Check results for 'STAR'

using R version 4.1.2 Patched (2021-11-25 r81257)
using platform: x86_64-pc-linux-gnu (64-bit)
using session charset: UTF-8
checking for file ‘STAR/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘STAR’ version ‘0.3-7’
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking serialization versions ... OK
checking whether package ‘STAR’ can be installed ... OK
checking package directory ... OK
checking for future file timestamps ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over 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 whether the package can be unloaded cleanly ... OK
checking whether the namespace can be loaded with stated dependencies ... OK
checking whether the namespace can be unloaded cleanly ... OK
checking loading without being on the library search path ... OK
checking use of S3 registration ... OK
checking dependencies in R code ... 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.
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [35s/41s] 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’
gsslockedTrain: no visible global function definition for ‘gssanova’
gsslockedTrain0: no visible global function definition for ‘gssanova0’
gsspsth: no visible global function definition for ‘gssanova’
gsspsth0: no visible global function definition for ‘gssanova0’
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’
mkM2U: no visible global function definition for ‘ssden’
mkM2U : <anonymous>: no visible global function definition for ‘dssden’
mkM2U : dFct: no visible global function definition for ‘dssden’
mkPostSimAnalysis: no visible global function definition for
  ‘findGlobals’
plot.ssanova: no visible global function definition for ‘X11’
plot.ssanova0: no visible global function definition for ‘X11’
qqDuration: no visible binding for global variable ‘yi’
qqDuration: no visible binding for global variable ‘si’
reportHTML.gam: no visible global function definition for ‘png’
reportHTML.gam: no visible global function definition for ‘dev.off’
reportHTML.repeatedTrain: no visible global function definition for
  ‘png’
reportHTML.repeatedTrain: no visible global function definition for
  ‘dev.off’
reportHTML.spikeTrain: no visible global function definition for ‘png’
reportHTML.spikeTrain: no visible global function definition for
  ‘dev.off’
reportHTML.spikeTrain : <anonymous>: no visible global function
  definition for ‘png’
reportHTML.spikeTrain : <anonymous>: no visible global function
  definition for ‘dev.off’
thinProcess: no visible binding for global variable ‘targetFct’
thinProcess: no visible binding for global variable ‘posMax’
Undefined global functions or variables:
  PoissonF X11 dev.off dssden findGlobals gfit gssanova gssanova0 lN.1
  png posMax si spikeTimes ssden st targetFct yi
Consider adding
  importFrom("grDevices", "X11", "dev.off", "png")
to your NAMESPACE file.
checking Rd files ... [3s/3s] OK
checking Rd metadata ... OK
checking Rd line widths ... 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.
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... OK
checking data for ASCII and uncompressed saves ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking pragmas in C/C++ headers and code ... OK
checking compilation flags used ... OK
checking compiled code ... OK
checking sizes of PDF files under ‘inst/doc’ ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [9s/10s] OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking re-building of vignette outputs ... [206s/231s] OK
checking PDF version of manual ... OK
checking for non-standard things in the check directory ... OK
DONE

Status: 3 NOTEs