> dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value</b></div><div style="margin:0px;font-size:12px">
<b> Referenced from: /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so</b></div><div style="margin:0px;font-size:12px"><b> Expected in: flat namespace</b></div><div style="margin:0px;font-size:12px"><b> in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so</b></div>
</div><div><br></div><div>Any idea why it is so? Any help would be appreciated. Thanks very much.</div><div><br></div><div><br></div><div>Best regards,</div><div>Yitping</div></div>
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