CRAN Package Check Results for Package STAR

Last updated on 2014-08-01 14:47:33.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3-7 5.89 69.49 75.38 NOTE --no-vignettes
r-devel-linux-x86_64-debian-gcc 0.3-7 5.82 69.00 74.82 NOTE --no-vignettes
r-devel-linux-x86_64-fedora-clang 0.3-7 516.29 NOTE --no-build-vignettes
r-devel-linux-x86_64-fedora-gcc 0.3-7 501.98 NOTE --no-build-vignettes
r-devel-osx-x86_64-clang 0.3-7 356.22 NOTE --no-build-vignettes
r-devel-windows-ix86+x86_64 0.3-7 19.00 125.00 144.00 NOTE --no-vignettes
r-patched-linux-x86_64 0.3-7 6.18 70.64 76.82 NOTE --no-vignettes
r-patched-solaris-sparc 0.3-7 924.10 NOTE --no-vignettes
r-patched-solaris-x86 0.3-7 1090.80 NOTE --no-build-vignettes
r-release-linux-ix86 0.3-7 7.22 85.02 92.24 NOTE --no-vignettes
r-release-linux-x86_64 0.3-7 6.07 70.22 76.29 NOTE --no-vignettes
r-release-osx-x86_64-mavericks 0.3-7 NOTE
r-release-osx-x86_64-snowleopard 0.3-7 NOTE
r-release-windows-ix86+x86_64 0.3-7 26.00 127.00 153.00 NOTE --no-vignettes
r-oldrel-windows-ix86+x86_64 0.3-7 25.00 134.00 159.00 NOTE --no-vignettes

Check Details

Version: 0.3-7
Flags: --no-vignettes
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to codetools which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     codetools gss
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter Creating R
    packages of the Writing R Extensions manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-ix86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.3-7
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following functions:
     plot.ssanova plot.ssanova0
    Found the platform-specific device:
     X11
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    as.spikeTrain: no visible global function definition for spikeTimes
    gamObj.gampsth: no visible binding for global variable PoissonF
    gammaMLE: multiple local function definitions for rFct with different
     formal arguments
    gssObj.gsspsth: no visible binding for global variable gfit
    gssObj.gsspsth0: no visible binding for global variable gfit
    invgaussMLE: multiple local function definitions for rFct with
     different formal arguments
    lines.CountingProcessSamplePath: no visible binding for global variable
     st
    mkAR: no visible binding for global variable lN.1
    qqDuration: no visible binding for global variable yi
    qqDuration: no visible binding for global variable si
    thinProcess: no visible binding for global variable targetFct
    thinProcess: no visible binding for global variable posMax
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-ix86, r-release-linux-x86_64

Version: 0.3-7
Flags: --no-build-vignettes
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to codetools which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     codetools gss
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter Creating R
    packages of the Writing R Extensions manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-solaris-x86

Version: 0.3-7
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following functions:
     plot.ssanova plot.ssanova0
    Found the platform-specific device:
     X11
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    as.spikeTrain: no visible global function definition for spikeTimes
    gamObj.gampsth: no visible binding for global variable PoissonF
    gammaMLE: multiple local function definitions for rFct with different
     formal arguments
    gssObj.gsspsth: no visible binding for global variable gfit
    gssObj.gsspsth0: no visible binding for global variable gfit
    invgaussMLE: multiple local function definitions for rFct with
     different formal arguments
    lines.CountingProcessSamplePath: no visible binding for global variable
     st
    mkAR: no visible binding for global variable lN.1
    qqDuration: no visible binding for global variable yi
    qqDuration: no visible binding for global variable si
    thinProcess: no visible binding for global variable targetFct
    thinProcess: no visible binding for global variable posMax
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-solaris-x86

Version: 0.3-7
Flags: --no-build-vignettes
Check: Rd line widths
Result: NOTE
    Rd file 'brt4df.Rd':
     \examples lines wider than 100 characters:
     n1S.fitA <- gam(event ~ te(rlN.1,rsN.1,bs="cr") + rtN.1,data=n1.cal2sDF,family=binomial(link="logit"))
    
    Rd file 'cockroachALData.Rd':
     \examples lines wider than 100 characters:
     plot(e060817mixN1PSTH$mids-0.02,e060817mixN1PSTH$ciUp,type="n",ylim=c(0,max(e060817mixN1PSTH$ciUp)),xlim=c(5,14),xlab="Time (s)",ylab=" ... [TRUNCATED]
     polygon(c(e060817mixN1PSTH$mids-0.02,rev(e060817mixN1PSTH$mids-0.02)),c(e060817mixN1PSTH$ciLow,rev(e060817mixN1PSTH$ciUp)),col=rgb(1,0, ... [TRUNCATED]
     polygon(c(e060817citronN1PSTH$mids,rev(e060817citronN1PSTH$mids)),c(e060817citronN1PSTH$ciLow,rev(e060817citronN1PSTH$ciUp)),col=rgb(1, ... [TRUNCATED]
     polygon(c(e060817terpiN1PSTH$mids-0.04,rev(e060817terpiN1PSTH$mids-0.04)),c(e060817terpiN1PSTH$ciLow,rev(e060817terpiN1PSTH$ciUp)),col= ... [TRUNCATED]
     plot(e060817mixN2PSTH$mids-0.02,e060817mixN2PSTH$ciUp,type="n",ylim=c(0,max(e060817mixN2PSTH$ciUp)),xlim=c(5,14),xlab="Time (s)",ylab=" ... [TRUNCATED]
     polygon(c(e060817mixN2PSTH$mids-0.02,rev(e060817mixN2PSTH$mids-0.02)),c(e060817mixN2PSTH$ciLow,rev(e060817mixN2PSTH$ciUp)),col=rgb(1,0, ... [TRUNCATED]
     polygon(c(e060817citronN2PSTH$mids,rev(e060817citronN2PSTH$mids)),c(e060817citronN2PSTH$ciLow,rev(e060817citronN2PSTH$ciUp)),col=rgb(1, ... [TRUNCATED]
     polygon(c(e060817terpiN2PSTH$mids-0.04,rev(e060817terpiN2PSTH$mids-0.04)),c(e060817terpiN2PSTH$ciLow,rev(e060817terpiN2PSTH$ciUp)),col= ... [TRUNCATED]
     plot(e060817mixN3PSTH$mids-0.02,e060817mixN3PSTH$ciUp,type="n",ylim=c(0,max(e060817mixN3PSTH$ciUp)),xlim=c(5,14),xlab="Time (s)",ylab=" ... [TRUNCATED]
     polygon(c(e060817mixN3PSTH$mids-0.02,rev(e060817mixN3PSTH$mids-0.02)),c(e060817mixN3PSTH$ciLow,rev(e060817mixN3PSTH$ciUp)),col=rgb(1,0, ... [TRUNCATED]
     polygon(c(e060817citronN3PSTH$mids,rev(e060817citronN3PSTH$mids)),c(e060817citronN3PSTH$ciLow,rev(e060817citronN3PSTH$ciUp)),col=rgb(1, ... [TRUNCATED]
     polygon(c(e060817terpiN3PSTH$mids-0.04,rev(e060817terpiN3PSTH$mids-0.04)),c(e060817terpiN3PSTH$ciLow,rev(e060817terpiN3PSTH$ciUp)),col= ... [TRUNCATED]
    
    Rd file 'crossGeneral.Rd':
     \examples lines wider than 100 characters:
     res <- crossGeneral(tMax=1,h=1/n,cFct=cFT1p1,bFct=bFT1p1.ii,withBounds=TRUE,Lplus=TRUE)
     res <- crossGeneral(tMax=1,h=1/n,cFct=cFT1p3,bFct=function(t) 3-2*t,withBounds=TRUE,Lplus=TRUE)
     res <- crossGeneral(tMax=1,h=1/n,cFct=cFT1p3,bFct=function(t) 3-2*t,withBounds=TRUE,Lplus=TRUE)
     res <- crossGeneral(tMax=1,h=1/n,cFct=function(t) 1+sin(t),bFct=function(t) cos(t),withBounds=TRUE,Lplus=TRUE)
     res <- crossGeneral(tMax=1,h=1/n,cFct=function(t) 1+sin(t),bFct=function(t) rep(0.5,length(t)),withBounds=TRUE,Lplus=T ... [TRUNCATED]
    
    Rd file 'df4counts.Rd':
     \examples lines wider than 100 characters:
     psth(CAL1V[["neuron 1"]],stimTimeCourse=c(4.49,4.99),breaks=c(bw=0.5,step=0.05),colCI=2,xlim=c(0,10))
    
    Rd file 'frt.Rd':
     \examples lines wider than 100 characters:
     n1S.fitA <- gam(event ~ te(rlN.1,rsN.1,bs="cr",fx=TRUE) + rtN.1,data=n1.cal2sDF,family=binomial(link="logit"))
    
    Rd file 'isi.Rd':
     \examples lines wider than 100 characters:
     e060517spontDFn1lGF <- gssanova(event ~ lN.1*isi1+isi2, data=e060517spontDFn1l, family="binomial", seed=20061001)
    
    Rd file 'mkGLMdf.Rd':
     \examples lines wider than 100 characters:
     interData.lt1v2 <- lockedTrain(interData[["post2"]],interData[["post1"]],laglim=c(-0.03,0.05),c(0,60))
     dfN2.fit0 <- gam(event ~ s(lN.1,bs="cr") + s(lN.2,bs="cr"), data=dfN2, family=poisson, subset=(dfN2$lN.1 <=0.1))
     plot(xx,exp(-cumsum(exp(predict(dfN2.fit0,data.frame(lN.1=rep(100,300)*0.001,lN.2=(1:300)*0.001))))),type="l")
     dfN2.fit1 <- gam(event ~ s(lN.1,bs="cr") + s(lN.2,bs="cr") + s(lN.3,bs="cr"), data=dfN2, family=poisson, subset=(dfN2$lN.1 <=0.1) & (df ... [TRUNCATED]
     dfN3.fit0 <- gam(event ~ s(lN.1,k=20,bs="cr") + s(lN.3,k=15,bs="cr"),data=dfN3,family=poisson, subset=(dfN3$lN.1 <=0.1))
     dfN4.fit0 <- gam(event ~ s(lN.1,k=20,bs="cr") + s(lN.4,k=15,bs="cr"),data=dfN4,family=poisson, subset=(dfN4$lN.1 <=0.1))
    
    Rd file 'plot.frt.Rd':
     \examples lines wider than 100 characters:
     n1S.fitA <- gam(event ~ te(rlN.1,rsN.1,bs="cr",fx=TRUE) + rtN.1,data=n1.cal2sDF,family=binomial(link="logit"))
    
    Rd file 'plot.transformedTrain.Rd':
     \examples lines wider than 100 characters:
     n1S.fitA <- gam(event ~ te(rlN.1,rsN.1,bs="cr",fx=TRUE) + rtN.1,data=n1.cal2sDF,family=binomial(link="logit"))
    
    Rd file 'predictLogProb.Rd':
     \examples lines wider than 100 characters:
     reportHTML(e060824spont[["neuron 1"]],filename="e060824spont_1",otherST=e060824spont[c(2)],maxiter=100)
     system.time(GF1 <- gssanova(event ~ e1t+i1t, data=subset(DFA,time<=29),family="binomial",seed=20061001))
     system.time(GF2 <- gssanova(event ~ e1t+i1t, data=subset(DFA,time>29),family="binomial",seed=20061001))
     system.time(GF3 <- gssanova(event ~ e1t*i1t, data=subset(DFA,time<=29),family="binomial",seed=20061001))
     system.time(GF4 <- gssanova(event ~ e1t*i1t, data=subset(DFA,time>29),family="binomial",seed=20061001))
    
    Rd file 'reportHTML.spikeTrain.Rd':
     \examples lines wider than 100 characters:
     reportHTML(e070528spont[["neuron 1"]],"e070528spontN1",otherST=e070528spont[-1],laglim=c(-1,1)*0.25,forceTT=FALSE)
    
    Rd file 'summary.transformedTrain.Rd':
     \examples lines wider than 100 characters:
     n1S.fitA <- gam(event ~ te(rlN.1,rsN.1,bs="cr",fx=TRUE) + rtN.1,data=n1.cal2sDF,family=binomial(link="logit"))
    
    Rd file 'thinProcess.Rd':
     \examples lines wider than 100 characters:
     reportHTML(e060824spont[["neuron 1"]],filename="e060824spont_1",otherST=e060824spont[c(2)],maxiter=100)
     (GF2.e060824spont.1.logProb <- predictLogProb(GF2.e060824spont.1[[1]][[1]],subset(DFA,time>29.5))+predictLogProb(GF2.e060824spont.1[[2] ... [TRUNCATED]
     (GF1.e060824spont.1.logProb <- predictLogProb(GF1.e060824spont.1[[1]][[1]],subset(DFA,time>29.5))+predictLogProb(GF1.e060824spont.1[[2] ... [TRUNCATED]
     PSAFct <- mkPostSimAnalysis(e060824spont[[1]],1,29.5,list(GF1.e060824spont.1[[1]][[1]],GF2.e060824spont.1[[1]][[1]]),mkDF.e060824spont. ... [TRUNCATED]
     plot(sim1.e060824spont.1.lpp1,sim1.e060824spont.1.lpp2,main="log prob with M2 vs log prob with M1 when M1 is true",xlab="log prob with ... [TRUNCATED]
     segments(e060824spont.1.lpp1,0,e060824spont.1.lpp1,sum(sim1.e060824spont.1.lpp1 <= e060824spont.1.lpp1)/nbRep,col=2,lwd=2)
     segments(-1600,sum(sim1.e060824spont.1.lpp1 <= e060824spont.1.lpp1)/nbRep,e060824spont.1.lpp1,sum(sim1.e060824spont.1.lpp1 <= e060824sp ... [TRUNCATED]
     segments(e060824spont.1.lpp2,0,e060824spont.1.lpp2,sum(sim1.e060824spont.1.lpp2 <= e060824spont.1.lpp2)/nbRep,col=2,lwd=2)
     segments(-1800,sum(sim1.e060824spont.1.lpp2 <= e060824spont.1.lpp2)/nbRep,e060824spont.1.lpp2,sum(sim1.e060824spont.1.lpp2 <= e060824sp ... [TRUNCATED]
     plot(ecdf(sim1.e060824spont.1.lpp1-sim1.e060824spont.1.lpp2),pch=".",main="log prob with M1 - log prob with M2 when M1 is true")
     segments(e060824spont.1.lppDiff,0,e060824spont.1.lppDiff,sum(sim1.e060824spont.1.lpp1-sim1.e060824spont.1.lpp2<=e060824spont.1.lppDiff) ... [TRUNCATED]
     segments(-10,sum(sim1.e060824spont.1.lpp1-sim1.e060824spont.1.lpp2<=e060824spont.1.lppDiff)/nbRep,e060824spont.1.lppDiff,sum(sim1.e0608 ... [TRUNCATED]
     plot(sim2.e060824spont.1.lpp1,sim2.e060824spont.1.lpp2,main="log prob with M2 vs log prob with M1 when M2 is true",xlab="log prob with ... [TRUNCATED]
     segments(e060824spont.1.lpp1,0,e060824spont.1.lpp1,sum(sim2.e060824spont.1.lpp1 <= e060824spont.1.lpp1)/nbRep,col=2,lwd=2)
     segments(-2000,sum(sim2.e060824spont.1.lpp1 <= e060824spont.1.lpp1)/nbRep,e060824spont.1.lpp1,sum(sim2.e060824spont.1.lpp1 <= e060824sp ... [TRUNCATED]
     segments(e060824spont.1.lpp2,0,e060824spont.1.lpp2,sum(sim2.e060824spont.1.lpp2 <= e060824spont.1.lpp2)/nbRep,col=2,lwd=2)
     segments(-2000,sum(sim2.e060824spont.1.lpp2 <= e060824spont.1.lpp2)/nbRep,e060824spont.1.lpp2,sum(sim2.e060824spont.1.lpp2 <= e060824sp ... [TRUNCATED]
     xlim=c(min(c(-e060824spont.1.lppDiff,sim2.e060824spont.1.lpp2-sim2.e060824spont.1.lpp1)),max(sim2.e060824spont.1.lpp2-sim2.e060824spont ... [TRUNCATED]
     plot(ecdf(sim2.e060824spont.1.lpp2-sim2.e060824spont.1.lpp1),pch=".",main="log prob with M2 - log prob with M1 when M2 is true",xlim=xl ... [TRUNCATED]
    
    Rd file 'transformedTrain.Rd':
     \examples lines wider than 100 characters:
     n1S.fitA <- gam(event ~ te(rlN.1,rsN.1,bs="cr",fx=TRUE) + rtN.1,data=n1.cal2sDF,family=binomial(link="logit"))
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.3-7
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    as.spikeTrain: no visible global function definition for 'spikeTimes'
    gamObj.gampsth: no visible binding for global variable 'PoissonF'
    gammaMLE: multiple local function definitions for 'rFct' with different
     formal arguments
    gssObj.gsspsth: no visible binding for global variable 'gfit'
    gssObj.gsspsth0: no visible binding for global variable 'gfit'
    invgaussMLE: multiple local function definitions for 'rFct' with
     different formal arguments
    lines.CountingProcessSamplePath: no visible binding for global variable
     'st'
    mkAR: no visible binding for global variable 'lN.1'
    qqDuration: no visible binding for global variable 'yi'
    qqDuration: no visible binding for global variable 'si'
    thinProcess: no visible binding for global variable 'targetFct'
    thinProcess: no visible binding for global variable 'posMax'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.3-7
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to codetools which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     codetools gss
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter Creating R
    packages of the Writing R Extensions manual.
Flavor: r-release-osx-x86_64-mavericks

Version: 0.3-7
Check: R code for possible problems
Result: NOTE
    as.spikeTrain: no visible global function definition for spikeTimes
    gamObj.gampsth: no visible binding for global variable PoissonF
    gammaMLE: multiple local function definitions for rFct with different
     formal arguments
    gssObj.gsspsth: no visible binding for global variable gfit
    gssObj.gsspsth0: no visible binding for global variable gfit
    invgaussMLE: multiple local function definitions for rFct with
     different formal arguments
    lines.CountingProcessSamplePath: no visible binding for global variable
     st
    mkAR: no visible binding for global variable lN.1
    qqDuration: no visible binding for global variable yi
    qqDuration: no visible binding for global variable si
    thinProcess: no visible binding for global variable targetFct
    thinProcess: no visible binding for global variable posMax
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 0.3-7
Check: dependencies in R code
Result: NOTE
     library or require call to codetools which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     codetools gss
     These packages need to be imported from for the case when
     this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter Creating R
    packages of the Writing R Extensions manual.
Flavor: r-release-osx-x86_64-snowleopard