turnoverFit: no visible binding for global variable 'IntCal13'
turnoverFit: no visible binding for global variable 'Hua2013'
initialize,NlModel : .local: no visible global function definition for
  'TransportDecompositionOperator.new'
Running the tests in 'tests/prediction-test.R' failed.
Last 13 lines of output:
  > stopifnot(predict(nsom, iris[1,1:4])==nsom$clustering[1])
  > stopifnot(identical(predict(nsom), nsom$clustering))
  > 
  > rsom <- trainSOM(dissim.lesmis, type="relational", maxit=10, scaling= "none")
  > stopifnot(identical(predict(rsom, dissim.lesmis), rsom$clustering))
  > stopifnot(predict(rsom, dissim.lesmis[1,])==rsom$clustering[1])
  > stopifnot(identical(predict(rsom), rsom$clustering))
  > 
  > rsom <- trainSOM(dissim.lesmis, type="relational", maxit=10, 
  +                  radius.type="letremy")
  > stopifnot(identical(predict(rsom, dissim.lesmis), rsom$clustering))
  Error: identical(predict(rsom, dissim.lesmis), rsom$clustering) is not TRUE
  Execution halted
plot3d: no visible global function definition for 'persp3d'
SOS: no visible global function definition for 'getCurlHandle'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sourceR.Rcheck/00install.out' for details.
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
glasso.miss: no visible global function definition for 'glasso'
glasso.miss: no visible global function definition for 'Solve'
space.miss: no visible global function definition for 'Solve'
SJ: no visible binding for global variable 'bs'
SJ: no visible global function definition for 'get.adjacency'
SJ : <anonymous>: no visible global function definition for
  'graph.adjacency'
SJ: no visible binding for global variable 'ecount'
SJ.dag: no visible binding for global variable 'bs'
SJ.dag : <anonymous>: no visible global function definition for
  'graph.adjacency'
SJ.dag: no visible binding for global variable 'ecount'
SJpath: no visible global function definition for 'get.adjacency'
SJpath : <anonymous>: no visible global function definition for
  'graph.adjacency'
generate.dag.data: no visible global function definition for 'vcount'
generate.dag.data: no visible global function definition for
  'topological.sort'
generate.dag.data: no visible global function definition for
  'neighbors'
grpsel: no visible global function definition for 'Matrix'
moralize: no visible global function definition for 'vcount'
moralize: no visible global function definition for 'as.undirected'
moralize: no visible global function definition for 'get.adjacency'
moralize: no visible global function definition for 'add.edges'
moralize: no visible global function definition for 'simplify'
plot.SJ: no visible global function definition for
  'layout.fruchterman.reingold'
plot.SJ.dag: no visible global function definition for
  'layout.fruchterman.reingold'
print.SJ: no visible binding for global variable 'ecount'
print.SJ: no visible global function definition for 'ecount'
print.SJ.dag: no visible binding for global variable 'ecount'
print.SJ.dag: no visible global function definition for 'ecount'
rdag: no visible global function definition for 'graph.adjacency'
cophen: no visible global function definition for 'Ntip'
get.descendants.of.node: no visible global function definition for
  'Ntip'
phy.deresolve: no visible global function definition for
  'branching.times'
phy.deresolve: no visible global function definition for 'Ntip'
phy.dotplot: no visible global function definition for 'tiplabels'
phy.nodetimes: no visible global function definition for 'Ntip'
phy.nodetimes: no visible global function definition for
  'branching.times'
reorderspacodiobj: no visible global function definition for 'drop.tip'
resamp.phy: no visible global function definition for 'Ntip'
resamp.phy: no visible global function definition for 'branching.times'
spacodi.all.nodes: no visible global function definition for 'subtrees'
spacodi.all.nodes: no visible global function definition for
  'branching.times'
spacodi.exp.nodes: no visible global function definition for 'subtrees'
spacodi.treeplot: no visible global function definition for
  'diverge_hcl'
spacodi.treeplot: no visible global function definition for
  'nodelabels'
Namespace in Imports field not imported from: 'rstudioapi'
  All declared Imports should be used.
livy_statement_parse_response : scalaTypeOfArray: possible error in
  regexec("^\\[L(.*);", scalaType, perl = TRUE): unused argument (perl
  = TRUE)
SPARQL: no visible binding for global variable 'getURL'
SPARQL: no visible binding for global variable 'xmlParse'
SPARQL: no visible global function definition for 'getNodeSet'
SPARQL: no visible global function definition for 'xpathApply'
SPARQL: no visible binding for global variable 'postForm'
get_attr: no visible global function definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'xmlDoc'
get_value: no visible global function definition for 'xmlDoc'
get_value: no visible global function definition for 'xpathSApply'
get_value: no visible binding for global variable 'xmlValue'
get_value: no visible global function definition for 'xpathApply'
get_value: no visible binding for global variable 'xmlGetAttr'
getcoef_list: no visible global function definition for 'drop0'
sparsepredict: no visible global function definition for
  'lambda.interp'
sparsepredict: no visible global function definition for 'nonzeroCoef'
bbox_to_SpatialPolygons: no visible global function definition for
  'CRS'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygon'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygons'
bbox_to_SpatialPolygons: no visible global function definition for
  'SpatialPolygons'
list.raster.files: no visible global function definition for 'CRS'
list.raster.files: no visible global function definition for
  'spTransform'
list.raster.files: no visible global function definition for
  'SpatialPolygonsDataFrame'
list.raster.files: no visible global function definition for 'spChFIDs'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'spTransform'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'CRS'
spatial_sync_raster: no visible global function definition for 'bbox'
spatial_sync_vector: no visible global function definition for
  'spTransform'
spatial_sync_vector: no visible global function definition for 'CRS'
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    data   3.4Mb
    doc    5.0Mb
    help   4.8Mb
    libs   1.2Mb
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
err.default: no visible global function definition for 'prediction'
err.default: no visible global function definition for 'performance'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sphereplot.Rcheck/00install.out' for details.
monophyly: no visible global function definition for 'prop.part'
monophylyBoot: no visible global function definition for 'nj'
monophylyBoot: no visible global function definition for 'boot.phylo'
monophylyBoot : <anonymous>: no visible global function definition for
  'root'
monophylyBoot : <anonymous>: no visible global function definition for
  'nj'
monophylyBoot: no visible global function definition for 'prop.part'
polyBalance: no visible global function definition for 'node.depth'
read.BOLD: no visible global function definition for 'as.DNAbin'
read.GB: no visible global function definition for 'as.DNAbin'
slideAnalyses: no visible global function definition for 'nj'
slideAnalyses: no visible global function definition for 'node.depth'
slideAnalyses: no visible binding for global variable 'nj'
tree.comp: no visible global function definition for 'unroot'
tree.comp: no visible global function definition for 'prop.part'
tree.comp: no visible global function definition for 'node.depth'
cv.spikeslab: no visible global function definition for 'mclapply'
gnet.get: no visible global function definition for 'lars'
gnet.get: no visible global function definition for 'predict.lars'
plot.spikeslab: no visible global function definition for 'plot.lars'
sparsePC.spikeslab : get.pc : <anonymous>: no visible global function
  definition for 'randomForest'
sparsePC.spikeslab: no visible global function definition for
  'randomForest'
spikeslab: no visible global function definition for 'randomForest'
SPIn: no visible global function definition for 'solve.QP'
Ell.Theta: no visible global function definition for 'ell.theta'
Namespace in Imports field not imported from: 'geoR'
  All declared Imports should be used.
Errors in running code in vignettes:
when running code in 'SQUAREM.Rnw'
  ...
+     Ap <- pvec * tA
+     pnew <- colMeans(t(Ap)/colSums(Ap))
+     pnew * (pnew > 0)
+ }

> library(interval)

  When sourcing 'SQUAREM.R':
Error: there is no package called 'interval'
Execution halted
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

See section 'Good practice' in '?.onAttach'.
fit.model: no visible global function definition for 'hadamard'
station: no visible binding for global variable 'WTdiff'
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
File 'StanHeaders/libs/i386/StanHeaders.dll':
  Found 'printf', possibly from 'printf' (C)
    Objects: 'cvodes/src/sundials/sundials_direct.o',
      'cvodes/src/nvec_ser/nvector_serial.o'
  Found 'putchar', possibly from 'putchar' (C)
    Objects: 'cvodes/src/sundials/sundials_direct.o',
      'cvodes/src/nvec_ser/nvector_serial.o'
File 'StanHeaders/libs/x64/StanHeaders.dll':
  Found 'printf', possibly from 'printf' (C)
    Objects: 'cvodes/src/sundials/sundials_direct.o',
      'cvodes/src/nvec_ser/nvector_serial.o'
  Found 'putchar', possibly from 'putchar' (C)
    Objects: 'cvodes/src/sundials/sundials_direct.o',
      'cvodes/src/nvec_ser/nvector_serial.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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'
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'
rg.robmva: no visible global function definition for 'cov.mve'
Namespaces in Imports field not imported from:
  'magrittr' 'rpart'
  All declared Imports should be used.
getHb: no visible binding for global variable 'masshb'
getHbgrid: no visible binding for global variable 'masshbgrid'
showComposition: no visible binding for global variable 'compositions'
testComposition: no visible binding for global variable 'compositions'
File 'stepPlr/libs/i386/stepPlr.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'cg_descent.o'
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Object: 'cg_descent.o'
File 'stepPlr/libs/x64/stepPlr.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'cg_descent.o'
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Object: 'cg_descent.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/StereoMorph.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'SnowballC' 'tm'
  All declared Imports should be used.
DetailOpLines: no visible global function definition for
  'tkProgressBar'
DetailOpLines: no visible global function definition for
  'setTkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'tkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'setTkProgressBar'
SimHistory: no visible global function definition for 'tkProgressBar'
SimHistory: no visible global function definition for
  'setTkProgressBar'
.rp.stan3d: no visible global function definition for 'rp.control'
.rp.stan3d: no visible global function definition for 'rp.slider'
.rp.stan3d: no visible global function definition for 'rp.button'
.rp.stan3d : <anonymous>: no visible global function definition for
  'par3d'
.rp.stan3d : <anonymous>: no visible global function definition for
  'rotationMatrix'
.rp.stan3d: no visible global function definition for 'rp.do'
.rp.stan3d: no visible global function definition for 'rp.block'
.setBG: no visible global function definition for 'surface3d'
.setPlot: no visible global function definition for 'plot3d'
.setPlot: no visible global function definition for 'axis3d'
.setPlot: no visible global function definition for 'par3d'
.setPlot: no visible global function definition for 'aspect3d'
.setPlot: no visible global function definition for 'rotationMatrix'
.stan3d.redraw: no visible global function definition for 'par3d'
.stan3d.redraw: no visible global function definition for 'rgl.pop'
.stan3d.redraw: no visible binding for global variable 'spheres3d'
rlgcp: no visible global function definition for 'bbox'
stan: no visible global function definition for 'lines3d'
stan: no visible global function definition for 'segments3d'
stan: no visible global function definition for 'points3d'
bin.info.cubature : compute.fun: no visible global function definition
  for 'adaptIntegrate'
tess.info : new.points: no visible global function definition for
  'as.points'
tess.info : new.points: no visible global function definition for 'csr'
tess.info.MISER : int.fun: no visible global function definition for
  'as.points'
tess.info.MISER : int.fun: no visible global function definition for
  'inpip'
tessdev: no visible global function definition for 'deldir'
tessdev: no visible global function definition for 'tile.list'
tessdev : sum.l: no visible global function definition for 'as.points'
tessdev : sum.l: no visible global function definition for 'inpip'
tessdev.info : all: no visible global function definition for
  'as.points'
tessdev.info : all: no visible global function definition for 'inpip'
tessresid: no visible global function definition for 'deldir'
tessresid: no visible global function definition for 'tile.list'
tessresid : num: no visible global function definition for 'as.points'
tessresid : num: no visible global function definition for 'inpip'
Namespace in Imports field not imported from: 'sna'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'broom' 'car' 'lmerTest' 'pbkrtest'
  All declared Imports should be used.
breakpoints.formula: no visible global function definition for
  '%dopar%'
breakpoints.formula: no visible binding for global variable 'i'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
plot,GBH-ANY : .local: no visible binding for global variable
  'sorted.hyp'
plot,GBH-ANY : .local: no visible binding for global variable 'pval'
plot,GBH-ANY : .local: no visible binding for global variable 'group'
plot,GBH-ANY : .local: no visible binding for global variable 'type'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/subprocess.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'ISwR' 'MASS' 'corpcor'
  All declared Imports should be used.
subsemble: no visible global function definition for 'detectCores'
subsemble : .make_Z_l: no visible global function definition for
  'parSapply'
subsemble : .make_Z_l: no visible global function definition for
  'makeCluster'
subsemble : .make_Z_l: no visible global function definition for
  'stopCluster'
subsemble: no visible global function definition for 'parSapply'
subsemble: no visible global function definition for 'makeCluster'
subsemble: no visible global function definition for 'stopCluster'
test_subtype_only: no visible global function definition for 'survdiff'
test_subtype_only: no visible global function definition for 'survfit'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to
  'digits'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to
  'width'
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol'
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of 'nr' to 'nrow'
superdiag: no visible global function definition for 'as.mcmc.list'
superdiag: no visible global function definition for 'as.mcmc'
superdiag: no visible global function definition for 'geweke.diag'
superdiag: no visible global function definition for 'heidel.diag'
superdiag: no visible global function definition for 'raftery.diag'
superdiag: no visible global function definition for 'gelman.diag'
gen.y.mat2: no visible global function definition for 'survfit'
superpc.cv: no visible global function definition for 'coxph'
superpc.cv: no visible global function definition for 'coxph.control'
superpc.fit.to.outcome: no visible global function definition for
  'coxph'
superpc.fit.to.outcome: no visible global function definition for
  'coxph.control'
superpc.lrtest.curv: no visible global function definition for 'coxph'
superpc.predictionplot: no visible binding for global variable
  'shrinkages'
superpc.predictionplot: no visible global function definition for
  'survfit'
surv.to.class2: no visible global function definition for 'survfit'
pbc.sample: no visible binding for global variable 'pbc'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

schemper: no visible global function definition for 'survfit'
Est.PH: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'coxph'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.5Mb
AER: no visible binding for global variable 'survexp.fr'
AER: no visible global function definition for 'survexp'
LR: no visible binding for global variable 'survexp.fr'
LR: no visible global function definition for 'survexp'
SMR: no visible binding for global variable 'survexp.fr'
SMR: no visible global function definition for 'survexp'
survexp_plot: no visible binding for global variable 'survexp.fr'
survexp_plot: no visible global function definition for 'survfit'
survexp_plot: no visible global function definition for 'survexp'
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
Running examples in 'survminer-Ex.R' failed
The error most likely occurred in:

> ### Name: ggcoxdiagnostics
> ### Title: Diagnostic Plots for Cox Proportional Hazards Model with ggplot2
> ### Aliases: ggcoxdiagnostics
> 
> ### ** Examples
> 
> 
> if(require(RTCGA.clinical)){
+ # TCGA data exmaple (http://cancergenome.nih.gov/)
+ # source("https://bioconductor.org/biocLite.R")
+ # biocLite("RTCGA.clinical") # data for examples
+ # library(RTCGA.clinical) # also loads 'RTCGA' package
+ survivalTCGA(BRCA.clinical, OV.clinical,
+             extract.cols = c("admin.disease_code", "patient.days_to_birth")) -> BRCAOV.survInfo
+ BRCAOV.survInfo$age  <- round((-as.numeric(BRCAOV.survInfo$patient.days_to_birth))/365,2)
+ 
+ library(survival)
+ coxph.fit <- coxph(Surv(times, patient.vital_status) ~ admin.disease_code + age,
+               data = BRCAOV.survInfo)
+ 
+ ggcoxdiagnostics(coxph.fit, ggtheme = theme_dark(), point.col = "white", point.aplha = 0.3)
+ ggcoxdiagnostics(coxph.fit, ggtheme = theme_RTCGA(), # library(RTCGA.clinical)
+  type = "deviance") + ylab('Deviance Residuals')
+ ggcoxdiagnostics(coxph.fit, ggtheme = theme_light(), linear.predictions = FALSE)
+ # ggcoxdiagnostics(coxph.fit, ggtheme = theme_void(), type = "deviance", linear.predictions = FALSE)
+ }
Loading required package: RTCGA.clinical
Loading required package: RTCGA
Loading required package: knitr
Welcome to the RTCGA (version: 1.0.2).
Error: could not find function "survivalTCGA"
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Loading required package: RTCGA
Welcome to the RTCGA (version: 1.0.2).
Quitting from lines 55-64 (Informative_Survival_Plots.Rmd) 
Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics:
could not find function "survivalTCGA"
Execution halted
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  'citation()' on how to cite R or R packages in publications.
  
  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > library(testthat)
  > library(svglite)
  > 
  > test_check("svglite")
  Error in loadNamespace(name) : there is no package called 'fontquiver'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Namespaces in Imports field not imported from:
  'MASS' 'graphics' 'methods' 'stats'
  All declared Imports should be used.
Package in Depends field not imported from: 'kernlab'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
roccurve: warning in formatC(sum(c1 * cumsum(c2)), digit = 4): partial
  argument match of 'digit' to 'digits'
svmmajtuning: warning in .svmmaj(Z[groups != i, ], y[groups != i],
  lambda = lambda[l], w = w[groups != i], increase.step =
  increase.step, hinge = newHinge, theta = theta, check.positive =
  FALSE, convergence = convergence, ...): partial argument match of
  'hinge' to 'hingef'
auc: no visible global function definition for 'error'
getUpdate: no visible global function definition for 'vanilladot'
getUpdate: no visible global function definition for 'kernelMatrix'
qhat.theta: no visible global function definition for 'kernelMatrix'
roccurve: no visible global function definition for 'error'
svmmaj.default: no visible binding for global variable 'vanilladot'
svmmaj.default: no visible global function definition for 'kpar'
svmmaj2.default: no visible binding for global variable 'vanilladot'
svmmaj2.default: no visible global function definition for 'kpar'
svmmajtuning: no visible binding for global variable 'vanilladot'
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
protocol_junit.svSuiteData: no visible global function definition for
  'xmlNode'
protocol_junit.svSuiteData: no visible global function definition for
  'addChildren'
protocol_junit.svSuiteData: no visible global function definition for
  'saveXML'
protocol_junit.svTestData: no visible global function definition for
  'xmlNode'
protocol_junit.svTestData: no visible global function definition for
  'addChildren'
adjust.linearmodel: no visible global function definition for 'rlm'
confounding: no visible global function definition for 'heatmap.2'
hca.plot: no visible global function definition for 'colorpanel'
hca.plot: no visible global function definition for 'hcluster'
hca.test: no visible global function definition for 'hcluster'
kill.pc: no visible global function definition for 'impute.knn'
prince: no visible global function definition for 'impute.knn'
prince.plot: no visible global function definition for 'heatmap.2'
prince.var.plot: no visible global function definition for 'impute.knn'
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
fj_pl: no visible global function definition for 'getbasismatrix'
fj_pl: no visible global function definition for 'create.bspline.basis'
fj_pl: no visible global function definition for 'getbasispenalty'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sybilSBML.Rcheck/00install.out' for details.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Namespaces in Imports field not imported from:
  'doParallel' 'foreach' 'parallel'
  All declared Imports should be used.
cleavogram : savecleavogram : savefic: warning in jpeg(file =
  filename): partial argument match of 'file' to 'filename'
fn.V: no visible global function definition for 'LowRankQP'
synth: no visible global function definition for 'LowRankQP'
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
cellgram: no visible global function definition for 'grid.rect'
cellgram: no visible global function definition for 'gpar'
cellgram: no visible global function definition for 'grid.segments'
cellgram: no visible global function definition for 'grid.circle'
cellgram: no visible global function definition for 'grid.polygon'
cellgram: no visible global function definition for 'grid.text'
cellgram: no visible global function definition for 'unit'
tableplot.colldiag: no visible global function definition for
  'colldiag'
tableplot.default: no visible global function definition for
  'grid.newpage'
tableplot.default: no visible global function definition for
  'grid.layout'
tableplot.default: no visible global function definition for 'unit'
tableplot.default: no visible global function definition for
  'pushViewport'
tableplot.default: no visible global function definition for 'viewport'
tableplot.default: no visible global function definition for
  'grid.text'
tableplot.default: no visible global function definition for
  'upViewport'
tableplot.default: no visible global function definition for 'gpar'
tableplot.default: no visible global function definition for
  'grid.rect'
tableplot.default: no visible global function definition for
  'popViewport'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.3Mb
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/TDA.Rcheck/00install.out' for details.
ConvDiffCoef: no visible global function definition for 'pascal'
DeconTrace: no visible global function definition for 'as.Zpg'
DeconTrace: no visible global function definition for 'butter'
MakeDPZ: no visible global function definition for 'bilinear'
MatchCoefDPZ: no visible global function definition for 'Zpg'
PZ2Coef: no visible global function definition for 'Poly'
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for global variable 'ID'
TER.deesc.1.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B: no visible binding for global variable 'ID'
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A3.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A2.f: no visible binding for global variable 'ID'
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : B1.f: no visible binding for global variable 'ID'
TER.deesc.A.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B: no visible binding for global variable 'ID'
installed size is 44.0Mb
  sub-directories of 1Mb or more:
    libs      13.0Mb
    tessdata  30.9Mb
test_pkg : <anonymous>: no visible global function definition for
  '.traceback'
Dif.Surv.Rec: no visible global function definition for 'survfitr'
Plot.Event.Rec: no visible global function definition for 'survfitr'
Plot.Surv.Rec: no visible global function definition for 'survfitr'
Plot.Surv.Rec: no visible global function definition for 'q.search'
Print.Summary: no visible global function definition for 'survfitr'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.5Mb
    libs   2.2Mb
Namespace in Imports field not imported from: 'irlba'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/textTinyR.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'DBI' 'broom' 'forcats' 'ggplot2' 'haven' 'hms' 'httr' 'jsonlite'
  'lubridate' 'modelr' 'readr' 'readxl' 'rvest' 'stringr' 'tidyr'
  'xml2'
  All declared Imports should be used.
determine_replications: no visible global function definition for
  'microbenchmark'
plot.timeit: no visible global function definition for 'ggplot'
plot.timeit: no visible global function definition for 'aes'
plot.timeit: no visible global function definition for 'geom_boxplot'
plot.timeit: no visible global function definition for 'geom_point'
plot.timeit: no visible global function definition for 'xlab'
plot.timeit: no visible global function definition for 'ylab'
plot.timeit: no visible global function definition for 'ggtitle'
plot.timeit: no visible global function definition for 'coord_flip'
timeline: no visible global function definition for 'ggplot'
timeline: no visible global function definition for 'geom_segment'
timeline: no visible global function definition for 'aes_string'
timeline: no visible global function definition for 'geom_rect'
timeline: no visible global function definition for 'geom_text'
timeline: no visible global function definition for 'theme'
timeline: no visible global function definition for 'element_blank'
timeline: no visible global function definition for 'xlab'
timeline: no visible global function definition for 'ylab'
timeline: no visible global function definition for 'xlim'
timeline: no visible global function definition for
  'scale_y_continuous'
timeline: no visible global function definition for 'geom_point'
timeline: no visible global function definition for 'scale_color_grey'
timeline: no visible global function definition for 'geom_hline'
is.Bizday: no visible global function definition for 'isWeekday'
plotCalendarHeatmap: no visible global function definition for 'ddply'
plotCalendarHeatmap: no visible global function definition for '.'
plotCalendarHeatmap: no visible binding for global variable 'year'
plotCalendarHeatmap: no visible binding for global variable 'month'
plotCalendarHeatmap: no visible binding for global variable 'week'
plotCalendarHeatmap: no visible global function definition for 'ggplot'
plotCalendarHeatmap: no visible global function definition for 'aes'
plotCalendarHeatmap: no visible binding for global variable 'monthweek'
plotCalendarHeatmap: no visible binding for global variable 'weekday'
plotCalendarHeatmap: no visible global function definition for
  'geom_tile'
plotCalendarHeatmap: no visible global function definition for
  'facet_grid'
plotCalendarHeatmap: no visible global function definition for
  'scale_fill_gradientn'
projectDate: no visible global function definition for 'holidayNYSE'
projectDate: no visible global function definition for
  'sparse.model.matrix'
boot_autocov: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'tsboot'
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dmvt'
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/tolerance.Rcheck/00install.out' for details.
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'colorspace'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: eval(code, new_test_environment)
  3: eval(expr, envir, enclos)
  4: expect_is(trakt.user.watchlist(user = sample_user, type = "movies", extended = "min"), 
         "data.frame") at test_user.R:25
  5: expect_that(object, is_a(class), info, label)
  6: condition(object)
  7: paste0(class(x), collapse = ", ")
  8: trakt.user.watchlist(user = sample_user, type = "movies", extended = "min")
  9: convert_datetime(response)
  10: stop("Object type not supported")
  
  Error: Test failures
  Execution halted
mytree.asymmetric.age: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.age: no visible global function definition for
  'drop.fossil'
mytree.asymmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.taxa: no visible global function definition for
  'drop.fossil'
mytree.symmetric.age: no visible global function definition for
  'collapse.singles'
mytree.symmetric.age: no visible global function definition for
  'drop.fossil'
mytree.symmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.symmetric.taxa: no visible global function definition for
  'drop.fossil'
plot.tkm: no visible global function definition for 'plotcluster'
plot.tkm: no visible global function definition for 'discrcoord'
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'gam'
sim.cont: no visible global function definition for 'lsoda'
TSget,character-TSfameLocalConnection : .local: no visible global
  function definition for 'zoo'
TSget,character-TSfameServerConnection : .local: no visible global
  function definition for 'zoo'
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
plotDominationGraph: no visible global function definition for
  'graph.adjacency'
plotDominationGraph: no visible global function definition for
  'layout.norm'
sampleCombinations: no visible global function definition for
  'qrng_alloc'
sampleCombinations: no visible global function definition for
  'qrng_get'
tunePareto: no visible global function definition for 'sfLibrary'
tunePareto : <anonymous>: no visible global function definition for
  'sfLibrary'
tunePareto: no visible global function definition for 'sfExport'
tunePareto: no visible global function definition for 'sfLapply'
tunePareto.NaiveBayes: no visible binding for global variable
  'NaiveBayes'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/uaparserjs.Rcheck/00install.out' for details.
uniCoxCV: no visible global function definition for 'coxph'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/uroot.Rcheck/00install.out' for details.
File 'UScensus2010/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage(paste("Package ", dscr$Package, ": ", dscr$Title,     "\n", "Version ", dscr$Version, " created on ", dscr$Date,     ".\n", sep = ""))
    packageStartupMessage(paste("Zack Almquist, University of California-Irvine\nne\n",     sep = ""))
    packageStartupMessage("For citation information, type citation(\"UScensus2010\").")
    packageStartupMessage("Type help(package=UScensus2010) to get started.")

See section 'Good practice' in '?.onAttach'.
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
mcmc.estimate: no visible global function definition for '%dopar%'
mcmc.estimate: no visible global function definition for 'foreach'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/valr.Rcheck/00install.out' for details.
SVEC: no visible global function definition for 'Null'
causality: no visible global function definition for 'ginv'
stability: no visible global function definition for 'efp'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.3Mb
Package required but not available: 'fontquiver'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
vioplot: warning in axis(1, at = at, label = label): partial argument
  match of 'label' to 'labels'
vioplot: warning in axis(2, at = at, label = label): partial argument
  match of 'label' to 'labels'
raster.proj: no visible global function definition for 'rasterFromXYZ'
.vdensecalc: no visible global function definition for 'contour3d'
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 65-67 (vtreatRareLevels.Rmd) 
Error: processing vignette 'vtreatRareLevels.Rmd' failed with diagnostics:
unused argument (left.open = TRUE)
Execution halted
ald: no visible global function definition for 'detectCores'
ald: no visible global function definition for 'mclapply'
coltheart.N: no visible global function definition for 'detectCores'
coltheart.N: no visible global function definition for 'mclapply'
hamming.distance: no visible global function definition for
  'stringdist'
ldknn: no visible global function definition for 'detectCores'
ldknn: no visible global function definition for 'mclapply'
levenshtein.damerau.distance: no visible global function definition for
  'stringdist'
levenshtein.distance: no visible global function definition for
  'stringdist'
plot.ldknn.run: no visible global function definition for 'histogram'
plot.ldknn.run: no visible global function definition for
  'theEconomist.theme'
plot.ldknn.run: no visible global function definition for 'xyplot'
plot.ldknn.run: no visible global function definition for 'as.layer'
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
color.factor: warning in rgb(red = t.rgb[1, ], green = t.rgb[2, ], blue
  = t.rgb[3, ], max = 255): partial argument match of 'max' to
  'maxColorValue'
p.flow_comp: warning in line_sumrain(xdata = xdata, cum_sum =
  cumsum(data[crain, ])/10, theMax = rain.max, col = "grey"): partial
  argument match of 'cum_sum' to 'cum_sum_rain'
Errors in running code in vignettes:
when running code in 'vignette.Rnw'
  ...

> library(waterData)

> q05054000 <- importDVs("05054000", code = "00060", 
+     stat = "00003", sdate = "2000-01-01", edate = "2010-12-31")
Unknown IO errorfailed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"

  When sourcing 'vignette.R':
Error: 1: Unknown IO error2: failed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 1 
Error : 1: Unknown IO error2: failed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"

Execution halted
WDI: no visible binding for global variable 'WDI_data'
WDIcache: no visible global function definition for 'fromJSON'
WDIsearch: no visible binding for global variable 'WDI_data'
getStationCode: no visible binding for global variable
  'USAirportWeatherStations'
getStationCode: no visible binding for global variable 'IntlWxStations'
File 'webvis/R/zzz.R':
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

[1] "Welcome to the webvis pacakge."
pairtest: no visible global function definition for 'p.value'
pairtest: no visible global function definition for 'single.snp.tests'
fun.load.hals.a: no visible global function definition for 'sfExport'
fun.load.hals.a: no visible global function definition for 'sfLibrary'
fun.load.hals.fill: no visible global function definition for
  'sfExport'
fun.load.hals.fill: no visible global function definition for
  'sfLibrary'
fun.load.widals.a: no visible global function definition for 'sfExport'
fun.load.widals.a: no visible global function definition for
  'sfLibrary'
fun.load.widals.fill: no visible global function definition for
  'sfExport'
fun.load.widals.fill: no visible global function definition for
  'sfLibrary'
screen.ttest: no visible global function definition for 'colttests'
widenet: no visible global function definition for 'mc.reset.stream'
widenet: no visible global function definition for 'mclapply'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
Namespace in Imports field not imported from: 'RMySQL'
  All declared Imports should be used.
wordcloud: no visible global function definition for 'Corpus'
wordcloud: no visible global function definition for 'VectorSource'
wordcloud: no visible global function definition for 'tm_map'
wordcloud: no visible binding for global variable 'removePunctuation'
wordcloud : <anonymous>: no visible global function definition for
  'removeWords'
wordcloud : <anonymous>: no visible global function definition for
  'stopwords'
wordcloud: no visible global function definition for
  'TermDocumentMatrix'
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
simul.wsvm: no visible binding for global variable 'mixture.example'
plot,x12Batch : .local: no visible binding for global variable 'xb'
x12,ts : .local: no visible binding for global variable 'out'
x12,x12Batch : .local: no visible global function definition for
  'mclapply'
x12,x12Single : .local: no visible binding for global variable 'out'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/xgboost.Rcheck/00install.out' for details.
Running examples in 'XGR-Ex.R' failed
The error most likely occurred in:

> ### Name: xCheckParallel
> ### Title: Function to check whether parallel computing should be used and
> ###   how
> ### Aliases: xCheckParallel
> 
> ### ** Examples
> 
> xCheckParallel(multicores=2)
Error in .check_ncores(length(names)) : 3 simultaneous processes spawned
Calls: xCheckParallel ... <Anonymous> -> makeCluster -> makePSOCKcluster -> .check_ncores
Execution halted
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
File 'xml2/libs/i386/xml2.dll':
  Found non-API call to R: 'getConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API call to R: 'getConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.1Mb
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile : .local: possible error in updateIds(doc, save = x):
  unused argument (save = x)
as.xts.ts: no visible global function definition for 'as.yearqtr'
as.xts.ts: no visible global function definition for 'as.yearmon'
rollapply.xts: no visible global function definition for 'na.fill'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'yacca/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat("Copyright (c) 2008, Carter T. Butts, University of California-Irvine\n")
    cat("For citation information, type citation(\"yacca\").\n")
    cat("Type help(\"yacca-package\") to get started.\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
tZC_NS: no visible global function definition for 'cmpfun'
tZC_NS_extra: no visible global function definition for 'cmpfun'
tZC_SV: no visible global function definition for 'cmpfun'
tZC_SV_extra: no visible global function definition for 'cmpfun'
Namespaces in Imports field not imported from:
  'DT' 'ggplot2' 'quantmod' 'sde' 'shinyBS' 'shinydashboard' 'shinyjs'
  'yuima'
  All declared Imports should be used.
epirice.weather: no visible binding for global variable
  'weather_SouthAsia'
maize.multisy: no visible binding for global variable
  'weather_EuropeEU'
maize.multisy240 : <anonymous>: no visible binding for global variable
  'weather_EuropeEU'
maize.weather: no visible binding for global variable
  'weather_FranceWest'
param.rtriangle: no visible global function definition for 'rtriangle'
population.age.model.ode: no visible global function definition for
  'ode'
population.age.model.ode: no visible global function definition for
  'rkMethod'
predator.prey.model: no visible global function definition for 'ode'
predator.prey.model: no visible global function definition for
  'rkMethod'
watbal.weather: no visible binding for global variable
  'weather_FranceWest'
Namespaces in Imports field not imported from:
  'dplyr' 'ggplot2' 'lubridate'
  All declared Imports should be used.