[R] Installing rgeos on Mac OS X 10.4 (was Re: "package 'stringr' does not have a name space"

Tue Oct 25 23:11:01 CEST 2011

I figured it out, at least enough to get rgeos's gSimplify 
function to work, which was my original goal; the stringr 
problem was with 0.2, however I got stringr 0.5 to install 
by changing the minimum version in DESCRIPTION from R2.11 to 
R 2.10. ...

Thanks for the help!

#############
# This is how I got rgeos to install in R GUI on my Intel 
Mac OS X 10.4:
#############

# stringr download source 0.5 from CRAN
# change DESCRIPTION, change R 2.11 to R 2.10
# install with:
install.packages("/Users/nick/Desktop/downloads/stringr", 
"/Library/Frameworks/R.framework/Resources/library/", NULL, 
type='source')

# Update sp to 0.9-91 (manual download from CRAN; my default 
server didn't have it)
remove.packages("sp")

install.packages("/Users/nick/Desktop/downloads/sp_0.9-91.tar.gz", 
"/Library/Frameworks/R.framework/Resources/library/", NULL, 
type='source')

# Manual install of GEOS 3.3

# Download GEOS 3.3 from:
http://www.kyngchaos.com/macosx/build/geos
http://trac.osgeo.org/geos/

./configure
make
sudo make install

# This installs to /usr/local/bin/geo-config which is an 
input to the rgeos install

# To find, in Terminal type:
locate geos-config

# I got a crash based on a missing definition of 
GEOSUnaryUnion_r, so...
# To get rgeos to install,

# delete from rgeos_topology.c this bit (line 33):
================================
#ifdef HAVEUNARYUNION
SEXP rgeos_unaryunion(SEXP env, SEXP obj, SEXP id, SEXP byid ) {
     return( rgeos_topologyfunc(env, obj, id, byid, 
&GEOSUnaryUnion_r) );
}
#endif
================================

# And this from line 35 of init.c
================================
#ifdef HAVEUNARYUNION
     {"rgeos_unaryunion", (DL_FUNC) &rgeos_unaryunion, 4},
#endif
================================

# Then remove failed installs if any
remove.packages("rgeos")

install.packages("/Users/nick/Desktop/downloads/rgeos", 
"/Library/Frameworks/R.framework/Resources/library/", NULL, 
type='source',
configure.args="--with-geos-config=/usr/local/bin/geos-config")

library(rgeos)

# (You may have to remove old .o and .so files from previous 
install attempts...)

On 10/25/11 1:09 PM, Nick Matzke wrote:
> Hi all,
>
> I have almost gotten rgeos to install, however I'm getting a
> peculiar error about a (successfully installed) other
> package, stringr:
>
> "Error : package 'stringr' does not have a name space"
>
> I have asked the r-sig-geo list, but this error looks like a
> more generic one, perhaps there is some simple command I
> could add to stringr to get the namespace correct?
>
> Any ideas much appreciated!
>
> Cheers,
> Nick
>
>
> PS Full error message below...yes, I'm still on Intel Mac OS
> X 10.4 and thus R 2.10.1, can't be helped at the moment...
>
> =========================================
>  > 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] stats grDevices utils datasets graphics methods base
>
> other attached packages:
> [1] stringr_0.2 plyr_0.1.9
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
>
>
>> install.packages("/Users/nick/Desktop/downloads/rgeos",
> "/Library/Frameworks/R.framework/Resources/library/", NULL,
> type='source',
> +
> configure.args="--with-geos-config=/usr/local/bin/geos-config")
> WARNING: ignoring environment value of R_HOME
> Loading ~/.Rprofile...
> Currently viewed PATH:
> /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/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
>
> * installing *source* package ‘rgeos’ ...
> geos-config: /usr/local/bin/geos-config
> GEOS: 3.2.3
> CPPFLAGS: -DHAVEUNARYUNION -I/usr/local/include
> LIBS: -L/usr/local/lib -lgeos
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> ** arch - i386
> make: Nothing to be done for `all'.
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: plyr
> Error : package 'stringr' does not have a name space
> ERROR: lazy loading failed for package ‘rgeos’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/2.10/Resources/library/rgeos’
>
> Warning message:
> In install.packages("/Users/nick/Desktop/downloads/rgeos",
> "/Library/Frameworks/R.framework/Resources/library/", :
> installation of package
> '/Users/nick/Desktop/downloads/rgeos' 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
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