[Phylobase-devl] failed mac build

[Marguerite Butler]

Hi Ben and Steve,

Luckily (I guess) I have not done a clean install on a laptop. So  
here's the build log and error messages.  I'll add it to the open  
ticket in a bit.

Marguerite




On Mar 31, 2008, at 11:17 AM, Steve Kembel wrote:

> Scratch that, was using the rev 104 tarball from the project home
> page, the nightly build tarball installs fine (with a non-fatal
> warning about In method for function "[": expanding the signature to
> include omitted arguments in definition: j = "missing",
> drop = "missing").
>
> Steve
>
> On Mar 31, 2008, at 2:09 PM, Steve Kembel wrote:
>> Thanks Ben... that worked. Actually that was a typo, meant to say R
>> 2.5.1 (I'm out of date but not *that* bad!), but I upgraded to 2.6.2
>> and now I can install via the install.packages("phylobase",  
>> repos="http://r-forge.r-project.org
>> ") command within R, but at the command line using the latest source
>> tarball with R CMD INSTALL phylobase I get the following errors. I
>> know this is the error that Thibaut was having before, what was the
>> resolution?:
>>
>> [...]
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> ** libs
>> g++ -I/usr/share/R/include -I/usr/share/R/include     -IRcppSrc -
>> Incl/ncl -fpic  -g -O2 -c NCLInterface.cpp -o NCLInterface.o
>> g++ -I/usr/share/R/include -I/usr/share/R/include     -IRcppSrc -
>> Incl/ncl -fpic  -g -O2 -c ReadWithNCL.cpp -o ReadWithNCL.o
>> g++ -shared  -o phylobase.so NCLInterface.o ReadWithNCL.o -LRcppSrc -
>> lRcpp -Lncl/ncl/.libs -lncl  -L/usr/lib64/R/lib -lR
>> /usr/bin/ld: ncl/ncl/.libs/libncl.a(nxsassumptionsblock.o):
>> relocation R_X86_64_32 against `a local symbol' can not be used when
>> making a shared object; recompile with -fPIC
>> ncl/ncl/.libs/libncl.a: could not read symbols: Bad value
>> collect2: ld returned 1 exit status
>> make: *** [phylobase.so] Error 1
>> chmod: cannot access `/usr/local/lib/R/site-library/phylobase/libs/
>> *': No such file or directory
>> ERROR: compilation failed for package 'phylobase'
>> ** Removing '/usr/local/lib/R/site-library/phylobase'
>>
>> <config.log>
>> _______________________________________________
>> Phylobase-devl mailing list
>> Phylobase-devl at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/ 
>> phylobase-devl
>
> ______________________________________________
> Dr. Steven Kembel - skembel at berkeley.edu
> http://www.phylodiversity.net/skembel/
>
>
> _______________________________________________
> Phylobase-devl mailing list
> Phylobase-devl at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/ 
> phylobase-devl

____________________________________________
Marguerite A. Butler
Department of Zoology
University of Hawaii
2538 McCarthy Mall, Edmondson 259
Honolulu, HI  96822

Phone: 808-956-4713
FAX:   808-956-9812
Dept: 808-956-8617
http://www2.hawaii.edu/~mbutler
http://www.hawaii.edu/zoology/

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