Hi all,
I am attempting to install a package called phylobase from
source directory. It all seems to work until the end, at
which point it looks like the last compile command fails
because the line is too long...perhaps because the g++
command line also includes "Loading ~/.Rprofile...", like this:
============================
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 [....etc....]
reorderRobust.o Loading ~/.Rprofile... Currently viewed
PATH:
/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/Library/Frameworks/Python.framework/Versions/Current/bin:[...etc...]
============================
Any hints on what might be going on? Is there a way to
access the makefile directly so that I can tinker with it?
Or tell INSTALL to not bother with .Rprofile?
I get similar errors when installing from zipfile, or from
using install.packages within R.
Cheers,
Nick
Full output:
===============================
[getting sessionInfo()]
mws2:~/Desktop/downloads nick$ R
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
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
> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-apple-darwin8.11.1
locale:
[1] C/en_US.UTF-8/C/C/C/C
attached base packages:
[1] stats grDevices utils datasets graphics
methods base
> quit()
Save workspace image? [y/n/c]: n
mws2:~/Desktop/downloads nick$
[install attempt with R CMD INSTALL]
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’
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