Check results for 'grasp'

using R version 2.8.0 Under development (unstable) (2008-07-05 r46037)
using session charset: UTF-8

checking for file 'grasp/DESCRIPTION' ... OK

this is package 'grasp' version '2.5-4'

checking package dependencies ... OK

checking if this is a source package ... OK

checking whether package 'grasp' can be installed ... OK

checking package directory ... OK

checking for portable file names ... OK

checking for sufficient/correct file permissions ... OK

checking DESCRIPTION meta-information ... OK

checking top-level files ... OK

checking index information ... OK

checking package subdirectories ... OK

checking R files for non-ASCII characters ... OK

checking R files for syntax errors ... OK

checking whether the package can be loaded ... OK

checking whether the package can be loaded with stated dependencies ... OK

checking for unstated dependencies in R code ... OK

checking S3 generic/method consistency ... OK

checking replacement functions ... OK

checking foreign function calls ... OK

checking R code for possible problems ... NOTE
grasp: no visible binding for global variable ‘XXXpred’
grasp: no visible binding for global variable ‘YYY’
grasp: no visible binding for global variable ‘XXX’
grasp: no visible binding for global variable ‘OPTIONS’
grasp: no visible binding for global variable ‘gr.modmask’
grasp: no visible binding for global variable ‘DATAFILTER’
grasp: no visible binding for global variable ‘WEIGHTS’
grasp.adm.dump: no visible binding for global variable ‘OPTIONS’
grasp.exp.cormat: no visible binding for global variable ‘gr.selX’
grasp.exp.cormat: no visible binding for global variable ‘OPTIONS’
grasp.exp.cormat: no visible binding for global variable ‘YYY’
grasp.exp.cormat: no visible binding for global variable ‘gr.selXCOR’
grasp.exp.cormat: no visible binding for global variable ‘XXX’
grasp.exp.cormat: no visible binding for global variable ‘gr.modmask’
grasp.exp.cormat : panel: no visible binding for global variable ‘YYY’
grasp.exp.cormat : panel: no visible binding for global variable
‘OPTIONS’
grasp.exp.datamap: no visible binding for global variable ‘YYY’
grasp.exp.datamap: no visible binding for global variable ‘OPTIONS’
grasp.exp.datamap: no visible binding for global variable ‘XXX’
grasp.exp.datamap: no visible binding for global variable ‘gr.modmask’
grasp.exp.datamap: no visible binding for global variable ‘CONTOURS’
grasp.exp.distry: no visible binding for global variable ‘OPTIONS’
grasp.exp.distry: no visible binding for global variable ‘YYY’
grasp.exp.distry: no visible binding for global variable ‘gr.modmask’
grasp.exp.distry: no visible global function definition for ‘chisq.gof’
grasp.exp.histo: no visible binding for global variable ‘gr.selX’
grasp.exp.histo: no visible binding for global variable ‘OPTIONS’
grasp.exp.histo: no visible binding for global variable ‘YYY’
grasp.exp.histo: no visible binding for global variable ‘gr.modmask’
grasp.exp.histo: no visible binding for global variable ‘XXX’
grasp.exp.RvsP: no visible binding for global variable ‘gr.selX’
grasp.exp.RvsP: no visible binding for global variable ‘YYY’
grasp.exp.RvsP: no visible binding for global variable ‘OPTIONS’
grasp.exp.RvsP: no visible binding for global variable ‘XXX’
grasp.exp.RvsP: no visible binding for global variable ‘gr.modmask’
grasp.exp.RvsP: no visible binding for global variable ‘WEIGHTS’
grasp.exp.summary: no visible binding for global variable ‘YYY’
grasp.exp.summary: no visible binding for global variable ‘OPTIONS’
grasp.exp.summary: no visible binding for global variable ‘gr.modmask’
grasp.exp.summary: no visible binding for global variable ‘XXX’
grasp.exp.summary: no visible binding for global variable ‘gr.selX’
grasp.exp.xpredplot: no visible binding for global variable ‘XXX’
grasp.exp.xpredplot: no visible binding for global variable ‘OPTIONS’
grasp.exp.xpredplot: no visible binding for global variable ‘XXXpred’
grasp.in: no visible binding for global variable ‘YYY’
grasp.in: no visible binding for global variable ‘XXX’
grasp.in: no visible binding for global variable ‘XXXpred’
grasp.in: no visible binding for global variable ‘DROP.CONTRIB’
grasp.in: no visible binding for global variable ‘ALONE.CONTRIB’
grasp.in: no visible binding for global variable ‘MODEL.CONTRIB’
grasp.in: no visible binding for global variable ‘gr.lastcontrib1’
grasp.in: no visible binding for global variable ‘gr.lastcontrib2’
grasp.in: no visible binding for global variable ‘gr.lastcontrib3’
grasp.in: no visible binding for global variable ‘contribution1’
grasp.in: no visible binding for global variable ‘contribution2’
grasp.in: no visible binding for global variable ‘contribution3’
grasp.in: no visible binding for global variable ‘VALIDATION’
grasp.in: no visible binding for global variable ‘OPTIONS’
grasp.in: no visible binding for global variable ‘WEIGHTS’
grasp.int.contplot: no visible binding for global variable ‘YYY’
grasp.int.contplot: no visible binding for global variable ‘OPTIONS’
grasp.int.contplot: no visible binding for global variable ‘MODELCALLS’
grasp.int.contplot: no visible binding for global variable ‘XXX’
grasp.int.contplot: no visible binding for global variable
‘DROP.CONTRIB’
grasp.int.contplot: no visible binding for global variable
‘MODEL.CONTRIB’
grasp.int.contplot: no visible binding for global variable
‘ALONE.CONTRIB’
grasp.int.contrib: no visible binding for global variable ‘YYY’
grasp.int.contrib: no visible binding for global variable ‘OPTIONS’
grasp.int.contrib: no visible binding for global variable ‘MODELCALLS’
grasp.int.contrib: no visible binding for global variable
‘ALONE.CONTRIB’
grasp.int.contrib: no visible binding for global variable
‘DROP.CONTRIB’
grasp.int.contrib: no visible binding for global variable
‘MODEL.CONTRIB’
grasp.int.contrib: no visible binding for global variable ‘XXX’
grasp.int.plot: no visible binding for global variable ‘YYY’
grasp.int.plot: no visible binding for global variable ‘OPTIONS’
grasp.int.plot: no visible binding for global variable ‘MODELCALLS’
grasp.int.plot: no visible binding for global variable ‘XXX’
grasp.int.plot: no visible global function definition for ‘plot.gam’
grasp.int.response: no visible binding for global variable ‘OPTIONS’
grasp.int.response : grasp.pred.lookup2: no visible binding for global
variable ‘MODELCALLS’
grasp.int.response : grasp.pred.lookup2: no visible binding for global
variable ‘XXX’
grasp.int.response : grasp.pred.lookup2: no visible binding for global
variable ‘gr.selX’
grasp.int.response : grasp.pred.lookup2: no visible binding for global
variable ‘gr.modmask’
grasp.int.response: no visible binding for global variable ‘gr.selX’
grasp.int.response: no visible binding for global variable ‘XXX’
grasp.int.response: no visible binding for global variable ‘YYY’
grasp.int.response: no visible binding for global variable ‘MODELCALLS’
grasp.mod.anova: no visible binding for global variable ‘YYY’
grasp.mod.anova: no visible binding for global variable ‘OPTIONS’
grasp.mod.anova: no visible binding for global variable ‘MODELCALLS’
grasp.mod.anova: no visible binding for global variable ‘XXX’
grasp.mod.validate: no visible binding for global variable ‘YYY’
grasp.mod.validate: no visible binding for global variable ‘OPTIONS’
grasp.mod.validate: no visible binding for global variable ‘MODELCALLS’
grasp.mod.validate: no visible binding for global variable ‘XXX’
grasp.mod.validate: no visible binding for global variable ‘VALIDATION’
grasp.mod.validate: no visible binding for global variable ‘gr.modmask’
grasp.mod.validate: no visible binding for global variable ‘gr.EVA.ROC’
grasp.msk.limits: no visible binding for global variable ‘OPTIONS’
grasp.msk.limits: no visible binding for global variable ‘YYY’
grasp.msk.limits: no visible binding for global variable ‘gr.modmask’
grasp.msk.limits: no visible binding for global variable ‘gr.predmask’
grasp.msk.limits: no visible binding for global variable ‘XXX’
grasp.msk.limits: no visible binding for global variable ‘XXXpred’
grasp.options: no visible binding for global variable ‘gr.selX’
grasp.options: no visible binding for global variable ‘XXXpred’
grasp.options: no visible binding for global variable ‘XXX’
grasp.pred: no visible binding for global variable ‘YYY’
grasp.pred: no visible binding for global variable ‘OPTIONS’
grasp.pred: no visible binding for global variable ‘MODELCALLS’
grasp.pred: no visible binding for global variable ‘XXX’
grasp.pred: no visible binding for global variable ‘gr.predmat’
grasp.pred: no visible binding for global variable ‘XXXpred’
grasp.pred: no visible binding for global variable ‘gr.predmask’
grasp.pred.export: no visible binding for global variable ‘YYY’
grasp.pred.export: no visible binding for global variable ‘OPTIONS’
grasp.pred.export: no visible binding for global variable ‘MODELCALLS’
grasp.pred.export: no visible binding for global variable ‘XXXpred’
grasp.pred.export: no visible binding for global variable ‘gr.predmat’
grasp.pred.lookup: no visible binding for global variable ‘YYY’
grasp.pred.lookup: no visible binding for global variable ‘OPTIONS’
grasp.pred.lookup: no visible binding for global variable ‘MODELCALLS’
grasp.pred.lookup: no visible binding for global variable ‘XXX’
grasp.pred.lookup: no visible binding for global variable ‘wc’
grasp.pred.lookup: no visible binding for global variable ‘XXXlut’
grasp.pred.lookup: no visible binding for global variable ‘XXXpred’
grasp.pred.lookup: no visible binding for global variable ‘gr.modmask’
grasp.pred.lookup: no visible binding for global variable ‘gr.predmask’
grasp.pred.plot: no visible binding for global variable ‘YYY’
grasp.pred.plot: no visible binding for global variable ‘OPTIONS’
grasp.pred.plot: no visible binding for global variable ‘XXXpred’
grasp.pred.plot: no visible binding for global variable ‘gr.predmat’
grasp.step: no visible binding for global variable ‘YYY’
grasp.step: no visible binding for global variable ‘OPTIONS’
grasp.step: no visible binding for global variable ‘MODELCALLS’
grasp.step: no visible binding for global variable ‘gr.modmask’
grasp.step: no visible binding for global variable ‘XXX’
grasp.step: no visible binding for global variable ‘WEIGHTS’
grasp.step.anova: no visible binding for global variable ‘OPTIONS’
grasp.step.bruto: no visible binding for global variable ‘YYY’
grasp.step.bruto : bruto.gam: no visible binding for global variable
‘OPTIONS’
grasp.step.bruto : bruto.gam: no visible binding for global variable
‘XXX’
grasp.step.bruto : bruto.gam: no visible binding for global variable
‘YYY’
grasp.step.bruto : bruto.gam: no visible binding for global variable
‘gr.modmask’
grasp.step.bruto : bruto.gam: no visible binding for global variable
‘WEIGHTS’
grasp.step.bruto: no visible binding for global variable ‘MODELCALLS’
grasp.step.bruto: no visible binding for global variable ‘gr.modmask’
grasp.step.bruto : bruto.scope: no visible binding for global variable
‘XXX’
grasp.step.bruto: no visible binding for global variable ‘XXX’
grasp.step.bruto: no visible binding for global variable ‘OPTIONS’
grasp.step.contrib: no visible binding for global variable ‘XXX’
grasp.step.contrib: no visible binding for global variable ‘wc’
grasp.step.contrib: no visible binding for global variable ‘OPTIONS’
grasp.step.cross: no visible binding for global variable ‘gr.statname’
grasp.step.cross: no visible binding for global variable ‘gr.StatSel’
grasp.step.cross: no visible binding for global variable ‘gr.CrossSel’
grasp.step.cross: no visible binding for global variable
‘PLOTCROSS.VAL’
grasp.step.cross: no visible binding for global variable
‘PLOTCROSS.CVAL’
grasp.step.cross: no visible binding for global variable ‘gr.Yi’
grasp.step.crossplot: no visible binding for global variable ‘YYY’
grasp.step.crossplot: no visible binding for global variable ‘OPTIONS’
grasp.step.crossplot: no visible binding for global variable
‘PLOTCROSS.VAL’
grasp.step.crossplot: no visible binding for global variable
‘PLOTCROSS.CVAL’
grasp.step.crossval: no visible binding for global variable ‘YYY’
grasp.step.crossval: no visible binding for global variable ‘gr.Yi’
grasp.step.crossval: no visible binding for global variable ‘OPTIONS’
grasp.step.crossval: no visible binding for global variable ‘XXX’
grasp.step.crossval: no visible binding for global variable
‘gr.modmask’
grasp.step.full: no visible binding for global variable ‘YYY’
grasp.step.full: no visible binding for global variable ‘OPTIONS’
grasp.step.full: no visible binding for global variable ‘MODELCALLS’
grasp.step.full: no visible binding for global variable ‘gr.modmask’
grasp.step.full: no visible binding for global variable ‘XXX’
grasp.step.scope: no visible binding for global variable ‘XXX’
grasp.step.scope: no visible binding for global variable ‘OPTIONS’
grasp.step.start: no visible binding for global variable ‘OPTIONS’
grasp.step.start: no visible binding for global variable ‘gr.selXCOR’
grasp.step.start: no visible binding for global variable ‘gr.Yi’
grasp.step.start: no visible binding for global variable ‘XXX’
grasp.step.start: no visible binding for global variable ‘YYY’
Found possibly global 'T' or 'F' in the following function:
grasp.exp.distry

checking Rd files ... OK

checking Rd cross-references ... OK

checking for missing documentation entries ... OK

checking for code/documentation mismatches ... OK

checking Rd \usage sections ... OK

checking data for non-ASCII characters ... OK

creating grasp-Ex.R ... OK

checking examples ... ERROR
Running examples in 'grasp-Ex.R' failed.
The error most likely occurred in:

> ### * grasp
>
> flush(stderr()); flush(stdout())
>
> ### Name: grasp
> ### Title: Generalized Regression Analysis and Spatial Prediction
> ### Aliases: grasp
> ### Keywords: models
>
> ### ** Examples
>
>
> data(YYY) # reads in YYY,XXX and XXXpred demo dataset
> data(XXX)
> data(XXXpred)
> grasp.in(YYY,XXX,XXXpred) # initialize a new grasp session
#
# FUNCTION: grasp.in
# (by A. Lehmann )
# initializes the GRASP objects
#
creates YYY
creates gr.modmask
creates XXX
creates XXXpred
creates gr.predmat
creates gr.predmask
INFO: old contributions removed
#
# FUNCTION: grasp.options (by A. Lehmann)
# Sets the OPTIONS that are used by the different grasp functions
#
####################### GRASP OPTIONS ##########################

========== SET OPTIONS ===========
GRASP:
TITLE : GRASP:
PATH : c:/temp
PATHPNG : c:/temp
PATHLOG : c:/temp
PATHLUT : c:/temp
PLOTPAR : c(3, 3)
NBAR : 10
NPAST : 0
LIM : and
SELXLIM : 2
CORLIM : 1
RECALCULATEWEIGHTS : FALSE
CORTHIN : 1
CORPLOT : TRUE
DF1 : c(NA, NA, NA, NA, NA, NA, NA, NA, NA)
DF2 : c(4, 4, 4, 4, 4, 4, 4, 4, 4)
SMOOTHER : s
TEST : F
PERCONT : FALSE
DIRECTION : both
P.limit : 0.05
MINCONTRIB : 0
STARTWITH : 2
RESETSTART : TRUE
SHOWDETAIL : FALSE
CONTPLOT : histo
CVGROUPS : 5
RESOLUTION : 2500
STDERROR : TRUE
FAM : binomial

=========================================
INFO: old datafilter removed
**********************************************************************
********** REUSE GRASP.IN EACH TIME YOU MODIFY YOUR DATA *************
**********************************************************************
[1] "INPUT OK"
>
> grasp(2:3,c(4:6,8:9), title = "GRASP: ", path = "", gr.fam = "binomial", weights = TRUE, make.summary = TRUE, plot.maps = TRUE, plot.distry = TRUE, plot.histograms = TRUE, plot.respvspred = TRUE, plot.xpred = TRUE,plot.correlation = TRUE, stepwise.models = TRUE, test = "AIC", contributions = TRUE, plot.contributions = TRUE, plot.models = TRUE, model.anova = TRUE, validate.models = TRUE, predictions = TRUE, plot.predictions = TRUE)
#
# FUNCTION: grasp.options (by A. Lehmann)
# Sets the OPTIONS that are used by the different grasp functions
#
####################### GRASP OPTIONS ##########################

========== SET OPTIONS ===========
GRASP:
TITLE : GRASP:
PATH :
PATHPNG :
PATHLOG :
PATHLUT :
PLOTPAR : c(3, 3)
NBAR : 10
NPAST : 10
LIM : and
SELXLIM : c(4, 5, 6, 8, 9)
CORLIM : 1
RECALCULATEWEIGHTS : TRUE
CORTHIN : 1
CORPLOT : TRUE
DF1 : c(NA, NA, NA, NA, NA, NA, NA, NA, NA)
DF2 : c(4, 4, 4, 4, 4, 4, 4, 4, 4)
SMOOTHER : s
TEST : AIC
PERCONT : FALSE
DIRECTION : both
P.limit : 0.05
MINCONTRIB : 0
STARTWITH : c(4, 5, 6, 8, 9)
RESETSTART : TRUE
SHOWDETAIL : FALSE
CONTPLOT : histo
CVGROUPS : 5
RESOLUTION : 2500
STDERROR : TRUE
FAM : binomial

=========================================

########################################################################################
GRASP: Generalized Regression Analysis and Spatial Prediction for R, v2.0
Copyrights: Landcare Research New Zealand & Swiss Centre for Faunal Cartography, 1999-2005
Ref: A. Lehmann, J.R. Leathwick & J.McC. Overton, 2002. GRASP. Ecological Modelling, 157: 189-207
########################################################################################
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status Under development (unstable)
major 2
minor 8.0
year 2008
month 07
day 05
svn rev 46037
language R
version.string R version 2.8.0 Under development (unstable) (2008-07-05 r46037)
Tue Jul 8 17:21:41 2008
========== SELECTED VARIABLES ===========
selected responses: 2 3
selected predictors: 4 5 6 8 9
============================================
========== SET OPTIONS ===========
GRASP:
TITLE : GRASP:
PATH :
PATHPNG :
PATHLOG :
PATHLUT :
PLOTPAR : c(3, 3)
NBAR : 10
NPAST : 10
LIM : and
SELXLIM : c(4, 5, 6, 8, 9)
CORLIM : 1
RECALCULATEWEIGHTS : TRUE
CORTHIN : 1
CORPLOT : TRUE
DF1 : c(NA, NA, NA, NA, NA, NA, NA, NA, NA)
DF2 : c(4, 4, 4, 4, 4, 4, 4, 4, 4)
SMOOTHER : s
TEST : AIC
PERCONT : FALSE
DIRECTION : both
P.limit : 0.05
MINCONTRIB : 0
STARTWITH : c(4, 5, 6, 8, 9)
RESETSTART : TRUE
SHOWDETAIL : FALSE
CONTPLOT : histo
CVGROUPS : 5
RESOLUTION : 2500
STDERROR : TRUE
FAM : binomial
abscol : grey
prescol : black
PNG : FALSE

=========================================

INFO: !!! Applying DATAFILTER !!!
Number of observations used applying datafilter:
SP1 SP2
7563 7563

INFO: !!! WEIGHTS: sum of weights of 0s = sum of weights of 1s
Weights of 0s for SP1 = 0.05998598
Weights of 0s for SP2 = 0.11994669

VVVVVVVVVVVV calculating summaries VVVVVVVVVVVV
#
# FUNCTION: grasp.exp.summary
# (by A. Lehmann using Splus summary function)
# calculate a summary of selected Ys and Xs
#

vvvvvvvvvv GRASP SUMMARY vvvvvvvvvv
Tue Jul 8 17:21:42 2008
Y:
RESPONSE NAME: SP1
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.00000 0.00000 0.00000 0.05659 0.00000 1.00000

XXX:
TEMP RAD PREC SLOPE ASPECT
Min. : 529 Min. :1970 Min. : 323 Min. : 0.00 NORTH:1844
1st Qu.:1313 1st Qu.:5584 1st Qu.: 924 1st Qu.: 3.00 NULL :1636
Median :1622 Median :6440 Median :1175 Median :12.00 SOUTH:4083
Mean :1533 Mean :6741 Mean :1179 Mean :13.21
3rd Qu.:1803 3rd Qu.:7844 3rd Qu.:1434 3rd Qu.:22.00
Max. :2186 Max. :9772 Max. :2377 Max. :55.00
********** GRASP SUMMARY END **********

#
# FUNCTION: grasp.exp.summary
# (by A. Lehmann using Splus summary function)
# calculate a summary of selected Ys and Xs
#

vvvvvvvvvv GRASP SUMMARY vvvvvvvvvv
Tue Jul 8 17:21:42 2008
Y:
RESPONSE NAME: SP2
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0000 0.0000 0.0000 0.1071 0.0000 1.0000

XXX:
TEMP RAD PREC SLOPE ASPECT
Min. : 529 Min. :1970 Min. : 323 Min. : 0.00 NORTH:1844
1st Qu.:1313 1st Qu.:5584 1st Qu.: 924 1st Qu.: 3.00 NULL :1636
Median :1622 Median :6440 Median :1175 Median :12.00 SOUTH:4083
Mean :1533 Mean :6741 Mean :1179 Mean :13.21
3rd Qu.:1803 3rd Qu.:7844 3rd Qu.:1434 3rd Qu.:22.00
Max. :2186 Max. :9772 Max. :2377 Max. :55.00
********** GRASP SUMMARY END **********

Tue Jul 8 17:21:42 2008

############ summaries calculated ############

VVVVVVVVVVVV plotting maps VVVVVVVVVVVV
Error in get(getOption("device")) : invalid first argument
Calls: grasp -> lapply -> FUN -> get
Execution halted