This is a list, others may know the answer better than the person you
named (me). Please ask on R-sig-mac. Note that Brian Ripley answered
questions regarding spatial packages on Mavericks there:
https://stat.ethz.ch/pipermail/r-sig-mac/2014-April/010860.html
and later
https://stat.ethz.ch/pipermail/r-sig-mac/2014-May/010871.html
with a resolution - re-install rgdal and rgeos from CRAN-extras. Then
you'll need to install maptools from source, I suppose. I don't know
enough to know whether R 3.0.2 runs on 10.9.* at all. You'll need to
specify a lot more about your underlying system (OS 10.9.3, which R
version build for which system, etc.). My guess is that you have mixtures
of versions of software.
maptools doesn't depend on rgdal or rgeos, but it hasn't been built for R
3.1.0/Mavericks because of an unprotected call to rgeos::gDistance which I
will protect, so maptools for OSX Mavericks should appear soon. This,
however, is not your problem, I think.
Roger
On Thu, 5 Jun 2014, jwm302 wrote:
Hi Roger
I am really battling to get maptools package to work on on my system (OS X
10.9.3 Mavericks - see session at bottom of message). Everything was working
fine but since I upgraded from R version 3.0 (2013-09-25) -- "Frisbee
Sailing” to R 3.0.2 “Spring Dance” (because suddenly the extract function
wasn’t working anymore things started to break.
rgdal seems to be working because I am able to do commands like this with no
error: surfWater <- readOGR("Surface_water/gns_swb", "gns_swb”)
I have spent hours sifting through forum posts and the like, but all to no
avail. Either I am missing something obvious, or I am not command line savy
enough to find a solution . This forum (right at the bottom) seems to
suggest that you don’t need to install map tools from source, that the
binaries are available on CRAN. But I see over here
(http://cran.r-project.org/web/packages/maptools/index.html) that OS X
Mavericks binaries are not available. I am confused because I get conflicted
results from my searching on forums.
I would just like to resolve the issue as soon as possible so that I can get
on with my work.
But as you can see, when I invoke maptools package I get a horrible looking
error and R crashes (the same happens when I perform the same code from the
command line
<http://r-sig-geo.2731867.n2.nabble.com/file/n7586556/Screen_Shot_2014-06-05_at_1.png>
)):
sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] splines grid stats graphics grDevices utils datasets
methods base
other attached packages:
[1] diagram_1.6.2 shape_1.4.1 data.table_1.9.2 tables_0.7.64
Hmisc_3.14-0 Formula_1.1-1 survival_2.37-7 lattice_0.20-29
xtable_1.7-1 texreg_1.32
[11] bootStepAIC_1.2-0 MASS_7.3-31 glm2_1.1.2 plyr_1.8
RMySQL_0.9-3 DBI_0.2-7 maps_2.3-6 maptools_0.8-29
gdalUtils_0.2.0 rgdal_0.8-16
[21] raster_2.2-12 sp_1.0-14
loaded via a namespace (and not attached):
[1] cluster_1.15.2 codetools_0.2-8 foreach_1.4.1
foreign_0.8-61 iterators_1.0.6 latticeExtra_0.6-26
RColorBrewer_1.0-5 reshape2_1.2.2 stringr_0.6.2
packageInstallLoad <- function(x){
+ for( i in x ){
+ # require returns TRUE invisibly if it was able to load package
+ if( ! require( i , character.only = TRUE ) ){
+ # If package was not able to be loaded then re-install
+ #setRepositories(ind = c(1,6))
+ install.packages( i , dependencies = T )
+ # Load package after installing
+ require( i , character.only = TRUE )
+ }
+ }
+ }
packageInstallLoad(c("raster", "rgdal", "gdalUtils", "maptools", "sp",
"maps", "RMySQL", "plyr", "stats", "glm2", "bootStepAIC", "texreg",
"xtable", "tables", "data.table", "diagram"))
Loading required package: gdalUtils
Loading required package: maps
Loading required package: RMySQL
Loading required package: DBI
Loading required package: plyr
Loading required package: glm2
Loading required package: bootStepAIC
Loading required package: MASS
Attaching package: ‘MASS’
The following objects are masked from ‘package:raster’:
area, select
Loading required package: texreg
Version: 1.32
Date: 2014-05-01
Author: Philip Leifeld (University of Konstanz)
Attaching package: ‘texreg’
The following object is masked from ‘package:raster’:
extract
Loading required package: xtable
Attaching package: ‘xtable’
The following object is masked from ‘package:maptools’:
label
Loading required package: tables
Loading required package: Hmisc
Loading required package: grid
Loading required package: lattice
Loading required package: survival
Loading required package: splines
Loading required package: Formula
Attaching package: ‘Hmisc’
The following objects are masked from ‘package:xtable’:
label, label<-
The following objects are masked from ‘package:plyr’:
is.discrete, summarize
The following objects are masked from ‘package:raster’:
mask, zoom
The following object is masked from ‘package:maptools’:
label
The following object is masked from ‘package:rgeos’:
translate
The following objects are masked from ‘package:base’:
format.pval, round.POSIXt, trunc.POSIXt, units
Loading required package: data.table
data.table 1.9.2 For help type: help("data.table")
Loading required package: diagram
Loading required package: shape
Attaching package: ‘diagram’
The following object is masked from ‘package:sp’:
coordinates
data(wrld_simpl)
kenya <- wrld_simpl[wrld_simpl$NAME == "Kenya",]
*** caught segfault ***
address 0x1150, cause 'memory not mapped'
Traceback:
1: .Call(bboxCalcR_c, y@polygons)
2: wrld_simpl[wrld_simpl$NAME == "Kenya", ]
3: wrld_simpl[wrld_simpl$NAME == "Kenya", ]
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Thanks and Regards
Justin Michell
--
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--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: roger.biv...@nhh.no
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