[R-sig-phylo] problem updating phylobase

Nick Matzke matzke at berkeley.edu
Sat Oct 29 21:53:54 CEST 2011


Looks like I have to update the OS on this computer to get a 
newer version of Rcpp to work, I've been avoiding that but 
I'll do it and report back.  Thanks!
Nick


On 10/29/11 9:52 AM, François Michonneau wrote:
>
> 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/PR
OJ.
>>
>> 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/PR
OJ.
>>
>> 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/PR
OJ.
>>
>> 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
>> ===========
>>
>>
>>

-- 
====================================================
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
1005 Valley Life Sciences Building #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



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