[Phylobase-devl] Compilation woes

Brian O'Meara bcomeara at nescent.org
Sun Aug 3 17:35:49 CEST 2008

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 ( http://r-forge.r-project.org/R/?group_id=111 
  ), clicking on R.check, and then clicking on the error file. The two  
main errors are of the types
Rcpp.cpp:885: error: 'strlen' is not a member of 'std'
[with additional errors for strcpy and strcat] and
nxsdiscretematrix.h:52: error: 'UINT_MAX' was not declared in this scope
with that error occurring in other files, too.
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.
Anyone have any ideas?

Support item #179, was opened at 2008-07-29 23:35
Status: Open
Priority: 3
Submitted By: Brian O'Meara (bcomeara)
Assigned to: Nobody (None)
Summary: Source version earlier than binary
Hardware: All
Operating System: None
Severity: blocker
URL: http://r-forge.r-project.org/src/contrib/phylobase_0.3-1.tar.gz

Initial Comment:
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 http://r-forge.r-project.org/R/? 
group_id=111 ), 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.


> Comment By: Stefan Theussl (stefan7th)
Date: 2008-07-29 23:54

Dear Brian,

Did you have at the build logs? There is an error when compiling the  
package sources:
nxsdiscretematrix.h:52: error: 'UINT_MAX' was not declared in this scope

Compiling the code is necessary even for tarballs as building the  
vignettes depends on it.

The windows build is even stranger:
R:/R/pkgs/phylobase/inst/doc/phylobase.tex:15: Extra
�:15: Emergency stop
�:15:  ==> Fatal error occurred, no output PDF file produced!texify:  
pdflatex failed for some reason (see log file).
buildVignettes(dir = '.')
Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =  
quiet) :
  running 'texi2dvi' on 'phylobase.tex' failed
Calls: buildVignettes -> texi2dvi
Execution halted

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.

Hope this helps.
Best Stefan

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

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