- using R version 4.0.3 Patched (2021-01-18 r79846)
- 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 ... [29s/34s] 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 ... 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 ... [208s/229s] OK
- checking PDF version of manual ... OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 3 NOTEs