Hi Nick, Could you please report if you also get this problem with the latest version of Rcpp?
Thanks,
-- François
On Fri, 2011-10-28 at 16:58 -0700, Nick Matzke wrote:
> Hi all,
>
> I've had phylobase installed and functioning for awhile, but
> I get a weird error while installing phylobase 0.6.2,
> despite the fact that it looks like all the files compile
> successfully and something weird happens while building
> phylobase.so.
>
> Any advice would be *much* appreciated...
>
> Install attempt:
> ==============
> mws2:~/Desktop/downloads nick$ R CMD INSTALL
> ~/Desktop/downloads/phylobase_0.6.2
>
> Loading ~/.Rprofile...
>
> Currently viewed PATH:
>
> /opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/Library/Frameworks/Python.framework/Versions/Current/bin:/usr/local/soylatte16-i386/bin:/Applications/muscle:/Applications/dssp:/opt/local/include:/Library/Frameworks/GDAL.framework/Programs:/Library/Frameworks/PROJ.framework/Programs:/sw/include/wx-2.8:/Library/Frameworks/PROJ.framework/Programs:_njm:/opt/git/bin:/Users/nick/gtk/inst/bin:/Users/nick/bin:/usr/local/mysql/bin:/opt/local/bin:/opt/local/sbin:/bioinformatics/ncbi_execs/sap:/bioinformatics/ncbi_execs/tcoffee565/bin:/usr/local/ActivePerl-5.10/bin:/bioinformatics/ncbi_execs/bin:/Users/nick:/bioinformatics:/bioinformatics/ncbi_execs/ncbi_tools/:/bioinformatics/pythonstuff/soylatte16-i386-1.0.3/bin:/bioinformatics/diva_mac:/usr/texbin/usr/ebiotools/staden/macosx-bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/ebiotools/ncbi/bin:/usr/ebiotools/bin:/usr/local/bin:/usr/texbin:/usr/X11R6/bin:/usr/texbin:/Applications/dssp:/Library/Frameworks/PROJ.framework/:/Library/Frameworks/PROJ.
>
> framework/Programs:/Library/Frameworks/PROJ.framework/Versions/4.6/Headers:/Library/Frameworks/GDAL.framework/Versions/1.6/Programs
>
> * installing to library ‘/Users/nick/Library/R/2.10/library’
>
> * installing *source* package ‘phylobase’ ...
>
> ** libs
>
> ** arch - i386
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c GetNCL.cpp -o GetNCL.o
>
> gcc -arch i386 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c ancestors.c -o ancestors.o
>
> gcc -arch i386 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c descendants.c -o descendants.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsassumptionsblock.cpp -o
> nxsassumptionsblock.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsblock.cpp -o nxsblock.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxscharactersblock.cpp -o
> nxscharactersblock.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxscxxdiscretematrix.cpp -o
> nxscxxdiscretematrix.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsdatablock.cpp -o nxsdatablock.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsdistancedatum.cpp -o nxsdistancedatum.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsdistancesblock.cpp -o nxsdistancesblock.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsemptyblock.cpp -o nxsemptyblock.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsexception.cpp -o nxsexception.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsmultiformat.cpp -o nxsmultiformat.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxspublicblocks.cpp -o nxspublicblocks.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsreader.cpp -o nxsreader.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxssetreader.cpp -o nxssetreader.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsstring.cpp -o nxsstring.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxstaxablock.cpp -o nxstaxablock.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxstoken.cpp -o nxstoken.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxstreesblock.cpp -o nxstreesblock.o
>
> g++ -arch i386
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c nxsunalignedblock.cpp -o nxsunalignedblock.o
>
> gcc -arch i386 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c phyloXX.c -o phyloXX.o
>
> gcc -arch i386 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c reorderBinary.c -o reorderBinary.o
>
> gcc -arch i386 -std=gnu99
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386 -I.
> -DHAVE_INTTYPES_H -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -fPIC -g -O2 -c reorderRobust.c -o reorderRobust.o
>
> g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names
> -mmacosx-version-min=10.4 -undefined dynamic_lookup
> -single_module -multiply_defined suppress -L/usr/local/lib
> -o phylobase.so GetNCL.o ancestors.o descendants.o
> nxsassumptionsblock.o nxsblock.o nxscharactersblock.o
> nxscxxdiscretematrix.o nxsdatablock.o nxsdistancedatum.o
> nxsdistancesblock.o nxsemptyblock.o nxsexception.o
> nxsmultiformat.o nxspublicblocks.o nxsreader.o
> nxssetreader.o nxsstring.o nxstaxablock.o nxstoken.o
> nxstreesblock.o nxsunalignedblock.o phyloXX.o
> reorderBinary.o reorderRobust.o Loading ~/.Rprofile...
> Currently viewed PATH:
> /opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/Library/Frameworks/Python.framework/Versions/Current/bin:/usr/local/soylatte16-i386/bin:/Applications/muscle:/Applications/dssp:/opt/local/include:/Library/Frameworks/GDAL.framework/Programs:/Library/Frameworks/PROJ.framework/Programs:/sw/include/wx-2.8:/Library/Frameworks/PROJ.framework/Programs:_njm:/opt/git/bin:/Users/nick/gtk/inst/bin:/Users/nick/bin:/usr/local/mysql/bin:/opt/local/bin:/opt/local/sbin:/bioinformatics/ncbi_execs/sap:/bioinformatics/ncbi_execs/tcoffee565/bin:/usr/local/ActivePerl-5.10/bin:/bioinformatics/ncbi_execs/bin:/Users/nick:/bioinformatics:/bioinformatics/ncbi_execs/ncbi_tools/:/bioinformatics/pythonstuff/soylatte16-i386-1.0.3/bin:/bioinformatics/diva_mac:/usr/texbin/usr/ebiotools/staden/macosx-bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/ebiotools/ncbi/bin:/usr/ebiotools/bin:/usr/local/bin:/usr/texbin:/usr/X11R6/bin:/usr/texbin:/Applications/dssp:/Library/Frameworks/PROJ.framework/:/Library/Frameworks/PROJ.
>
> framework/Programs:/Library/Frameworks/PROJ.framework/Versions/4.6/Headers:/Library/Frameworks/GDAL.framework/Versions/1.6/Programs:/usr/texbin:/Applications/dssp:/Library/Frameworks/PROJ.framework/:/Library/Frameworks/PROJ.framework/Programs:/Library/Frameworks/PROJ.framework/Versions/4.6/Headers:/Library/Frameworks/GDAL.framework/Versions/1.6/Programs
>
> /Library/Frameworks/R.framework/Versions/2.10/Resources/library/Rcpp/lib/i386/libRcpp.a
>
> -F/Library/Frameworks/R.framework/.. -framework R
> -Wl,-framework -Wl,CoreFoundation
>
> i686-apple-darwin8-g++-4.2.1: Loading: No such file or directory
>
> i686-apple-darwin8-g++-4.2.1: ~/.Rprofile...: No such file
> or directory
>
> i686-apple-darwin8-g++-4.2.1: Currently: No such file or
> directory
>
> i686-apple-darwin8-g++-4.2.1: viewed: No such file or directory
>
> i686-apple-darwin8-g++-4.2.1: PATH:: No such file or directory
>
> i686-apple-darwin8-g++-4.2.1:
> /opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/Library/Frameworks/Python.framework/Versions/Current/bin:/usr/local/soylatte16-i386/bin:/Applications/muscle:/Applications/dssp:/opt/local/include:/Library/Frameworks/GDAL.framework/Programs:/Library/Frameworks/PROJ.framework/Programs:/sw/include/wx-2.8:/Library/Frameworks/PROJ.framework/Programs:_njm:/opt/git/bin:/Users/nick/gtk/inst/bin:/Users/nick/bin:/usr/local/mysql/bin:/opt/local/bin:/opt/local/sbin:/bioinformatics/ncbi_execs/sap:/bioinformatics/ncbi_execs/tcoffee565/bin:/usr/local/ActivePerl-5.10/bin:/bioinformatics/ncbi_execs/bin:/Users/nick:/bioinformatics:/bioinformatics/ncbi_execs/ncbi_tools/:/bioinformatics/pythonstuff/soylatte16-i386-1.0.3/bin:/bioinformatics/diva_mac:/usr/texbin/usr/ebiotools/staden/macosx-bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/ebiotools/ncbi/bin:/usr/ebiotools/bin:/usr/local/bin:/usr/texbin:/usr/X11R6/bin:/usr/texbin:/Applications/dssp:/Library/Frameworks/PROJ.framework/:/Library/Frameworks/PROJ.
>
> framework/Programs:/Library/Frameworks/PROJ.framework/Versions/4.6/Headers:/Library/Frameworks/GDAL.framework/Versions/1.6/Programs:/usr/texbin:/Applications/dssp:/Library/Frameworks/PROJ.framework/:/Library/Frameworks/PROJ.framework/Programs:/Library/Frameworks/PROJ.framework/Versions/4.6/Headers:/Library/Frameworks/GDAL.framework/Versions/1.6/Programs:
>
> File name too long
>
> make: *** [phylobase.so] Error 1
>
> ERROR: compilation failed for package ‘phylobase’
>
> * removing ‘/Users/nick/Library/R/2.10/library/phylobase’
>
> * restoring previous
> ‘/Users/nick/Library/R/2.10/library/phylobase’
> ==============
>
>
>
> Using intel mac, sessionInfo():
>
> sessionInfo():
> ===========
> R version 2.10.1 (2009-12-14)
> i386-apple-darwin8.11.1
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid stats grDevices utils datasets
> graphics methods base
>
> other attached packages:
> [1] Rcpp_0.8.3 phylobase_0.5 ape_2.7-3
>
> loaded via a namespace (and not attached):
> [1] gee_4.13-14 lattice_0.17-26 nlme_3.1-96
> tools_2.10.1
> Warning message:
> In install.packages(c("phylobase"), lib =
> "/Library/Frameworks/R.framework/Resources/library/", :
> installation of package 'phylobase' had non-zero exit status
> ===========
>
>
>
signature.asc
Description: This is a digitally signed message part
_______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
