<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Phylobase is no longer compiling for Linux on R-Forge. The errors we're getting are in code that hasn't changed in several months. You can see the build failures by going to the phylobase build page ( <a href="http://r-forge.r-project.org/R/?group_id=111">http://r-forge.r-project.org/R/?group_id=111</a> ), clicking on R.check, and then clicking on the error file. The two main errors are of the types<div><pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; white-space: normal;">Rcpp.cpp:885: error: 'strlen' is not a member of 'std' </span></font></pre><pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; white-space: normal;">[with additional errors for strcpy and strcat] and </span></font></pre><pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; white-space: normal;"><pre><font class="Apple-style-span" face="Helvetica"><span class="Apple-style-span" style="white-space: normal;">nxsdiscretematrix.h:52: error: 'UINT_MAX' was not declared in this scope</span></font></pre><pre><font class="Apple-style-span" face="Helvetica"><span class="Apple-style-span" style="white-space: normal;">with that error occurring in other files, too.</span></font></pre><pre><font class="Apple-style-span" face="Helvetica"><span class="Apple-style-span" style="white-space: normal;">I've tried poking around a bit, but I am having trouble identifying and fixing the actual error. I emailed R-forge for help, and got the following reply. </span></font></pre><pre><font class="Apple-style-span" face="Helvetica"><span class="Apple-style-span" style="white-space: normal;">Anyone have any ideas?</span></font></pre><pre><font class="Apple-style-span" face="Helvetica"><span class="Apple-style-span" style="white-space: normal;">Thanks,</span></font></pre><pre><font class="Apple-style-span" face="Helvetica"><span class="Apple-style-span" style="white-space: normal;">Brian</span></font></pre><pre><br></pre><pre><font class="Apple-style-span" face="Helvetica"><span class="Apple-style-span" style="white-space: normal;">Support item #179, was opened at 2008-07-29 23:35<br>Status: Open<br>Priority: 3<br>Submitted By: Brian O'Meara (bcomeara)<br>Assigned to: Nobody (None)<br>Summary: Source version earlier than binary <br>Hardware: All<br>Operating System: None<br>Severity: blocker<br>URL: <a href="http://r-forge.r-project.org/src/contrib/phylobase_0.3-1.tar.gz">http://r-forge.r-project.org/src/contrib/phylobase_0.3-1.tar.gz</a><br><br><br>Initial Comment:<br>We are running a class using phylobase. We patched an error in the trunk eight days ago. Some of the students who downloaded the package three days ago had the fixed version, the others did not. To fix this, two days ago we updated the project version in its DESCRIPTION to 0.3-1, so we could track which students have which version upon updating their packages. Users on Windows, linux, and some macs can't get the newest version, while others can. The .tar.gz file is actually empty (see link from URL <a href="http://r-forge.r-project.org/R/?group_id=111">http://r-forge.r-project.org/R/?group_id=111</a> ), which might be the cause of the problem. Users trying to install using the GUI in Mac R have a link to 0.3-1 if they want to download from binary but 0.3 if they try to install from source.<br><br>----------------------------------------------------------------------<br><br><blockquote type="cite">Comment By: Stefan Theussl (stefan7th)<br></blockquote>Date: 2008-07-29 23:54<br><br>Message:<br>Dear Brian,<br><br>Did you have at the build logs? There is an error when compiling the package sources:<br>nxsdiscretematrix.h:52: error: 'UINT_MAX' was not declared in this scope<br><br>Compiling the code is necessary even for tarballs as building the vignettes depends on it.<br><br>The windows build is even stranger:<br>R:/R/pkgs/phylobase/inst/doc/phylobase.tex:15: Extra <br>�:15: Emergency stop<br>�:15: ==> Fatal error occurred, no output PDF file produced!texify: pdflatex failed for some reason (see log file).<br>buildVignettes(dir = '.')<br>Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet = quiet) : <br> running 'texi2dvi' on 'phylobase.tex' failed<br>Calls: buildVignettes -> texi2dvi<br>Execution halted<br><br>it basically says that building the vignette fails. I really don't know why. But fixing the source code, so that it gets build on linux machine would probably solve Windows builds as well because we then use the tarball on Windows for creating the binary. In the tarball there is the vignette included and we don't build it on Windows again.<br><br>Hope this helps.<br>Best Stefan<br><br>PS: building starts on 3 o'clock CET. so if you fix this by then it will be available 2 hours later at the latest<br><br></span></font></pre></span></font></pre></div></body></html>