A correspondant suggests it would help if I said the OS,
it's Intel Mac OS X 10.4...yes I should update but I'm
trying to hold off a little longer due to numerous other
things I don't want to have to reinstall just yet...
On 10/28/11 10:54 AM, Nick Matzke wrote:> 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/PRO
J.>
>
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/PRO
J.>
>
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/PRO
J.>
>
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/PRO
J.>
>
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?
> ==============================
--
===================================================Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Graduate Student Instructor, IB200B
Principles of Phylogenetics: Ecology and Evolution
http://ib.berkeley.edu/courses/ib200b/
http://phylo.wikidot.com/
Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page:
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page:
http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu
Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
-----------------------------------------------------
"[W]hen people thought the earth was flat, they were wrong.
When people thought the earth was spherical, they were
wrong. But if you think that thinking the earth is spherical
is just as wrong as thinking the earth is flat, then your
view is wronger than both of them put together."
Isaac Asimov (1989). "The Relativity of Wrong." The
Skeptical Inquirer, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm