[GRASS-stats] errors on spgrass Yosemite / homebrew
Rainer M Krug
Rainer at krugs.de
Wed Jan 21 00:39:25 PST 2015
Hi
I tried to run
--8<---------------cut here---------------start------------->8---
library(spgrass)
examples(spgrass)
--8<---------------cut here---------------end--------------->8---
but I got an error - transcript below.
Let me know if I should try something out.
Cheers,
Rainer
,----
| 09:30:33 ~$ grass70 ~/Documents/spearfish60_grass7/user1/
| Cleaning up temporary files...
| Starting GRASS GIS...
|
| __________ ___ __________ _______________
| / ____/ __ \/ | / ___/ ___/ / ____/ _/ ___/
| / / __/ /_/ / /| | \__ \\_ \ / / __ / / \__ \
| / /_/ / _, _/ ___ |___/ /__/ / / /_/ // / ___/ /
| \____/_/ |_/_/ |_/____/____/ \____/___//____/
|
| Welcome to GRASS 7.0.0beta3
| GRASS homepage: http://grass.osgeo.org
| This version running through: Bash Shell (/usr/local/bin/bash)
| Help is available with the command: g.manual -i
| See the licence terms with: g.version -c
| Start the GUI with: g.gui wxpython
| When ready to quit enter: exit
|
| GRASS 7.0.0beta3 (spearfish60_grass7):~ > R
|
| R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
| Copyright (C) 2014 The R Foundation for Statistical Computing
| Platform: x86_64-apple-darwin14.1.0 (64-bit)
|
| 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.
|
| [Previously saved workspace restored]
|
| > library(spgrass)
| Loading required package: sp
| Loading required package: XML
| GRASS GIS interface loaded with GRASS version: GRASS 7.0.0beta3 (2014)
| and location: spearfish60_grass7
| > example(spgrass)
|
| spgrss> if (nchar(Sys.getenv("GISRC")) > 0) {
| spgrss+ require(rgdal)
| spgrss+ soilsph <- readRAST("soils.ph", ignore.stderr=TRUE, plugin=FALSE)
| spgrss+ summary(soilsph)
| spgrss+ grd <- gmeta2grd(ignore.stderr=TRUE)
| spgrss+ grd
| spgrss+ set.seed(1)
| spgrss+ pts <- spsample(soilsph, 200, "random")
| spgrss+ smple <- SpatialPointsDataFrame(pts, data=over(pts, soilsph))
| spgrss+ summary(smple)
| spgrss+ writeVECT(smple, "sp_dem", v.in.ogr_flags="overwrite", ignore.stderr=TRUE)
| spgrss+ bugsDF <- readVECT("bugsites", ignore.stderr=TRUE, mapset="PERMANENT")
| spgrss+ summary(bugsDF)
| spgrss+ vInfo("streams", ignore.stderr=TRUE)
| spgrss+ vColumns("streams", ignore.stderr=TRUE)
| spgrss+ vDataCount("streams", ignore.stderr=TRUE)
| spgrss+ streams <- readVECT("streams", type="line,boundary",
| spgrss+ remove.duplicates=FALSE, ignore.stderr=TRUE, plugin=FALSE)
| spgrss+ summary(streams)
| spgrss+ }
| Loading required package: rgdal
| rgdal: version: 0.9-1, (SVN revision 518)
| Geospatial Data Abstraction Library extensions to R successfully loaded
| Loaded GDAL runtime: GDAL 1.11.1, released 2014/09/24
| Path to GDAL shared files: /usr/local/Cellar/gdal/1.11.1_3/share/gdal
| Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480]
| Path to PROJ.4 shared files: (autodetected)
| Command: v.in.ogr
| Description: Imports vector data into a GRASS vector map using OGR library.
| Keywords: vector, import, OGR
| Parameters:
| name: dsn, type: string, required: yes, multiple: no
| [Examples:
| ESRI Shapefile: directory containing shapefiles
| MapInfo File: directory containing mapinfo files]
| name: layer, type: string, required: no, multiple: yes
| [Examples:
| ESRI Shapefile: shapefile name
| MapInfo File: mapinfo file name]
| name: output, type: string, required: no, multiple: no
| keydesc: name, keydesc_count: 1
| [Name for output vector map]
| name: spatial, type: float, required: no, multiple: yes
| keydesc: xmin,ymin,xmax,ymax, keydesc_count: 4
| [Format: xmin,ymin,xmax,ymax - usually W,S,E,N]
| name: where, type: string, required: no, multiple: no
| keydesc: sql_query, keydesc_count: 1
| [Example: income < 1000 and inhab >= 10000]
| name: min_area, type: float, required: no, multiple: no
| default: 0.0001
| [Smaller areas and islands are ignored. Should be greater than snap^2]
| name: type, type: string, required: no, multiple: yes
| default:
| [Optionally change default input type]
| name: snap, type: float, required: no, multiple: no
| default: -1
| ['-1' for no snap]
| name: location, type: string, required: no, multiple: no
| keydesc: name, keydesc_count: 1
| [Name for new location to create]
| name: cnames, type: string, required: no, multiple: yes
| [List of column names to be used instead of original names, first is used for category column]
| name: encoding, type: string, required: no, multiple: no
| [Overrides encoding interpretation, useful when importing ESRI Shapefile]
| name: key, type: string, required: no, multiple: no
| [If not given, categories are generated as unique values and stored in 'cat' column]
| Flags:
| name: f [List supported OGR formats and exit] {TRUE}
| name: l [List available OGR layers in data source and exit] {TRUE}
| name: c [Do not clean polygons (not recommended)] {FALSE}
| name: 2 [Useful if input is 3D but all z coordinates are identical] {FALSE}
| name: t [Do not create attribute table] {FALSE}
| name: o [Override dataset projection (use location's projection)] {FALSE}
| name: r [Limit import to the current region] {FALSE}
| name: e [Also updates the default region if in the PERMANENT mapset] {FALSE}
| name: w [Change column names to lowercase characters] {FALSE}
| name: i [Create the location specified by the "location" parameter and exit. Do not import the vector data.] {FALSE}
| name: overwrite [Allow output files to overwrite existing files] {FALSE}
| name: help [Print usage summary] {FALSE}
| name: verbose [Verbose module output] {FALSE}
| name: quiet [Quiet module output] {FALSE}
| Error in insert_required(pcmd = pcmd, parameters = parameters, pt = pt, :
| required parameters with no defaults missing: dsn
|
| > traceback()
| 10: stop(paste("required parameters with no defaults missing:", paste(nadefnms1,
| collapse = " ")))
| 9: insert_required(pcmd = pcmd, parameters = parameters, pt = pt,
| req = req, suppress_required = suppress_required)
| 8: doGRASS(cmd, flags = flags, ..., parameters = parameters, echoCmd = echoCmd,
| legacyExec = legacyExec)
| 7: execGRASS("v.in.ogr", flags = v.in.ogr_flags, input = GDSN, output = vname,
| layer = LAYER, ignore.stderr = ignore.stderr)
| 6: writeVECT(smple, "sp_dem", v.in.ogr_flags = "overwrite", ignore.stderr = TRUE) at Rex5d28289dfd2d#18
| 5: eval(expr, envir, enclos)
| 4: eval(ei, envir)
| 3: withVisible(eval(ei, envir))
| 2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
| getOption("prompt")), continue.echo = paste0(prompt.prefix,
| getOption("continue")), verbose = verbose, max.deparse.length = Inf,
| encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
| 1: example(spgrass)
| > version
| _
| platform x86_64-apple-darwin14.1.0
| arch x86_64
| os darwin14.1.0
| system x86_64, darwin14.1.0
| status
| major 3
| minor 1.2
| year 2014
| month 10
| day 31
| svn rev 66913
| language R
| version.string R version 3.1.2 (2014-10-31)
| nickname Pumpkin Helmet
| > sessionInfo()
| R version 3.1.2 (2014-10-31)
| Platform: x86_64-apple-darwin14.1.0 (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] stats graphics grDevices utils datasets methods base
|
| other attached packages:
| [1] rgdal_0.9-1 spgrass_0.1-0 XML_3.98-1.1 sp_1.0-16
|
| loaded via a namespace (and not attached):
| [1] grid_3.1.2 lattice_0.20-29 tools_3.1.2
| >
`----
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer at krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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