R Development Page

ctds log file (check_x86_64_linux)

Thu Aug 18 14:09:01 2016: Checking package ctds (SVN revision 9) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/ctds.Rcheck’
* using R version 3.3.1 Patched (2016-08-17 r71112)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘ctds/DESCRIPTION’ ... OK
* this is package ‘ctds’ version ‘0.5.3.1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Ephraim M. Hanks ’

New submission

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘raster’ ‘crawl’ ‘fda’ ‘Matrix’ ‘glmnet’ ‘statmod’ ‘sde’ ‘mvtnorm’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package ‘ctds’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    ‘Ephraim M. Hanks’
  Authors@R: ‘Ephraim Hanks [aut, cre]’

Maintainer field differs from that derived from Authors@R
  Maintainer: ‘Ephraim M. Hanks ’
  Authors@R:  ‘Ephraim Hanks ’

* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... WARNING
Empty file ‘INDEX’.
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
* 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
Package in Depends field not imported from: ‘mvtnorm’
  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 ... WARNING
plot:
  function(x, ...)
plot.ani.interact:
  function(sim.obj.list, rast, times, output, save.folder, pdfname,
           col.list, ...)

plot:
  function(x, ...)
plot.betas:
  function(mi.out, spline.list, times.betas, col.list, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  plot.ani.interact plot.betas
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FindCenters: no visible global function definition for ‘dist’
ctds.bayes.lasso: no visible global function definition for ‘rgamma’
ctds.bayes.lasso: no visible global function definition for ‘rmvnorm’
ctds.bayes.lasso: no visible global function definition for ‘dmvnorm’
ctds.bayes.lasso: no visible global function definition for ‘runif’
ctds.bayes.lasso: no visible binding for global variable ‘sd’
ctds.bayes.mh: no visible global function definition for ‘rmvnorm’
ctds.bayes.mh: no visible global function definition for ‘rnorm’
ctds.bayes.mh: no visible global function definition for ‘dmvnorm’
ctds.bayes.mh: no visible global function definition for ‘runif’
ctds.bayes.mh: no visible binding for global variable ‘sd’
ctds.bayes.mh: no visible global function definition for ‘sd’
ctds.glm.MI: no visible binding for global variable ‘sd’
ctds.glm.MI: no visible global function definition for ‘glm’
ctds.glm.MI: no visible binding for global variable ‘var’
make.Phi.mat: no visible global function definition for ‘approx’
make.Phi.mat: no visible global function definition for ‘ctds.bbsim’
plot.ani.interact: no visible global function definition for ‘pdf’
plot.ani.interact: no visible global function definition for ‘points’
plot.ani.interact: no visible global function definition for ‘dev.off’
plot.ani.interact: no visible global function definition for ‘jpeg’
plot.betas: no visible global function definition for ‘dev.new’
plot.betas: no visible global function definition for ‘points’
Undefined global functions or variables:
  approx ctds.bbsim dev.new dev.off dist dmvnorm glm jpeg pdf points
  rgamma rmvnorm rnorm runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "jpeg", "pdf")
  importFrom("graphics", "points")
  importFrom("stats", "approx", "dist", "glm", "rgamma", "rnorm",
             "runif", "sd", "var")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: FindCenters.Rd:73-75: Dropping empty section \note
prepare_Rd: FindCenters.Rd:67-69: Dropping empty section \references
prepare_Rd: FindCenters.Rd:79-81: Dropping empty section \seealso
prepare_Rd: ctds.MI.prep.Rd:52-54: Dropping empty section \details
prepare_Rd: ctds.MI.prep.Rd:55-61: Dropping empty section \value
prepare_Rd: ctds.MI.prep.Rd:68-70: Dropping empty section \note
prepare_Rd: ctds.MI.prep.Rd:62-64: Dropping empty section \references
prepare_Rd: ctds.MI.prep.Rd:74-76: Dropping empty section \seealso
prepare_Rd: ctds.MI.prep.Rd:77-79: Dropping empty section \examples
prepare_Rd: ctds.bayes.lasso.Rd:7-9: Dropping empty section \description
prepare_Rd: ctds.bayes.lasso.Rd:70-72: Dropping empty section \details
prepare_Rd: ctds.bayes.lasso.Rd:73-79: Dropping empty section \value
prepare_Rd: ctds.bayes.lasso.Rd:86-88: Dropping empty section \note
prepare_Rd: ctds.bayes.lasso.Rd:83-85: Dropping empty section \author
prepare_Rd: ctds.bayes.lasso.Rd:80-82: Dropping empty section \references
prepare_Rd: ctds.bayes.lasso.Rd:92-94: Dropping empty section \seealso
checkRd: (5) ctds.bayes.lasso.Rd:0-180: Must have a \description
prepare_Rd: ctds.bayes.mh.Rd:8-10: Dropping empty section \description
prepare_Rd: ctds.bayes.mh.Rd:59-61: Dropping empty section \details
prepare_Rd: ctds.bayes.mh.Rd:62-68: Dropping empty section \value
prepare_Rd: ctds.bayes.mh.Rd:75-77: Dropping empty section \note
prepare_Rd: ctds.bayes.mh.Rd:72-74: Dropping empty section \author
prepare_Rd: ctds.bayes.mh.Rd:69-71: Dropping empty section \references
prepare_Rd: ctds.bayes.mh.Rd:81-83: Dropping empty section \seealso
checkRd: (5) ctds.bayes.mh.Rd:0-146: Must have a \description
prepare_Rd: ctds.glm.MI.Rd:40-42: Dropping empty section \details
prepare_Rd: ctds.glm.MI.Rd:43-49: Dropping empty section \value
prepare_Rd: ctds.glm.MI.Rd:56-58: Dropping empty section \note
prepare_Rd: ctds.glm.MI.Rd:53-55: Dropping empty section \author
prepare_Rd: ctds.glm.MI.Rd:50-52: Dropping empty section \references
prepare_Rd: ctds.glm.MI.Rd:62-64: Dropping empty section \seealso
prepare_Rd: eval.spline.list.Rd:22-24: Dropping empty section \details
prepare_Rd: eval.spline.list.Rd:25-31: Dropping empty section \value
prepare_Rd: eval.spline.list.Rd:38-40: Dropping empty section \note
prepare_Rd: eval.spline.list.Rd:35-37: Dropping empty section \author
prepare_Rd: eval.spline.list.Rd:32-34: Dropping empty section \references
prepare_Rd: eval.spline.list.Rd:44-46: Dropping empty section \seealso
prepare_Rd: get.betas.Rd:26-28: Dropping empty section \details
prepare_Rd: get.betas.Rd:40-42: Dropping empty section \note
prepare_Rd: get.betas.Rd:34-36: Dropping empty section \references
prepare_Rd: get.betas.Rd:46-48: Dropping empty section \seealso
prepare_Rd: get.betas.Rd:49-64: Dropping empty section \examples
prepare_Rd: get.betas.sd.Rd:26-28: Dropping empty section \details
prepare_Rd: get.betas.sd.Rd:40-42: Dropping empty section \note
prepare_Rd: get.betas.sd.Rd:34-36: Dropping empty section \references
prepare_Rd: get.betas.sd.Rd:46-48: Dropping empty section \seealso
prepare_Rd: get.betas.sd.Rd:49-64: Dropping empty section \examples
prepare_Rd: get.crawl.path.Rd:8-10: Dropping empty section \description
prepare_Rd: get.crawl.path.Rd:32-34: Dropping empty section \details
prepare_Rd: get.crawl.path.Rd:35-41: Dropping empty section \value
prepare_Rd: get.crawl.path.Rd:48-50: Dropping empty section \note
prepare_Rd: get.crawl.path.Rd:45-47: Dropping empty section \author
prepare_Rd: get.crawl.path.Rd:42-44: Dropping empty section \references
prepare_Rd: get.crawl.path.Rd:54-56: Dropping empty section \seealso
checkRd: (5) get.crawl.path.Rd:0-91: Must have a \description
prepare_Rd: lion.pair.Rd:316-318: Dropping empty section \format
prepare_Rd: lion.pair.Rd:319-321: Dropping empty section \details
prepare_Rd: lion.pair.Rd:322-324: Dropping empty section \source
prepare_Rd: lion.pair.Rd:325-327: Dropping empty section \references
prepare_Rd: make.Phi.mat.Rd:52-54: Dropping empty section \details
prepare_Rd: make.Phi.mat.Rd:55-61: Dropping empty section \value
prepare_Rd: make.Phi.mat.Rd:68-70: Dropping empty section \note
prepare_Rd: make.Phi.mat.Rd:65-67: Dropping empty section \author
prepare_Rd: make.Phi.mat.Rd:62-64: Dropping empty section \references
prepare_Rd: make.Phi.mat.Rd:74-76: Dropping empty section \seealso
prepare_Rd: make.fourier.list.Rd:8-10: Dropping empty section \description
prepare_Rd: make.fourier.list.Rd:32-34: Dropping empty section \details
prepare_Rd: make.fourier.list.Rd:35-41: Dropping empty section \value
prepare_Rd: make.fourier.list.Rd:48-50: Dropping empty section \note
prepare_Rd: make.fourier.list.Rd:45-47: Dropping empty section \author
prepare_Rd: make.fourier.list.Rd:42-44: Dropping empty section \references
prepare_Rd: make.fourier.list.Rd:54-56: Dropping empty section \seealso
checkRd: (5) make.fourier.list.Rd:0-114: Must have a \description
prepare_Rd: make.spline.list.Rd:31-33: Dropping empty section \details
prepare_Rd: make.spline.list.Rd:44-46: Dropping empty section \note
prepare_Rd: make.spline.list.Rd:41-43: Dropping empty section \author
prepare_Rd: make.spline.list.Rd:38-40: Dropping empty section \references
prepare_Rd: make.spline.list.Rd:50-52: Dropping empty section \seealso
prepare_Rd: plot.ani.interact.Rd:41-43: Dropping empty section \details
prepare_Rd: plot.ani.interact.Rd:44-50: Dropping empty section \value
prepare_Rd: plot.ani.interact.Rd:57-59: Dropping empty section \note
prepare_Rd: plot.ani.interact.Rd:54-56: Dropping empty section \author
prepare_Rd: plot.ani.interact.Rd:51-53: Dropping empty section \references
prepare_Rd: plot.ani.interact.Rd:63-65: Dropping empty section \seealso
prepare_Rd: plot.betas.Rd:8-10: Dropping empty section \description
prepare_Rd: plot.betas.Rd:32-34: Dropping empty section \details
prepare_Rd: plot.betas.Rd:35-41: Dropping empty section \value
prepare_Rd: plot.betas.Rd:48-50: Dropping empty section \note
prepare_Rd: plot.betas.Rd:45-47: Dropping empty section \author
prepare_Rd: plot.betas.Rd:42-44: Dropping empty section \references
prepare_Rd: plot.betas.Rd:54-56: Dropping empty section \seealso
checkRd: (5) plot.betas.Rd:0-87: Must have a \description
prepare_Rd: rast.grad.Rd:19-21: Dropping empty section \details
prepare_Rd: rast.grad.Rd:22-28: Dropping empty section \value
prepare_Rd: rast.grad.Rd:35-37: Dropping empty section \note
prepare_Rd: rast.grad.Rd:32-34: Dropping empty section \author
prepare_Rd: rast.grad.Rd:29-31: Dropping empty section \references
prepare_Rd: rast.grad.Rd:41-43: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'FindCenters.Rd':
  \usage lines wider than 90 characters:
     FindCenters(ani, max.dist = 200, max.time.dist = 6, mintime = min(ani$locs[, 3]), maxtime = max(ani$locs[, 3]),nightonly=FALSE,nightsta ... [TRUNCATED]

Rd file 'ctds.bayes.lasso.Rd':
  \usage lines wider than 90 characters:
     ctds.bayes.lasso(sim.obj, spline.list, stack.static, stack.grad, conspecifics.list = NULL, crw = TRUE, path.aug.interval = 0, spline.pe ... [TRUNCATED]

Rd file 'ctds.bayes.mh.Rd':
  \usage lines wider than 90 characters:
     ctds.bayes.mh(sim.obj, spline.list, stack.static, stack.grad, conspecifics.list = NULL, crw = TRUE, path.aug.interval = 0, spline.perio ... [TRUNCATED]

Rd file 'ctds.glm.MI.Rd':
  \usage lines wider than 90 characters:
     ctds.glm.MI(ctds.obj, nfolds = 10, nlambda = 100, plot.cv = FALSE, method = "Stacked.cv", cv.param = "min", ...)

Rd file 'lion.pair.Rd':
  \examples lines wider than 100 characters:
     ini.list <- list(a1.x=c(lion1$locs[1,1], 0),a1.y=c(lion1$locs[1,2], 0),P1.x=diag(c(1,1)),P1.y=diag(c(1,1)))
     crawl.fit=crwMLE(data=lion1$locs,coord=c("UTM_X","UTM_Y"),Time.name="datetime",drift.model=FALSE,err.model=list(x=~1, y=~1),initial.sta ... [TRUNCATED]
     predObj <- crwPredict(object.crwFit=crawl.fit, pred.times, speedEst=TRUE, flat=FALSE,getUseAvail=TRUE)
     ini.list <- list(a1.x=c(lion2$locs[1,1], 0),a1.y=c(lion2$locs[1,2], 0),P1.x=diag(c(1,1)),P1.y=diag(c(1,1)))
     crawl.fit=crwMLE(data=lion2$locs,coord=c("UTM_X","UTM_Y"),Time.name="datetime",drift.model=FALSE,err.model=list(x=~1, y=~1),initial.sta ... [TRUNCATED]
     predObj <- crwPredict(object.crwFit=crawl.fit, pred.times, speedEst=TRUE, flat=FALSE,getUseAvail=TRUE)
     NotForest=stack.cropped[[1]]+stack.cropped[[2]]+stack.cropped[[3]]+stack.cropped[[4]]+stack.cropped[[6]]
     knot.intervals=list(static=knot.intervals.static,grad=knot.intervals.grad,ani=knot.intervals.ani,crw=knot.intervals.crw)
     ctds.AM80=ctds.MI.prep(AM80$sim.obj,spl.list,NotForest,d2kill,conspecifics.list=list(AF79$sim.obj),num.crawl.paths=10,crw=TRUE,path.aug ... [TRUNCATED]
     ctds.AM80.bayes=ctds.bayes.mh(AM80$sim.obj,spl.list,NotForest,d2kill,conspecifics.list=list(AF79$sim.obj),crw=TRUE,path.aug.interval=t. ... [TRUNCATED]
     beta.names.AM80 <- c("(a)  Static Cover - Not Forest","(b) Dynamic Covariate - Direction to Nearest Potential Kill Site","(c) Dynamic C ... [TRUNCATED]
     knot.intervals=list(static=knot.intervals.static,grad=knot.intervals.grad,ani=knot.intervals.ani,crw=knot.intervals.crw)
     ctds.AM80=ctds.MI.prep(AM80$sim.obj,spl.list,NotForest,d2kill,conspecifics.list=list(AF79$sim.obj),num.crawl.paths=10,crw=TRUE,path.aug ... [TRUNCATED]
     ctds.AM80.bayes.lasso=ctds.bayes.lasso(AM80$sim.obj,spl.list,NotForest,d2kill,conspecifics.list=list(AF79$sim.obj),crw=TRUE,path.aug.in ... [TRUNCATED]
     beta.names.AM80 <- c("(a) Static Cover - Not Forest","(b) Dynamic Covariate - Direction to Nearest Potential Kill Site","(c) Dynamic Co ... [TRUNCATED]
     beta.names.AM80 <- c("(a) Cover - Not Forest","(b) Direction to Nearest PKS","(c) Direction to Conspecific","(d) CRW Autoregressive Par ... [TRUNCATED]
       plot(times.betas*24,betas.lasso[,i],col="black",type="l",lwd=3,main=beta.names.AM80[i],ylim=c(min.val,max.val),xlab="Hour of the Day" ... [TRUNCATED]
           legend("bottomright",legend=c("Lasso Estimate","Bayesian Posterior Mean","Bayesian Posterior CI"),lty=c(2,1,3),lwd=2)

Rd file 'make.Phi.mat.Rd':
  \usage lines wider than 90 characters:
     make.Phi.mat(sim.obj, spline.list, stack.static, stack.grad, other.sim.list = list(), crw = TRUE, normalize.gradients = TRUE, grad.poin ... [TRUNCATED]

Rd file 'make.fourier.list.Rd':
  \examples lines wider than 100 characters:
                         spline.list[[length(spline.list) + 1]] = create.fourier.basis(rangeval = c(mintime, 
                         spline.list[[length(spline.list) + 1]] = create.fourier.basis(rangeval = c(mintime, 
                       spline.list[[length(spline.list) + 1]] = create.constant.basis(rangeval = c(mintime, 

Rd file 'make.spline.list.Rd':
  \examples lines wider than 100 characters:
                       spline.list[[length(spline.list) + 1]] = create.bspline.basis(rangeval = c(mintime, 
                       spline.list[[length(spline.list) + 1]] = create.constant.basis(rangeval = c(mintime, 

Rd file 'plot.ani.interact.Rd':
  \usage lines wider than 90 characters:
     plot.ani.interact(sim.obj.list, rast, times, output = "pdf", save.folder = "./", pdfname = "ani.pdf", col.list = c("red", "blue", "gree ... [TRUNCATED]

Rd file 'plot.betas.Rd':
  \usage lines wider than 90 characters:
     plot.betas(mi.out, spline.list, times.betas, col.list = c("red", "blue", "green", "purple", "black"), ...)

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 ... WARNING
Undocumented arguments in documentation object 'make.spline.list'
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object 'plot.ani.interact':
  ‘plot.ani.interact’

S3 methods shown with full name in documentation object 'plot.betas':
  ‘plot.betas’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 examples ... [16s/18s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
FindCenters 11.784    0.1  13.002
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 NOTEs
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/ctds.Rcheck/00check.log’
for details.


Run time: 152.31 seconds.