CRAN Package Check Results for Package STAR

Last updated on 2014-07-24 16:48:07.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3-7 6.30 69.78 76.08 NOTE --no-vignettes
r-devel-linux-x86_64-debian-gcc 0.3-7 5.85 68.64 74.49 NOTE --no-vignettes
r-devel-linux-x86_64-fedora-clang 0.3-7 533.28 NOTE --no-build-vignettes
r-devel-linux-x86_64-fedora-gcc 0.3-7 522.17 NOTE --no-build-vignettes
r-devel-osx-x86_64-clang 0.3-7 353.24 NOTE --no-build-vignettes
r-devel-windows-ix86+x86_64 0.3-7 18.00 118.00 136.00 NOTE --no-vignettes
r-patched-linux-x86_64 0.3-7 6.93 68.70 75.63 NOTE --no-vignettes
r-patched-solaris-sparc 0.3-7 904.70 NOTE --no-vignettes
r-patched-solaris-x86 0.3-7 1067.80 NOTE --no-build-vignettes
r-release-linux-ix86 0.3-7 7.26 86.01 93.26 NOTE --no-vignettes
r-release-linux-x86_64 0.3-7 5.77 69.88 75.65 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 17.00 119.00 136.00 NOTE --no-vignettes
r-oldrel-windows-ix86+x86_64 0.3-7 18.00 122.00 140.00 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