Package suggested but not available for checking: ‘INLA’
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of ‘dig’ to ‘digits’
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of ‘env’ to ‘envir’
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of ‘env’ to ‘envir’
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of ‘dig’ to ‘digits’
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of ‘env’ to ‘envir’
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of ‘env’ to ‘envir’
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  ‘wid’ to ‘width’
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Vignette.Rmd’
Malformed Description field: should contain one or more complete sentences.
index.citations: no visible global function definition for
  ‘txtProgressBar’
read.exsic: no visible global function definition for ‘read.csv’
update.pb: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpdcgx82/R.INSTALLc15278a7a06/extdplyr/man/check_missing.Rd:24: file link ‘summarize_at’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpdcgx82/R.INSTALLc15278a7a06/extdplyr/man/reexports.Rd:14: file link ‘%>%’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/extdplyr.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
extfunnel: no visible global function definition for ‘qnorm’
extfunnel: no visible global function definition for ‘meta.summaries’
extfunnel: no visible global function definition for ‘flush.console’
extfunnel: no visible global function definition for ‘qt’
extfunnel: no visible global function definition for ‘dev.new’
extfunnel: no visible global function definition for ‘par’
extfunnel: no visible global function definition for ‘polygon’
extfunnel: no visible global function definition for ‘segments’
extfunnel: no visible global function definition for ‘abline’
extfunnel: no visible global function definition for ‘axis’
extfunnel: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "polygon",
             "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
bars: no visible global function definition for ‘segments’
cv.binomial: no visible binding for global variable ‘var’
cv.binomial: no visible global function definition for ‘abline’
cv.normal: no visible binding for global variable ‘var’
cv.normal: no visible global function definition for ‘abline’
cv.poisson: no visible binding for global variable ‘var’
cv.poisson: no visible global function definition for ‘abline’
plot.extlasso: no visible global function definition for ‘matplot’
plot.extlasso: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
exbio: no visible global function definition for ‘as.formula’
exbio: no visible global function definition for ‘glm’
exbio: no visible binding for global variable ‘gaussian’
exbio: no visible global function definition for ‘Gamma’
exbio: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  Gamma as.formula gaussian glm pchisq
Consider adding
  importFrom("stats", "Gamma", "as.formula", "gaussian", "glm", "pchisq")
to your NAMESPACE file.
Rd file 'exbio.Rd':
  \usage lines wider than 90 characters:
     exbio(R, R.alt, cc, n, tol = 0.001, a.start = 1, b.start = 1, max.it = 1000, digits = NULL, model.maf = TRUE)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6y7Zsf/R.INSTALL17aa23e100e1/extraDistr/man/GammaPoiss.Rd:84: file link ‘Gamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6y7Zsf/R.INSTALL17aa23e100e1/extraDistr/man/Multinomial.Rd:54: file link ‘Multinomial’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/extraDistr.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
font_install: no visible global function definition for
  ‘installed.packages’
font_install: no visible global function definition for
  ‘install.packages’
fonttable_add: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  install.packages installed.packages write.csv
Consider adding
  importFrom("utils", "install.packages", "installed.packages",
             "write.csv")
to your NAMESPACE file.
toJavaMatrix2D: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘temp.Rdata’
Found the following significant warnings:
  Rd warning: /tmp/RtmpMiTSel/R.INSTALL406d63df925a/extremeStat/man/q_gpd.Rd:68: file link ‘gpdFit’ in package ‘fExtremes’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/extremeStat.Rcheck/00install.out’ for details.
bootstrapCMLE: no visible global function definition for ‘qweibull’
bootstrapCMLE: no visible binding for global variable ‘sd’
bootstrapCMLE: no visible global function definition for ‘quantile’
bootstrapCenWbMix: no visible binding for global variable ‘sd’
bootstrapCenWbMix: no visible global function definition for ‘quantile’
cenWeibullMLE: no visible global function definition for ‘sd’
expmx.p2.censor: no visible global function definition for ‘dweibull’
expmx.p2.censor: no visible global function definition for ‘pweibull’
genWbMixIni: no visible global function definition for ‘runif’
log.llh.p2.censor: no visible global function definition for ‘dweibull’
log.llh.p2.censor: no visible global function definition for ‘pweibull’
quanWbMix : t.fun: no visible global function definition for ‘pweibull’
quanWbMix: no visible global function definition for ‘uniroot’
quanWbMix.int : t.fun: no visible global function definition for
  ‘pweibull’
quanWbMix.int: no visible global function definition for ‘uniroot’
simWbMix: no visible global function definition for ‘rbinom’
simWbMix: no visible global function definition for ‘rweibull’
Undefined global functions or variables:
  dweibull pweibull quantile qweibull rbinom runif rweibull sd uniroot
Consider adding
  importFrom("stats", "dweibull", "pweibull", "quantile", "qweibull",
             "rbinom", "runif", "rweibull", "sd", "uniroot")
to your NAMESPACE file.
Package suggested but not available for checking: ‘exuberdata’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4OM5ji/R.INSTALL11355062fa9b/eyelinker/man/grapes-In-grapes.Rd:19: file link ‘distance_to_nearest’ in package ‘intervals’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4OM5ji/R.INSTALL11355062fa9b/eyelinker/man/whichInterval.Rd:20: file link ‘which_nearest’ in package ‘intervals’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/eyelinker.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Rd file 'distance2point.Rd':
  \usage lines wider than 90 characters:
     distance2point(x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
  \examples lines wider than 100 characters:
     function( x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight ) {

Rd file 'subtendedAngle.Rd':
  \usage lines wider than 90 characters:
     subtendedAngle(x1, y1, x2, y2, viewerDistance = 58.74, viewerHeight = 4.55, resolutionX = 1280, resolutionY = 1024, screenWidth = 33.97 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     function( x1, y1, x2, y2, viewerDistance=58.74, viewerHeight=4.55, resolutionX=1280, resolutionY=1024, screenWidth=33.97, screenHeight= ... [TRUNCATED]
         d1 <- distance2point(x1, y1, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
         d2 <- distance2point(x2, y2, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUIzyOO/R.INSTALL36bd2e029b00/ezec/man/get_EC.Rd:24: file link ‘ED’ in package ‘drc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ezec.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPSjCuS/R.INSTALL75403ee48081/ezknitr/man/ezknitr_core.Rd:136: file link ‘setup_ezknit_test’ in package ‘ezknitr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPSjCuS/R.INSTALL75403ee48081/ezknitr/man/ezknitr_core.Rd:137: file link ‘setup_ezspin_test’ in package ‘ezknitr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPSjCuS/R.INSTALL75403ee48081/ezknitr/man/open_output_dir.Rd:10: file link ‘ezspin’ in package ‘ezknitr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPSjCuS/R.INSTALL75403ee48081/ezknitr/man/open_output_dir.Rd:11: file link ‘ezknit’ in package ‘ezknitr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPSjCuS/R.INSTALL75403ee48081/ezknitr/man/setup_test.Rd:47: file link ‘ezspin’ in package ‘ezknitr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPSjCuS/R.INSTALL75403ee48081/ezknitr/man/setup_test.Rd:49: file link ‘ezknit’ in package ‘ezknitr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ezknitr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpNvaYi3/R.INSTALL466764465b7f/ezpickr/man/pick.Rd:18: file link ‘read_stata’ in package ‘haven’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNvaYi3/R.INSTALL466764465b7f/ezpickr/man/picko.Rd:16: file link ‘read_stata’ in package ‘haven’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNvaYi3/R.INSTALL466764465b7f/ezpickr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ezpickr.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following files/directories:
  ‘facilitationmovie.gif’ ‘ts.gif’
gibbs2: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘test_30iter.RData’ ‘test_50iter.RData’ ‘test_v2_50iter.RData’
Malformed Description field: should contain one or more complete sentences.
fma: no visible global function definition for ‘factanal’
fma: no visible global function definition for ‘runif’
fma: no visible global function definition for ‘kmeans’
fma: no visible global function definition for ‘var’
fma.em.alg: no visible global function definition for ‘var’
misc : q: no visible global function definition for ‘name’
Undefined global functions or variables:
  factanal kmeans name runif var
Consider adding
  importFrom("stats", "factanal", "kmeans", "runif", "var")
to your NAMESPACE file.
Rd file 'fma.Rd':
  \usage lines wider than 90 characters:
     fma(y, k, r, x.z = NULL, x.w = NULL, it = 15, eps = 1e-04, seed = 4, scaling = FALSE, init = NULL)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
Found the following significant warnings:
  Rd warning: /tmp/RtmpX4PyUp/R.INSTALL44191d19436e/factoextra/man/fviz_dend.Rd:72: file link ‘layout.auto’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpX4PyUp/R.INSTALL44191d19436e/factoextra/man/fviz_dend.Rd:73: file link ‘layout.gem’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpX4PyUp/R.INSTALL44191d19436e/factoextra/man/fviz_dend.Rd:74: file link ‘layout.mds’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/factoextra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmppxAaRk/R.INSTALL772f8d44265/FactorsR/man/Factors.Rd:168: file link ‘panel.hist’ in package ‘SciViews’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmppxAaRk/R.INSTALL772f8d44265/FactorsR/man/Factors.Rd:168: file link ‘panel.reg’ in package ‘SciViews’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FactorsR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpaVMfmA/R.INSTALL5f8a26b9a6a8/factory/man/digested_is.Rd:14: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/factory.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createFactualConnection: no visible global function definition for
  ‘new’
factualGetSchema: no visible global function definition for ‘fromJSON’
factualRead: no visible global function definition for ‘curlEscape’
factualRead: no visible global function definition for ‘fromJSON’
processFactualReadJSON: no visible global function definition for ‘new’
processFactualSchemaJSON: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  curlEscape fromJSON new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'factualR.Rd':
  \usage lines wider than 90 characters:
     factualRead(connection , tableID , sort = NULL , limit = NULL , offset = NULL , filters = NULL , subject_key = NULL , reformatNames , v ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpyDkr8B/R.INSTALL42ec2785b540/FADA/man/FADA.Rd:84: file link ‘sda-package’ in package ‘sda’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FADA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpNRvlz3/R.INSTALL603c3234c6c9/fail/man/fail.Rd:112: file link ‘as.list’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNRvlz3/R.INSTALL603c3234c6c9/fail/man/sail.Rd:33: file link ‘suppressMessages’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fail.Rcheck/00install.out’ for details.
faisalconjoint: no visible global function definition for ‘barplot’
faisalconjoint: no visible global function definition for ‘text’
faisalconjoint: no visible global function definition for ‘jpeg’
faisalconjoint: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
Found the following files/directories:
  ‘FCMgraph.jpg’
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp82T5OV/R.INSTALL43eb29ebe45d/fam2r/man/FamiliasConditional.Rd:14: file link ‘paramlink’ in package ‘paramlink’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp82T5OV/R.INSTALL43eb29ebe45d/fam2r/man/paramlinkConditional.Rd:5: file link ‘paramlink’ in package ‘paramlink’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp82T5OV/R.INSTALL43eb29ebe45d/fam2r/man/paramlinkConditional.Rd:52: file link ‘marker’ in package ‘paramlink’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fam2r.Rcheck/00install.out’ for details.
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in '?.onAttach'.
coef.FAMILY: no visible global function definition for ‘glm’
coef.FAMILY: no visible global function definition for ‘lm’
fm2v: no visible global function definition for ‘na.omit’
l_inf_prox: no visible global function definition for ‘tail’
predict.FAMILY: no visible global function definition for ‘coef’
predict.FAMILY: no visible global function definition for ‘lm’
predict.FAMILY: no visible global function definition for ‘predict’
predict.FAMILY: no visible global function definition for ‘glm’
predict.FAMILY: no visible global function definition for ‘predict.glm’
v2fm: no visible global function definition for ‘tail’
Undefined global functions or variables:
  coef glm lm na.omit predict predict.glm tail
Consider adding
  importFrom("stats", "coef", "glm", "lm", "na.omit", "predict",
             "predict.glm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘impute’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmpHkvCtk/R.INSTALL140055b3b731/fanovaGraph/man/fanovaGraph-package.Rd:41: file link ‘igraph-package’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHkvCtk/R.INSTALL140055b3b731/fanovaGraph/man/plot.graphlist.Rd:5: file link ‘igraph-package’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHkvCtk/R.INSTALL140055b3b731/fanovaGraph/man/plot.graphlist.Rd:8: file link ‘igraph-package’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHkvCtk/R.INSTALL140055b3b731/fanovaGraph/man/plot.graphlist.Rd:23: file link ‘igraph-package’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHkvCtk/R.INSTALL140055b3b731/fanovaGraph/man/simAdditive.Rd:50: file link ‘simulate’ in package ‘DiceKriging’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fanovaGraph.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUCZpSS/R.INSTALL7d6a3f2fd78/fansi/man/strsplit_ctl.Rd:35: file link ‘regular expression’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUCZpSS/R.INSTALL7d6a3f2fd78/fansi/man/strtrim_ctl.Rd:33: file link ‘as.character’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUCZpSS/R.INSTALL7d6a3f2fd78/fansi/man/strwrap_ctl.Rd:72: file link ‘as.character’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fansi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpAUDD8n/R.INSTALL47eb65bbb7b8/fasstr/man/compute_annual_trends.Rd:168: file link ‘zyp-package’ in package ‘zyp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fasstr.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘default5.eps’
Found the following significant warnings:
  Rd warning: /private/var/folders/vl/55n5rm_939zcrwpnd8p42w4w0000gn/T/RtmphjaR8q/Rbuild74c7dd20539/FastGaSP/man/FastGaSP-package.Rd:45: file link ‘FastGaSP’ in package ‘FastGaSP’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FastGaSP.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘quick-usage-guide-to-the-fastglm-package.Rmd’
basis_hica: no visible global function definition for ‘princomp’
energy_hica: no visible global function definition for ‘dev.new’
energy_hica: no visible global function definition for ‘points’
energy_hica: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dev.new legend points princomp
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "princomp")
to your NAMESPACE file.
Package suggested but not available for checking: ‘coxKM’
Found the following significant warnings:
  Rd warning: /tmp/RtmpaK9ztq/R.INSTALL7e5279776c49/fastmaRching/man/spFastMarch.Rd:15: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fastmaRching.Rcheck/00install.out’ for details.
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘alr3’
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
Found the following significant warnings:
  Rd warning: /tmp/Rtmp22nWJV/R.INSTALL15fe27ea63fc/fastshap/man/autoplot.explain.Rd:69: file link ‘geom_col’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp22nWJV/R.INSTALL15fe27ea63fc/fastshap/man/explain.Rd:47: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp22nWJV/R.INSTALL15fe27ea63fc/fastshap/man/explain.Rd:92: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp22nWJV/R.INSTALL15fe27ea63fc/fastshap/man/grid.arrange.Rd:14: file link ‘grid.arrange’ in package ‘gridExtra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fastshap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpKriiVg/R.INSTALL18a5268c5d39/FatTailsR/man/fitkienerX.Rd:242: file link ‘parApply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKriiVg/R.INSTALL18a5268c5d39/FatTailsR/man/getDSdata.Rd:54: file link ‘TimeSeriesData’ in package ‘timeSeries’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FatTailsR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnqsxJ7/R.INSTALL166b3ae8ef35/faux/man/pipe.Rd:10: file link ‘%>%’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/faux.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpy4G0dJ/R.INSTALL525f55234ae9/fBasics/man/fBasics-deprecated.Rd:19: file link ‘dstable’ in package ‘stabledist’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpy4G0dJ/R.INSTALL525f55234ae9/fBasics/man/stableSlider.Rd:25: file link ‘dstable’ in package ‘stabledist’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fBasics.Rcheck/00install.out’ for details.
FBN.histogramMaxima: no visible global function definition for ‘hist’
FBN.kmeans: no visible global function definition for ‘median’
FBN.kmeans: no visible global function definition for ‘kmeans’
FBNormalization: no visible global function definition for ‘read.table’
FBNormalization: no visible global function definition for ‘median’
FBNormalization: no visible global function definition for ‘hist’
FBNormalization: no visible global function definition for ‘par’
FBNormalization: no visible global function definition for ‘dev.print’
FBNormalization: no visible binding for global variable ‘bmp’
FBNormalization: no visible global function definition for ‘sd’
FBNormalization: no visible global function definition for
  ‘write.table’
medianFilter: no visible global function definition for ‘median’
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'FBNormalization.Rd':
  \usage lines wider than 90 characters:
             normDataFileName = NULL, debugFlag = FALSE, plotFlag = FALSE, plotAndSaveFlag = FALSE)

These lines will be truncated in the PDF manual.
'library' or 'require' calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘glmnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for ‘kmeans’
fcd.start: no visible global function definition for ‘ginv’
fcd.start: no visible global function definition for ‘glmnet’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
mis.cluster: no visible global function definition for ‘permn’
spectral.clustering: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
PTSingleAssetBarrierOption2: no visible global function definition for
  ‘new’
newton: no visible global function definition for ‘abline’
probInRange: no visible global function definition for ‘pnorm’
shortfall_risk: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline new pnorm
Consider adding
  importFrom("graphics", "abline")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/RtmpZhN0BL/R.INSTALL6e10323313fb/fclust/man/plot.fclust.Rd:18: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fclust.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Found the following files/directories:
  ‘.Rprofile’
Found the following significant warnings:
  Rd warning: /tmp/RtmpCm3LR4/R.INSTALL16426e436664/fda/man/create.bspline.basis.Rd:171: file link ‘spline.des’ in package ‘splines’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCm3LR4/R.INSTALL16426e436664/fda/man/create.bspline.basis.Rd:174: file link ‘spline.des’ in package ‘splines’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCm3LR4/R.INSTALL16426e436664/fda/man/create.bspline.basis.Rd:199: file link ‘spline.des’ in package ‘splines’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fda.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpMgu8WL/R.INSTALL3a5a4cb6cc49/fda.usc/man/fdata.methods.Rd:88: file link ‘Summary’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMgu8WL/R.INSTALL3a5a4cb6cc49/fda.usc/man/fdata.methods.Rd:88: file link ‘Complex’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fda.usc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/GRADIENTBOOSTING.Rd:43: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/SOM.Rd:42: file link ‘som’ in package ‘kohonen’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/closegraphics.Rd:21: file link ‘dev.off’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/cookies.Rd:38: file link ‘labp’ in package ‘fds’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/cookies.Rd:38: file link ‘labc’ in package ‘fds’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/cookies.Rd:38: file link ‘nirp’ in package ‘fds’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/cookies.Rd:38: file link ‘nirc’ in package ‘fds’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/query.docs.Rd:36: file link ‘sim2’ in package ‘text2vec’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/query.words.Rd:38: file link ‘sim2’ in package ‘text2vec’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmEVitp/R.INSTALL5fe456176e96/fdm2id/man/som-class.Rd:23: file link ‘som’ in package ‘kohonen’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fdm2id.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘vert.txt’
FDRreg: no visible global function definition for ‘dnorm’
colnormalize: no visible global function definition for ‘sd’
efron: no visible global function definition for ‘median’
efron: no visible global function definition for ‘hist’
efron: no visible global function definition for ‘glm’
efron: no visible binding for global variable ‘poisson’
efron: no visible global function definition for ‘qchisq’
efron: no visible global function definition for ‘predict’
efron: no visible global function definition for ‘quantile’
efron: no visible global function definition for ‘lm’
efron: no visible global function definition for ‘coef’
make.bspline.matrix: no visible global function definition for
  ‘quantile’
plotFDR: no visible global function definition for ‘hist’
plotFDR: no visible global function definition for ‘par’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘lines’
plotFDR: no visible global function definition for ‘legend’
plotFDR: no visible global function definition for ‘rug’
plotFDR: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par poisson predict
  qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par", "rug",
             "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘treesAll.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpCaF8mu/R.INSTALL30294941817a/features/man/features.Rd:49: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCaF8mu/R.INSTALL30294941817a/features/man/fget.features.Rd:31: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/features.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1Cx947/R.INSTALL365870cc3c83/ffbase/man/as.character.ff.Rd:28: file link ‘as.character’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1Cx947/R.INSTALL365870cc3c83/ffbase/man/duplicated.ff.Rd:64: file link ‘ffdforder’ in package ‘ff’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1Cx947/R.INSTALL365870cc3c83/ffbase/man/ffrep.int.Rd:40: file link ‘rep.int’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1Cx947/R.INSTALL365870cc3c83/ffbase/man/ffseq_len.Rd:37: file link ‘seq_len’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1Cx947/R.INSTALL365870cc3c83/ffbase/man/is.na.ff.Rd:41: file link ‘is.na’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1Cx947/R.INSTALL365870cc3c83/ffbase/man/is.na.ff.Rd:41: file link ‘ffvecapply’ in package ‘ff’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ffbase.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gridExtra’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for ‘ggplot’
FFieldPtRepDemo: no visible binding for global variable ‘mtcars’
FFieldPtRepDemo: no visible global function definition for ‘aes’
FFieldPtRepDemo: no visible binding for global variable ‘mpg’
FFieldPtRepDemo: no visible global function definition for ‘geom_point’
FFieldPtRepDemo: no visible global function definition for ‘geom_text’
FFieldPtRepDemo: no visible global function definition for ‘ggtitle’
FFieldPtRepDemo: no visible global function definition for
  ‘geom_segment’
FFieldPtRepDemo: no visible global function definition for
  ‘grid.arrange’
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
ftest: no visible global function definition for ‘wilcox.test’
ftest: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4w8Vml/R.INSTALL4bcb7001e0e4/fgdr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fgdr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbM250g/R.INSTALL19d517c545ec/fgeo.analyze/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fgeo.analyze.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZA6P1Y/R.INSTALL1a704be4e093/fgeo.plot/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fgeo.plot.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpgvax2N/R.INSTALL4c972ec1dbe9/fgeo/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fgeo.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dmymvnorm: no visible global function definition for ‘dmvnorm’
dmymvt: no visible global function definition for ‘dmvt’
gof.test: no visible global function definition for ‘quantile’
gof.test : ecdf: no visible global function definition for ‘mecdf’
gof.test: no visible global function definition for ‘jacobian’
gof.test: no visible global function definition for ‘var’
gradCdfT: no visible global function definition for ‘dt’
gradCdfT: no visible global function definition for ‘pt’
gradCdfT: no visible global function definition for ‘pmvt’
influFun: no visible global function definition for ‘jacobian’
mult.sim: no visible global function definition for ‘rnorm’
plackettFormula: no visible global function definition for ‘pt’
plackettFormula: no visible global function definition for ‘pmvt’
pmymvnorm: no visible global function definition for ‘GenzBretz’
pmymvnorm: no visible global function definition for ‘TVPACK’
pmymvnorm : <anonymous>: no visible global function definition for
  ‘pmvnorm’
pmymvt: no visible global function definition for ‘GenzBretz’
pmymvt: no visible global function definition for ‘TVPACK’
pmymvt : <anonymous>: no visible global function definition for ‘pmvt’
rmymvnorm: no visible global function definition for ‘rmvnorm’
rmymvt: no visible global function definition for ‘rmvt’
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpgFI9Ok/R.INSTALL4acf1f7b7d9f/FHtest/man/FHtesticp.Rd:26: file link ‘permTS’ in package ‘perm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpgFI9Ok/R.INSTALL4acf1f7b7d9f/FHtest/man/FHtesticp.Rd:58: file link ‘icfit.default’ in package ‘interval’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpgFI9Ok/R.INSTALL4acf1f7b7d9f/FHtest/man/FHtestics.Rd:55: file link ‘icfit.default’ in package ‘interval’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpgFI9Ok/R.INSTALL4acf1f7b7d9f/FHtest/man/FHtestrcp.Rd:20: file link ‘permTS’ in package ‘perm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FHtest.Rcheck/00install.out’ for details.
fieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘dataframe.dump’ ‘list.dump’ ‘myDB’
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘filehash’ ‘DBI’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for ‘dbDriver’
createSQLite: no visible global function definition for ‘dbConnect’
createSQLite: no visible global function definition for
  ‘dbUnloadDriver’
createSQLite: no visible global function definition for ‘dbGetQuery’
initializeSQLite: no visible global function definition for ‘dbDriver’
initializeSQLite: no visible global function definition for ‘dbConnect’
initializeSQLite: no visible global function definition for ‘new’
dbDelete,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbDisconnect,filehashSQLite: no visible global function definition for
  ‘dbUnloadDriver’
dbFetch,filehashSQLite-character: no visible global function definition
  for ‘dbGetQuery’
dbInsert,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbList,filehashSQLite: no visible global function definition for
  ‘dbGetQuery’
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘myTestDB’
Found the following significant warnings:
  Rd warning: /tmp/RtmpoYA281/R.INSTALL4b9f20ae9a1e/FinancialInstrument/man/buildSpread.Rd:21: file link ‘.parseISO8601’ in package ‘xts’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoYA281/R.INSTALL4b9f20ae9a1e/FinancialInstrument/man/getSymbols.FI.Rd:53: file link ‘indexTZ’ in package ‘xts’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoYA281/R.INSTALL4b9f20ae9a1e/FinancialInstrument/man/update_instruments.yahoo.Rd:57: file link ‘stockSymbols’ in package ‘TTR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FinancialInstrument.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpJPqEnt/R.INSTALL44d36a41308a/FinePop2/man/pop_pairwiseFST.Rd:27: file link ‘as.dist’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJPqEnt/R.INSTALL44d36a41308a/FinePop2/man/pop_pairwiseFST.Rd:27: file link ‘as.dendrogram’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FinePop2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpalXZUn/R.INSTALL4475480b9ae2/FinePop/man/EBFST.Rd:37: file link ‘as.dist’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpalXZUn/R.INSTALL4475480b9ae2/FinePop/man/EBFST.Rd:37: file link ‘as.dendrogram’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FinePop.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpdu6EiZ/R.INSTALL75b94407ceb7/finiteruinprob/man/rriskproc.Rd:30: file link ‘rexp’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpdu6EiZ/R.INSTALL75b94407ceb7/finiteruinprob/man/rriskproc.Rd:31: file link ‘rgamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpdu6EiZ/R.INSTALL75b94407ceb7/finiteruinprob/man/rriskproc.Rd:31: file link ‘rlnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpdu6EiZ/R.INSTALL75b94407ceb7/finiteruinprob/man/rriskproc.Rd:62: file link ‘rhypoexp’ in package ‘sdprisk’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/finiteruinprob.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpb6IWBo/R.INSTALL220e66209553/firebase/man/reqSignin.Rd:10: file link ‘tags’ in package ‘shiny’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpb6IWBo/R.INSTALL220e66209553/firebase/man/reqSignout.Rd:10: file link ‘tags’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/firebase.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘tkrplot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'POICalc.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'POIcoords_-.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'plotPOI.Rd':
  \examples lines wider than 100 characters:
          graphPOI@docs <- matrix(c(seq(1:nrow(graphPOI@objeto)), seq(1:nrow(graphPOI@objeto))), ncol = 2)
        graphPOI@objeto <- graphPOI@objeto <- rbind(c(0,.05), c(.05,0), c(0,-.05), c(-.05,0) ,round(circulo(0,0,.3,PLOT = FALSE),2))
        usaPOI@wordsInQuery <- c(paste('High', names(USArrests[,c(1,2,4)])), paste('Low', names(USArrests[,c(1,2,4)])))

These lines will be truncated in the PDF manual.
lsmacof: no visible global function definition for ‘cmdscale’
plotInc: no visible global function definition for ‘rainbow’
prepareCalib: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmdscale lm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
fishmove : coefs: no visible global function definition for ‘coef’
fishmove : coefs: no visible global function definition for ‘pf’
fishmove: no visible global function definition for ‘lm’
fishmove: no visible global function definition for ‘predict.lm’
fishmove.estimate: no visible global function definition for ‘quantile’
fishmove.estimate : ddoublenorm: no visible global function definition
  for ‘dnorm’
fishmove.query: no visible global function definition for ‘hasArg’
fishmove.query : f: no visible global function definition for ‘pnorm’
fishmove.query: no visible global function definition for ‘uniroot’
pdk: no visible global function definition for ‘hasArg’
pdk : eq: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm",
             "quantile", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘converted_AMR_raw.txt’ ‘converted_SMR_raw.txt’ ‘fishresp.txt’
  ‘results.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpZM6oaR/R.INSTALL1cb42c7db33/fishualize/man/scale_fish.Rd:90: file link ‘scale_fill_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZM6oaR/R.INSTALL1cb42c7db33/fishualize/man/scale_fish.Rd:90: file link ‘scale_color_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fishualize.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘FitAR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FitARMA: no visible global function definition for ‘PacfDL’
FitARMA: no visible global function definition for ‘GetARMeanMLE’
FitARMA: no visible global function definition for
  ‘BackcastResidualsAR’
FitARMA: no visible global function definition for ‘LjungBoxTest’
GetFitARMA: no visible global function definition for ‘LoglikelihoodAR’
GetFitARMA: no visible global function definition for ‘ChampernowneD’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘PacfToAR’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘PacfDL’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘FastLoglikelihoodAR’
GetFitARMA: no visible global function definition for ‘PacfToAR’
InformationMatrixARMA: no visible global function definition for
  ‘InvertibleQ’
TacvfARMA: no visible global function definition for ‘InvertibleQ’
Undefined global functions or variables:
  BackcastResidualsAR ChampernowneD FastLoglikelihoodAR GetARMeanMLE
  InvertibleQ LjungBoxTest LoglikelihoodAR PacfDL PacfToAR
Found the following significant warnings:
  Rd warning: /tmp/RtmpOI0MbS/R.INSTALLeb56f0db9d5/FitAR/man/cts.Rd:47: file link ‘as.zooreg’ in package ‘zoo’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FitAR.Rcheck/00install.out’ for details.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘leaps’ ‘ltsa’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘bestglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'GetLeapsAR.Rd':
  \usage lines wider than 90 characters:
     GetLeapsAR(z, lag.max = 15, Criterion = "UBIC", Best = 3, Candidates=5, t="default", ExactQ=FALSE)

Rd file 'PlotARSdf.Rd':
  \usage lines wider than 90 characters:
     PlotARSdf(phi = NULL, theta = NULL, units = "radial", logSdf = FALSE, InnovationVariance = 1, main = NULL, sub = NULL, lwd=3, col="blue ... [TRUNCATED]

Rd file 'SelectModel.Rd':
  \usage lines wider than 90 characters:
     SelectModel(z, lag.max = 15, ARModel = c("AR", "ARz", "ARp"), Criterion = "default", Best = 3, Candidates = 5, t="default")

Rd file 'UnitRootTest.Rd':
  \usage lines wider than 90 characters:
     UnitRootTest(z, method = c("MLE", "ExactMLE", "LS", "All"), statistic = c("Z", "T"), NumBoot = 1000, PValueMethod = c("DH", "ET"))

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpJrSBr4/R.INSTALL4e273df36faa/fitdc/man/unpack.Rd:14: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fitdc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpEF169f/R.INSTALL8fe279d1d49/fitdistrplus/man/bootdist.Rd:44: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEF169f/R.INSTALL8fe279d1d49/fitdistrplus/man/bootdist.Rd:80: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fitdistrplus.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpBnpqsU/R.INSTALL1c596a42a848/fit.models/man/vcor.Rd:19: file link ‘cov2cor’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fit.models.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ihs’
'library' or 'require' calls in package code:
  ‘devEMF’ ‘doMC’ ‘foreach’ ‘grDevices’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘modelfile.dat’ ‘plots’ ‘scorefile.dat’
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Found the following significant warnings:
  Rd warning: /tmp/RtmpV67CUx/R.INSTALL2470444ff79d/flacco/man/features.Rd:474: file link ‘ResampleDesc’ in package ‘mlr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/flacco.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmpF8jb/R.INSTALL25172c7e7b5a/flair/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/flair.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/RtmpFSQoot/R.INSTALL621e47af2485/flexclust/man/propBarchart.Rd:39: file link ‘barchart’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFSQoot/R.INSTALL621e47af2485/flexclust/man/propBarchart.Rd:42: file link ‘barchart’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFSQoot/R.INSTALL621e47af2485/flexclust/man/propBarchart.Rd:46: file link ‘barchart’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFSQoot/R.INSTALL621e47af2485/flexclust/man/propBarchart.Rd:47: file link ‘bwplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFSQoot/R.INSTALL621e47af2485/flexclust/man/propBarchart.Rd:76: file link ‘bwplot,kcca-method’ in package ‘flexclust’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/flexclust.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxI7IBA/R.INSTALL44e2f42b5c5/flexCWM/man/plot.Rd:34: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/flexCWM.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘fmp.Rmd’
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpeXNVaL/R.INSTALL78cf610e28c7/flexsurv/man/GenF.Rd:96: file link ‘Llogis’ in package ‘eha’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeXNVaL/R.INSTALL78cf610e28c7/flexsurv/man/GenF.Rd:98: file link ‘dllogis’ in package ‘eha’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeXNVaL/R.INSTALL78cf610e28c7/flexsurv/man/Gompertz.Rd:79: file link ‘dgompertz’ in package ‘eha’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeXNVaL/R.INSTALL78cf610e28c7/flexsurv/man/Llogis.Rd:71: file link ‘dllogis’ in package ‘eha’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeXNVaL/R.INSTALL78cf610e28c7/flexsurv/man/flexsurvreg.Rd:440: file link ‘dEV’ in package ‘eha’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeXNVaL/R.INSTALL78cf610e28c7/flexsurv/man/flexsurvreg.Rd:440: file link ‘pEV’ in package ‘eha’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeXNVaL/R.INSTALL78cf610e28c7/flexsurv/man/flexsurvspline.Rd:138: file link ‘dllogis’ in package ‘eha’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/flexsurv.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpZtqYZA/R.INSTALL4fae10ea5f6b/FLightR/man/get.tags.data.Rd:19: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZtqYZA/R.INSTALL4fae10ea5f6b/FLightR/man/get.tags.data.Rd:19: file link ‘url’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZtqYZA/R.INSTALL4fae10ea5f6b/FLightR/man/get.tags.data.Rd:21: file link ‘POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZtqYZA/R.INSTALL4fae10ea5f6b/FLightR/man/get.tags.data.Rd:23: file link ‘POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZtqYZA/R.INSTALL4fae10ea5f6b/FLightR/man/map.FLightR.ggmap.Rd:27: file link ‘stat_density2d’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZtqYZA/R.INSTALL4fae10ea5f6b/FLightR/man/plot_util_distr.Rd:39: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FLightR.Rcheck/00install.out’ for details.
RIind: no visible global function definition for ‘aggregate’
RIind: no visible binding for global variable ‘sd’
RIpop: no visible global function definition for ‘aggregate’
RIpop: no visible binding for global variable ‘sd’
SI: no visible global function definition for ‘sd’
SI2: no visible global function definition for ‘sd’
SI3: no visible global function definition for ‘aggregate’
SI3: no visible global function definition for ‘pairs’
SI3: no visible global function definition for ‘cor’
SI4: no visible global function definition for ‘aggregate’
SI4: no visible global function definition for ‘sd’
fCV: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate cor pairs sd
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "aggregate", "cor", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GCV: no visible global function definition for ‘lm’
GCV: no visible global function definition for ‘resid’
ffplot: no visible global function definition for ‘par’
ffplot: no visible global function definition for ‘points’
ffplot: no visible global function definition for ‘legend’
flowfield: no visible global function definition for ‘write.table’
gpr: no visible global function definition for ‘quantile’
gpr: no visible global function definition for ‘var’
smoothp: no visible global function definition for ‘lm’
smoothp: no visible global function definition for ‘predict’
smoothp: no visible global function definition for ‘resid’
smoothp: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  legend lm optimize par points predict quantile resid var write.table
Consider adding
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp10iAIs/R.INSTALL21cd4a0e5be4/flowr/man/flowopts.Rd:35: file link ‘get_opts’ in package ‘params’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp10iAIs/R.INSTALL21cd4a0e5be4/flowr/man/flowopts.Rd:36: file link ‘set_opts’ in package ‘params’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp10iAIs/R.INSTALL21cd4a0e5be4/flowr/man/flowopts.Rd:37: file link ‘load_opts’ in package ‘params’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/flowr.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpenxtQi/R.INSTALL1ba55f6f0f7e/flux/man/lips.Rd:36: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpenxtQi/R.INSTALL1ba55f6f0f7e/flux/man/reco.bulk.Rd:34: file link ‘min’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpenxtQi/R.INSTALL1ba55f6f0f7e/flux/man/reco.bulk.Rd:34: file link ‘max’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpenxtQi/R.INSTALL1ba55f6f0f7e/flux/man/round.POSIXlt.Rd:9: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/flux.Rcheck/00install.out’ for details.
export: no visible global function definition for ‘write.table’
flux.odae : <anonymous>: no visible global function definition for
  ‘combn’
mf.flux: no visible global function definition for ‘runsd’
plot.fluss: no visible global function definition for ‘dev.new’
plot.fluss: no visible global function definition for ‘pdf’
plot.fluss: no visible global function definition for ‘dev.off’
plot.fluxes: no visible global function definition for ‘dev.new’
plot.fluxes: no visible global function definition for ‘devAskNewPage’
plot.fluxes: no visible global function definition for ‘pdf’
plot.fluxes: no visible global function definition for ‘dev.off’
plot.fluxxes: no visible global function definition for ‘dev.new’
plot.fluxxes: no visible global function definition for ‘devAskNewPage’
plot.fluxxes: no visible global function definition for ‘pdf’
plot.fluxxes: no visible global function definition for ‘dev.off’
reco.bulk : get.out: no visible global function definition for
  ‘boxplot.stats’
Undefined global functions or variables:
  boxplot.stats combn dev.new dev.off devAskNewPage pdf runsd
  write.table
Consider adding
  importFrom("grDevices", "boxplot.stats", "dev.new", "dev.off",
             "devAskNewPage", "pdf")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘flux.CH4.txt’
BSOptionValue: no visible global function definition for ‘pnorm’
ImpliedVol: no visible global function definition for ‘uniroot’
callFMstable: no visible global function definition for ‘integrate’
fitGivenQuantile: no visible global function definition for ‘uniroot’
matchQuartiles: no visible global function definition for ‘optim’
putFMstable: no visible global function definition for ‘integrate’
standardStableQuantile: no visible global function definition for
  ‘qnorm’
tailsGstable: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate optim pnorm qnorm uniroot
Consider adding
  importFrom("stats", "integrate", "optim", "pnorm", "qnorm", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpaD9etU/R.INSTALL5d6313b45529/folderfun/man/setff.Rd:31: file link ‘globalenv’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaD9etU/R.INSTALL5d6313b45529/folderfun/man/setff.Rd:32: file link ‘parent.frame’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/folderfun.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXTRdxb/R.INSTALL297b1ee5b51/fontHind/man/import_hind.Rd:5: file link ‘hrbrthemes-package’ in package ‘hrbrthemes’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXTRdxb/R.INSTALL297b1ee5b51/fontHind/man/import_hind.Rd:10: file link ‘hrbrthemes-package’ in package ‘hrbrthemes’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXTRdxb/R.INSTALL297b1ee5b51/fontHind/man/theme_ipsum_hind.Rd:42: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fontHind.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPwG6Nf/R.INSTALL29f319098d16/fontMPlus/man/theme_ipsum_mplus_c1.Rd:45: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPwG6Nf/R.INSTALL29f319098d16/fontMPlus/man/theme_ipsum_mplus_c2.Rd:45: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPwG6Nf/R.INSTALL29f319098d16/fontMPlus/man/theme_ipsum_mplus_m1.Rd:45: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPwG6Nf/R.INSTALL29f319098d16/fontMPlus/man/theme_ipsum_mplus_m2.Rd:45: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPwG6Nf/R.INSTALL29f319098d16/fontMPlus/man/theme_ipsum_mplus_mn1.Rd:45: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPwG6Nf/R.INSTALL29f319098d16/fontMPlus/man/theme_ipsum_mplus_p1.Rd:45: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPwG6Nf/R.INSTALL29f319098d16/fontMPlus/man/theme_ipsum_mplus_p2.Rd:45: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fontMPlus.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following significant warnings:
  Rd warning: /tmp/RtmpOWbYVm/R.INSTALL5f52bbea442/foolbox/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/foolbox.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpODVvf7/R.INSTALL1b603a25cec1/forcats/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/forcats.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5VnI5P/R.INSTALL24d167ba3307/ForecastComb/man/comb_WA.Rd:74: file link ‘winsor.mean’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ForecastComb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpdqofZM/R.INSTALL4607683a3b0e/forecastHybrid/man/hybridModel.Rd:35: file link ‘stlm’ in package ‘forecast’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpdqofZM/R.INSTALL4607683a3b0e/forecastHybrid/man/hybridModel.Rd:36: file link ‘snaive’ in package ‘forecast’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpdqofZM/R.INSTALL4607683a3b0e/forecastHybrid/man/hybridModel.Rd:50: file link ‘stlm’ in package ‘forecast’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpdqofZM/R.INSTALL4607683a3b0e/forecastHybrid/man/hybridModel.Rd:56: file link ‘snaive’ in package ‘forecast’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpdqofZM/R.INSTALL4607683a3b0e/forecastHybrid/man/hybridModel.Rd:118: file link ‘stlm’ in package ‘forecast’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpdqofZM/R.INSTALL4607683a3b0e/forecastHybrid/man/hybridModel.Rd:155: file link ‘stlm’ in package ‘forecast’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpdqofZM/R.INSTALL4607683a3b0e/forecastHybrid/man/plot.hybridModel.Rd:15: file link ‘plot.tbats’ in package ‘forecast’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/forecastHybrid.Rcheck/00install.out’ for details.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘combinat’ ‘genetics’
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘forensic/R/zzz.R’:
  .First.lib calls:
    cat("## Statistical Methods in Forensic Genetics \n")
    cat("## The work was supported by the project 1M06014 of the Ministry of \n        Education, Youth and Sports of the Czech Republic. \n")
    require(genetics, quietly = TRUE)
    require(combinat, quietly = TRUE)

Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘sim.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpD0kuQQ/R.INSTALL27ea5933ccf9/forestecology/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/forestecology.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2E2bLO/R.INSTALL47607fd367d2/forestmangr/man/pipe.Rd:8: file link ‘magrittr’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2E2bLO/R.INSTALL47607fd367d2/forestmangr/man/round_df.Rd:22: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2E2bLO/R.INSTALL47607fd367d2/forestmangr/man/tee.Rd:7: file link ‘magrittr’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/forestmangr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpHtHWUr/R.INSTALL45e85950c9ba/forestmodel/man/forest_model.Rd:89: file link ‘tidy’ in package ‘broom’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHtHWUr/R.INSTALL45e85950c9ba/forestmodel/man/forest_rma.Rd:30: file link ‘rma’ in package ‘metafor’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHtHWUr/R.INSTALL45e85950c9ba/forestmodel/man/forest_rma.Rd:79: file link ‘rma’ in package ‘metafor’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/forestmodel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpoE9qTB/R.INSTALL65e56bf630da/forestplot/man/fpDrawCI.Rd:113: file link ‘convertX’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoE9qTB/R.INSTALL65e56bf630da/forestplot/man/heightDetails.xaxis.Rd:16: file link ‘xaxisGrob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoE9qTB/R.INSTALL65e56bf630da/forestplot/man/heightDetails.xaxis.Rd:10: file link ‘xaxisGrob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoE9qTB/R.INSTALL65e56bf630da/forestplot/man/prFpDrawLine.Rd:28: file link ‘convertX’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoE9qTB/R.INSTALL65e56bf630da/forestplot/man/prFpGetConfintFnList.Rd:29: file link ‘as.call’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoE9qTB/R.INSTALL65e56bf630da/forestplot/man/prGridPlotTitle.Rd:10: file link ‘textGrob’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/forestplot.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpVRvVbN/R.INSTALL125f5c52dd4c/forge/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/forge.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
ForImp: no visible global function definition for ‘head’
ForImp: no visible global function definition for ‘tail’
ForImp: no visible global function definition for ‘dist’
medianimp: no visible global function definition for ‘quantile’
rancatmat: no visible global function definition for ‘runif’
transfmatcat: no visible global function definition for ‘qnorm’
transfmatcat: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
INFCvpe: no visible binding for global variable ‘INFCstats’
INFCvpe: no visible binding for global variable ‘INFCdomain’
Undefined global functions or variables:
  INFCdomain INFCstats
Found the following significant warnings:
  Rd warning: /tmp/RtmpjrIUjx/R.INSTALL40637bc4979c/formula.tools/man/get.vars.Rd:80: file link ‘all.vars’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjrIUjx/R.INSTALL40637bc4979c/formula.tools/man/get.vars.Rd:89: file link ‘all.vars’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/formula.tools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: C:/Users/Usuario/AppData/Local/Temp/Rtmp2fu5qC/Rbuild41b45aa61aa/FORTLS/man/tree.detection.Rd:104: file link ‘write.csv’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FORTLS.Rcheck/00install.out’ for details.
ForwardSearch.fit: no visible global function definition for ‘glm.fit’
ForwardSearch.plot: no visible global function definition for ‘lines’
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for ‘qnorm’
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  dnorm glm.fit lines qnorm
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "dnorm", "glm.fit", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
GenObs: no visible global function definition for ‘rnorm’
GenObs.T: no visible global function definition for ‘rt’
MeasL: no visible global function definition for ‘rbeta’
OutDet: no visible global function definition for ‘median’
RanCur: no visible global function definition for ‘rnorm’
init: no visible global function definition for ‘prcomp’
Undefined global functions or variables:
  median prcomp rbeta rnorm rt
Consider adding
  importFrom("stats", "median", "prcomp", "rbeta", "rnorm", "rt")
to your NAMESPACE file.
Rd file 'fpca.mle.Rd':
  \usage lines wider than 90 characters:
     fpca.mle(data.m, M.set,r.set, ini.method="EM", basis.method="bs", sl.v=rep(0.5,10), max.step=50,
  \examples lines wider than 100 characters:
      ##model selection result: the true model M=5, r=3 is selected with the smallest CV score among all converged models
      ##look at the CV scores and convergence for each model: note that model (M=5, r=4) does not converge. 
     #get predicted trajectories on a fine grid: the same grid for which mean and eigenfunctions are evaluated
     plot(t.c,y.c,ylim=range(pred[,id]),xlab="time",ylab="obs", main=paste("predicted trajectory of curve", id))
      ##model selection result: the true model M=5, r=3 is selected with the smallest CV score among all converged models
      plot(grids.new,result$eigenfunctions[i,],ylim=range(result$eigenfunctions),xlab="time",ylab=paste("eigenfunction",i))
      ##look at the CV scores and convergence for each model: note that model (M=5, r=4) does not converge. 

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpFwhp4x/R.INSTALL6c3136808c01/fplot/man/fit.off.Rd:43: file link ‘jpeg_fit’ in package ‘fplot’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFwhp4x/R.INSTALL6c3136808c01/fplot/man/png_fit.Rd:75: file link ‘bmp’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFwhp4x/R.INSTALL6c3136808c01/fplot/man/png_fit.Rd:75: file link ‘jpeg’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFwhp4x/R.INSTALL6c3136808c01/fplot/man/png_fit.Rd:75: file link ‘tiff’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fplot.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
'library' or 'require' calls in package code:
  ‘pcaPP’ ‘snowFT’ ‘wavelets’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ComputeDCT2FFT: no visible global function definition for ‘fft’
ComputeSemipgramFFT: no visible global function definition for ‘fft’
WaveVarFD: no visible global function definition for ‘modwt’
do.fd.estimate: no visible global function definition for
  ‘performParallel’
do.fd.estimate2d.simple: no visible global function definition for
  ‘median’
fd.Genton: no visible global function definition for ‘qn’
fd.estimate.matrix: no visible global function definition for
  ‘performParallel’
fd.plot.legend: no visible global function definition for ‘legend’
fd.plot.loglog: no visible global function definition for ‘points’
fd.plot.loglog: no visible global function definition for ‘abline’
summary.FractalDim: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline fft legend median modwt performParallel points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpoMB0LW/R.INSTALL164164c02117/frair/man/fr_emdII.Rd:31: file link ‘lambertW0’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoMB0LW/R.INSTALL164164c02117/frair/man/fr_flexpnr.Rd:39: file link ‘lambertW0’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoMB0LW/R.INSTALL164164c02117/frair/man/fr_rogersII.Rd:33: file link ‘lambertW0’ in package ‘lamW’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/frair.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
custom.draw.circle: no visible global function definition for ‘lines’
frcc: no visible binding for global variable ‘sd’
frcc: no visible global function definition for ‘cor.shrink’
frcc: no visible global function definition for ‘cor’
frcc: no visible global function definition for ‘p.asym’
generate_multivariate_normal_sample: no visible global function
  definition for ‘mvrnorm’
plot_units: no visible binding for global variable ‘sd’
plot_units: no visible global function definition for ‘points’
plot_units: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘points’
plot_variables: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘segments’
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpRsISbb/R.INSTALL765a1c1ca497/freqdom/man/rar.Rd:38: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRsISbb/R.INSTALL765a1c1ca497/freqdom/man/rar.Rd:39: file link ‘rmvt’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRsISbb/R.INSTALL765a1c1ca497/freqdom/man/rma.Rd:39: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRsISbb/R.INSTALL765a1c1ca497/freqdom/man/rma.Rd:40: file link ‘rmvt’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/freqdom.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpAliaoB/R.INSTALL57b011124776/FrF2.catlg128/man/Catalogues.Rd:37: file link ‘catlg’ in package ‘FrF2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAliaoB/R.INSTALL57b011124776/FrF2.catlg128/man/Catalogues.Rd:79: file link ‘catlg’ in package ‘FrF2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FrF2.catlg128.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘FrF2.catlg128-Ex.R’
Package in Depends field not imported from: ‘FrF2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmprkfvnI/R.INSTALL58165eeaaf8/FrF2/man/BsProb.design.Rd:102: file link ‘BsMD’ in package ‘BsMD’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprkfvnI/R.INSTALL58165eeaaf8/FrF2/man/CIG.Rd:47: file link ‘layout’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprkfvnI/R.INSTALL58165eeaaf8/FrF2/man/CIG.Rd:60: file link ‘independent.vertex.sets’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprkfvnI/R.INSTALL58165eeaaf8/FrF2/man/godolphin.Rd:85: file link ‘rerandomize.design’ in package ‘DoE.base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprkfvnI/R.INSTALL58165eeaaf8/FrF2/man/godolphin.Rd:146: file link ‘factor.names<-’ in package ‘DoE.base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FrF2.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'dggrids', 'INLA'
Packages in Depends field not imported from:
  ‘Rmpfr’ ‘partitions’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Bell : nways: no visible global function definition for ‘setparts’
Bell: no visible global function definition for ‘restrictedparts’
CalIncLapInt : Deriv: no visible global function definition for ‘D’
CalIncLapInt: no visible global function definition for ‘is.whole’
CalIncLapInt: no visible global function definition for ‘mpfr’
CalIncLapInt: no visible global function definition for ‘chooseMpfr’
derivErfc : Deriv: no visible global function definition for ‘D’
derivErfc : Erfc: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  D chooseMpfr is.whole mpfr pnorm restrictedparts setparts
Consider adding
  importFrom("stats", "D", "pnorm")
to your NAMESPACE file.
ROCscore: no visible global function definition for ‘par’
ROCscore: no visible global function definition for ‘axis’
ROCscore: no visible global function definition for ‘mtext’
ROCscore: no visible global function definition for ‘legend’
alphafrontier.2d: no visible global function definition for ‘par’
alphafrontier.2d: no visible global function definition for ‘polygon’
alphafrontier.2d: no visible global function definition for ‘lines’
alphafrontier.2d: no visible global function definition for ‘points’
alphafrontier.3d: no visible global function definition for ‘layout’
alphafrontier.3d: no visible global function definition for ‘barplot’
alphafrontier.3d: no visible global function definition for ‘axis’
alphafrontier.3d: no visible global function definition for ‘lines’
alphafrontier.3d: no visible global function definition for ‘na.omit’
ordermfrontier.2d: no visible global function definition for ‘par’
ordermfrontier.2d: no visible global function definition for ‘polygon’
ordermfrontier.2d: no visible global function definition for ‘lines’
ordermfrontier.2d: no visible global function definition for ‘points’
ordermscore.boot: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Introduction.Rmd’
Package suggested but not available for checking: ‘foba’
Found the following significant warnings:
  Rd warning: /tmp/RtmpDCCFSx/R.INSTALL53b5529a480d/FSelectorRcpp/man/information_gain.Rd:51: file link ‘gain.ratio’ in package ‘FSelector’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDCCFSx/R.INSTALL53b5529a480d/FSelectorRcpp/man/information_gain.Rd:51: file link ‘symmetrical.uncertainty’ in package ‘FSelector’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FSelectorRcpp.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Non-standard files/directories found at top level:
  ‘COPYRIGHT’ ‘pmden.R’
Copyright information should be in file inst/COPYRIGHTS
Rd file 'ftnonpar-internal.Rd':
  \usage lines wider than 90 characters:
     genmrcheck(y,yhat,thresh=-1,sigma=1,DYADIC=FALSE,beta=0.5,method=1,thr.const=2,schwelle = 1e+09)

Rd file 'genpmreg.Rd':
  \usage lines wider than 90 characters:
     genpmreg(y, beta = 0.5, squeezing.factor = 0.5, verbose = FALSE, localsqueezing = TRUE, DYADIC = TRUE, thr.const = 2, extrema.nr = -1,  ... [TRUNCATED]

Rd file 'l1pmreg.Rd':
  \usage lines wider than 90 characters:
     quantpmreg(y, beta = 0.5, squeezing.factor = 0.5, verbose = FALSE, localsqueezing = TRUE, DYADIC = TRUE, thr.const = 2, extrema.nr = -1 ... [TRUNCATED]
     l1pmreg(y, beta=0.5, squeezing.factor = 0.5, verbose = FALSE, localsqueezing = TRUE, DYADIC = TRUE, thr.const = 2, extrema.nr = -1, ban ... [TRUNCATED]

Rd file 'mintvmon.Rd':
  \usage lines wider than 90 characters:
     mintvmon(y, sigma = -1, DYADIC = TRUE, thresh = -1, method = 2, MONCONST = TRUE, CONVCONST = FALSE)

Rd file 'pmden.Rd':
  \usage lines wider than 90 characters:
     pmden(x, DISCR=FALSE,verbose = FALSE, bandwidth=-1, extrema.nr = -1, accuracy = mad(x)/1000,  extrema.mean = TRUE,maxkuipnr=19,asympbou ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘snowfall’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fugeR.evo: no visible global function definition for ‘runif’
fugeR.sfRun: no visible global function definition for ‘sfInit’
fugeR.sfRun: no visible global function definition for ‘sfLibrary’
fugeR.sfRun: no visible global function definition for ‘sfExport’
fugeR.sfRun: no visible global function definition for ‘sfLapply’
fugeR.sfRun: no visible global function definition for ‘sfStop’
Undefined global functions or variables:
  runif sfExport sfInit sfLapply sfLibrary sfStop
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Dependence on R version ‘3.5.1’ not with patchlevel 0
Found the following significant warnings:
  Rd warning: /tmp/Rtmpjthniw/R.INSTALL4d183c12e31c/funcharts/man/geom_mfd.Rd:35: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjthniw/R.INSTALL4d183c12e31c/funcharts/man/geom_mfd.Rd:37: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjthniw/R.INSTALL4d183c12e31c/funcharts/man/geom_mfd.Rd:39: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjthniw/R.INSTALL4d183c12e31c/funcharts/man/geom_mfd.Rd:41: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjthniw/R.INSTALL4d183c12e31c/funcharts/man/geom_mfd.Rd:43: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjthniw/R.INSTALL4d183c12e31c/funcharts/man/geom_mfd.Rd:45: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjthniw/R.INSTALL4d183c12e31c/funcharts/man/geom_mfd.Rd:51: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjthniw/R.INSTALL4d183c12e31c/funcharts/man/scale_mfd.Rd:49: file link ‘sd.fd’ in package ‘fda’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/funcharts.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘copying’
Found the following significant warnings:
  Rd warning: /tmp/RtmpnmMrIY/R.INSTALL19404252c5bd/FuncMap/man/FuncMap.Rd:15: file link ‘mvbutils’ in package ‘mvbutils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnmMrIY/R.INSTALL19404252c5bd/FuncMap/man/FuncMap.Rd:53: file link ‘mvbutils’ in package ‘mvbutils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FuncMap.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/RtmpMTnWrB/R.INSTALL4fb1880063f/functools/man/Mapply.Rd:16: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMTnWrB/R.INSTALL4fb1880063f/functools/man/Reduce_Right.Rd:13: file link ‘Reduce’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMTnWrB/R.INSTALL4fb1880063f/functools/man/Reduce_Right.Rd:10: file link ‘Reduce’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMTnWrB/R.INSTALL4fb1880063f/functools/man/Reduce_Right.Rd:16: file link ‘Reduce’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMTnWrB/R.INSTALL4fb1880063f/functools/man/Sapply.Rd:21: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMTnWrB/R.INSTALL4fb1880063f/functools/man/Sapply.Rd:24: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMTnWrB/R.INSTALL4fb1880063f/functools/man/Vapply.Rd:21: file link ‘vapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMTnWrB/R.INSTALL4fb1880063f/functools/man/Vapply.Rd:24: file link ‘vapply’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/functools.Rcheck/00install.out’ for details.
.FunFEM.main: no visible global function definition for ‘kmeans’
.FunFEM.main: no visible global function definition for ‘rmultinom’
.FunFEM.main: no visible global function definition for ‘cutree’
.FunFEM.main: no visible global function definition for ‘hclust’
.FunFEM.main: no visible global function definition for ‘dist’
.FunFEM.main: no visible global function definition for ‘par’
.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov cutree dist hclust kmeans par rmultinom
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPlsB1o/R.INSTALL5e4a44a6cf47/fungible/man/Ledermann.Rd:38: file link ‘ceiling’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPlsB1o/R.INSTALL5e4a44a6cf47/fungible/man/Ledermann.Rd:39: file link ‘floor’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPlsB1o/R.INSTALL5e4a44a6cf47/fungible/man/promaxQ.Rd:134: file link ‘promax’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fungible.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnmZgr8/R.INSTALL2bc4bc3a5bc/fun/man/sliding_puzzle.Rd:26: file link ‘X11’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fun.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘FusionLearn.Rmd’
Packages in Depends field not imported from:
  ‘RUnit’ ‘futile.options’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.validateGuardExpression: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  ‘d’ to ‘digits’
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  ‘d’ to ‘digits’
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  ‘d’ to ‘digits’
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
Found the following files/directories:
  ‘tmp-alloc.R’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp51Id97/R.INSTALL34e51207f299/fuzzyjoin/man/genome_join.Rd:38: file link ‘findOverlaps’ in package ‘IRanges’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp51Id97/R.INSTALL34e51207f299/fuzzyjoin/man/genome_join.Rd:49: file link ‘findOverlaps’ in package ‘IRanges’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp51Id97/R.INSTALL34e51207f299/fuzzyjoin/man/interval_join.Rd:45: file link ‘findOverlaps’ in package ‘IRanges’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp51Id97/R.INSTALL34e51207f299/fuzzyjoin/man/interval_join.Rd:37: file link ‘findOverlaps’ in package ‘IRanges’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fuzzyjoin.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpE6naw1/R.INSTALLe25257c9e89/FuzzyQ/man/AOplot.Rd:36: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FuzzyQ.Rcheck/00install.out’ for details.
NeedsCompilation field must take value ‘yes’ or ‘no’
'library' or 'require' call to ‘splines’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gensurf: no visible global function definition for ‘persp’
gensurf: no visible global function definition for ‘rainbow’
plotMF: no visible global function definition for ‘plot.new’
plotMF: no visible global function definition for ‘plot.window’
plotMF: no visible global function definition for ‘runif’
plotMF: no visible global function definition for ‘predict’
plotMF: no visible global function definition for ‘interpSpline’
plotMF: no visible global function definition for ‘lines’
plotMF: no visible global function definition for ‘text’
plotMF: no visible global function definition for ‘title’
plotMF: no visible global function definition for ‘axis’
plotMF: no visible global function definition for ‘box’
Undefined global functions or variables:
  axis box interpSpline lines persp plot.new plot.window predict
  rainbow runif text title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "persp", "plot.new",
             "plot.window", "text", "title")
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
Rd file 'newFIS.Rd':
  \usage lines wider than 90 characters:
     newFIS(FISName, FISType = "mamdani", version = "1.0", andMethod = "min", orMethod = "max", impMethod = "min", aggMethod = "max", defuzz ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘MASS’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DBNScoreStep1: no visible global function definition for ‘lm’
DBNScoreStep1: no visible global function definition for ‘rlm’
DBNScoreStep1: no visible global function definition for ‘pt’
DBNScoreStep2: no visible global function definition for ‘lm’
DBNScoreStep2: no visible global function definition for ‘rlm’
DBNScoreStep2: no visible global function definition for ‘pt’
SimulGeneExpressionAR1: no visible global function definition for
  ‘rnorm’
SimulGeneExpressionAR1: no visible global function definition for ‘ts’
SimulNetworkAdjMatrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  lm pt rlm rnorm runif ts
Consider adding
  importFrom("stats", "lm", "pt", "rnorm", "runif", "ts")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ArrayBin’
crossover: no visible global function definition for ‘runif’
exchangeSols: no visible global function definition for ‘runif’
fps: no visible global function definition for ‘runif’
mutation: no visible global function definition for ‘runif’
plotBicluster: no visible global function definition for ‘gray’
plotBicluster: no visible global function definition for ‘heatmap’
reproduction: no visible global function definition for ‘runif’
Undefined global functions or variables:
  gray heatmap runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "heatmap", "runif")
to your NAMESPACE file.
FPTsimul: no visible global function definition for ‘runif’
histplot: no visible global function definition for ‘dev.new’
histplot: no visible global function definition for ‘hist’
histplot: no visible global function definition for ‘par’
histplot: no visible global function definition for ‘legend’
mdt: no visible binding for global variable ‘deltat’
plot.FPTdensity: no visible global function definition for ‘dev.new’
res_summary: no visible global function definition for ‘write.table’
res_summary: no visible global function definition for ‘sd’
res_summary: no visible global function definition for ‘median’
vdt: no visible binding for global variable ‘deltat’
Undefined global functions or variables:
  deltat dev.new hist legend median par runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘results_Wiener1.out’
CI.RMSEA: no visible global function definition for ‘qchisq’
CI.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘par’
GAIPE.RMSEA: no visible global function definition for ‘abline’
GAIPE.RMSEA: no visible global function definition for ‘colors’
GAIPE.RMSEA: no visible global function definition for ‘text’
GAIPE.RMSEA: no visible global function definition for ‘arrows’
GAIPE.RMSEA: no visible global function definition for ‘points’
GAIPE.RMSEA: no visible global function definition for ‘axis’
GAIPE.RMSEA: no visible global function definition for ‘lines’
GAIPE.RMSEA: no visible global function definition for ‘legend’
GAIPE.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘qchisq’
GAIPE.RMSEA: no visible global function definition for ‘mtext’
GAIPE.RMSEA: no visible global function definition for ‘title’
PA.RMSEA: no visible global function definition for ‘pchisq’
PA.RMSEA: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq points qchisq
  text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: C:/Users/Benjamin (PEI)/AppData/Local/Temp/RtmpSKpGwt/Rbuild10202bff2c6e/gamboostLSS/man/cvrisk.Rd:60: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpgfEg6e/R.INSTALL175a3c2865d2/gamboostLSS/man/families.Rd:227: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Benjamin (PEI)/AppData/Local/Temp/RtmpSKpGwt/Rbuild10202bff2c6e/gamboostLSS/man/mboostLSS.Rd:100: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpgfEg6e/R.INSTALL175a3c2865d2/gamboostLSS/man/methods.Rd:285: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gamboostLSS.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
cvriskMSM: no visible global function definition for ‘predict’
plotcvriskMSM: no visible binding for global variable ‘lines’
plotcvriskMSM: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines predict
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpezaOs5/R.INSTALL38ec17c79022/gameofthrones/man/scale_got.Rd:97: file link ‘scale_fill_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpezaOs5/R.INSTALL38ec17c79022/gameofthrones/man/scale_got.Rd:97: file link ‘scale_color_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gameofthrones.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpTcTJsf/Rbuild7e3a7ca930fe/gamlss.lasso/man/gamlss.lasso-package.Rd:44: file link ‘gamlss.add’ in package ‘gamlss.add’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gamlss.lasso.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘gamlss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘gamlss:::.gamlss.bi.list’
  See the note in ?`:::` about the use of this operator.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following calls to attach():
File ‘gamlss.nl/R/nlgamlss.R’:
  attach(data)
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  Rd warning: /private/var/folders/94/71j6vmsn3zvf95p0_hlnxcfr0000gn/T/Rtmpa8RvrZ/Rbuildbd1fd39c5bc/gamlss/man/gamlss-package.Rd:48: file link ‘gamlss.dist’ in package ‘gamlss.dist’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gamlss.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpaFgn9t/R.INSTALL4ef3c904ed9/gamlss.tr/man/fitTail.Rd:65: file link ‘logSurv’ in package ‘gamlss’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gamlss.tr.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Introduction.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpqYLh5V/R.INSTALL3b236e142a70/gapfill/man/Image.Rd:105: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gapfill.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpr2THYE/R.INSTALL17af4d0834fe/GA/man/ga.Rd:116: file link ‘stopCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpr2THYE/R.INSTALL17af4d0834fe/GA/man/gaisl.Rd:123: file link ‘stopCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpjNAElx/R.INSTALL1a6a423a1aa1/gargle/man/Gargle-class.Rd:29: file link ‘Token’ in package ‘httr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjNAElx/R.INSTALL1a6a423a1aa1/gargle/man/Gargle-class.Rd:29: file link ‘Token2.0’ in package ‘httr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjNAElx/R.INSTALL1a6a423a1aa1/gargle/man/GceToken.Rd:16: file link ‘Token’ in package ‘httr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjNAElx/R.INSTALL1a6a423a1aa1/gargle/man/GceToken.Rd:16: file link ‘Token2.0’ in package ‘httr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gargle.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGw7S0B/R.INSTALL13f64a55e684/gaston/man/write.bed.matrix.Rd:37: file link ‘saveRDS’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gaston.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘orthopolynom’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘orthopolynom’ ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGaBgUC/R.INSTALL3e035f924d1e/GB2group/man/fitgroup.gb2.Rd:135: file link ‘gini.gb2’ in package ‘GB2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GB2group.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpfQi3Qo/R.INSTALL66d062009afe/GB2/man/Thomae.Rd:49: file link ‘genhypergeo_series’ in package ‘hypergeo’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GB2.Rcheck/00install.out’ for details.
contindic.gb2: no visible global function definition for ‘contour’
contindic.gb2: no visible global function definition for ‘box’
contindic.gb2: no visible global function definition for ‘mtext’
contprof.gb2: no visible global function definition for ‘image’
contprof.gb2: no visible global function definition for ‘heat.colors’
contprof.gb2: no visible global function definition for ‘contour’
contprof.gb2: no visible global function definition for ‘text’
contprof.gb2: no visible global function definition for ‘box’
dplot.cavgb2: no visible global function definition for ‘par’
dplot.cavgb2: no visible global function definition for ‘curve’
dplot.cavgb2: no visible global function definition for ‘legend’
dplot.cavgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘curve’
dplot.cgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘legend’
plotsML.gb2: no visible global function definition for ‘par’
plotsML.gb2: no visible global function definition for ‘abline’
plotsML.gb2: no visible global function definition for ‘curve’
plotsML.gb2: no visible global function definition for ‘legend’
saveplot : <local>: no visible global function definition for ‘dev.set’
saveplot : <local>: no visible global function definition for
  ‘dev.print’
saveplot : <local>: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "text")
to your NAMESPACE file.
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
coeplot: no visible global function definition for ‘axis’
coeplot: no visible global function definition for ‘lines’
coeplot: no visible global function definition for ‘title’
coeplot: no visible global function definition for ‘legend’
corplot: no visible global function definition for ‘par’
corplot: no visible global function definition for ‘pairs’
corplot: no visible global function definition for ‘strwidth’
lm.estimate: no visible global function definition for ‘as.formula’
lm.estimate: no visible global function definition for ‘glm’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
panel.smooth.r: no visible global function definition for ‘par’
panel.smooth.r: no visible global function definition for ‘points’
panel.smooth.r: no visible global function definition for ‘lines’
posplot: no visible global function definition for ‘par’
posplot: no visible global function definition for ‘barplot’
posplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
gcat.test: no visible global function definition for ‘pnorm’
generate_sub: no visible global function definition for ‘runif’
pfcn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm runif
Consider adding
  importFrom("stats", "pnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gputools’
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/ans.Rd:14: file link ‘.Last.value’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/ans.Rd:20: file link ‘.Last.value’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/first.Rd:34: file link ‘tail’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/left.Rd:27: file link ‘tail’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/read.xls.Rd:66: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/reorder.Rd:56: file link ‘reorder’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/trim.Rd:37: file link ‘sub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/trim.Rd:37: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/unmatrix.Rd:23: file link ‘as.vector’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTmVizi/R.INSTALL75d77300285c/gdata/man/upperTriangle.Rd:47: file link ‘upper.tri’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gdata.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DownloadGdelt: no visible global function definition for
  ‘packageVersion’
DownloadGdelt: no visible global function definition for
  ‘download.file’
GdeltZipToDataframe: no visible global function definition for
  ‘read.delim’
GdeltZipToDataframe: no visible global function definition for ‘unzip’
GetSizeOfGDELT: no visible global function definition for ‘read.delim’
IsValidGDELT: no visible global function definition for ‘read.delim’
IsValidGDELT: no visible global function definition for ‘md5sum’
NormEventCounts: no visible global function definition for
  ‘download.file’
NormEventCounts: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  download.file md5sum packageVersion read.csv read.delim unzip
Consider adding
  importFrom("utils", "download.file", "packageVersion", "read.csv",
             "read.delim", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpX7zcGe/R.INSTALL69703dca16e9/gdns/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gdns.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZvkfJX/R.INSTALL78264947abd8/gdtools/man/version_cairo.Rd:15: file link ‘packageVersion’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gdtools.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gdxrrw’
Non-standard files/directories found at top level:
  ‘README.too’ ‘blurb’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3VYufc/R.INSTALL52a57397d4c/geiger/man/geiger-defunct.Rd:47: file link ‘disparity’ in package ‘geiger’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3VYufc/R.INSTALL52a57397d4c/geiger/man/geiger-defunct.Rd:63: file link ‘load’ in package ‘geiger’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3VYufc/R.INSTALL52a57397d4c/geiger/man/geiger-defunct.Rd:65: file link ‘drop.random’ in package ‘geiger’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3VYufc/R.INSTALL52a57397d4c/geiger/man/geiger-defunct.Rd:66: file link ‘bd.km’ in package ‘geiger’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3VYufc/R.INSTALL52a57397d4c/geiger/man/geiger-defunct.Rd:71: file link ‘disparity’ in package ‘geiger’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3VYufc/R.INSTALL52a57397d4c/geiger/man/ratematrix.Rd:14: file link ‘rescale.phylo’ in package ‘geiger’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3VYufc/R.INSTALL52a57397d4c/geiger/man/sim.bd.Rd:21: file link ‘bd.km’ in package ‘geiger’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3VYufc/R.INSTALL52a57397d4c/geiger/man/sim.bd.Rd:31: file link ‘bd.km’ in package ‘geiger’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3VYufc/R.INSTALL52a57397d4c/geiger/man/sim.bdtree.Rd:36: file link ‘rbdtree’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geiger.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘GEint_example.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpq6NEGv/R.INSTALL2c6471d9b960/GenAlgo/man/maha.Rd:23: file link ‘cov.mve’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpq6NEGv/R.INSTALL2c6471d9b960/GenAlgo/man/maha.Rd:45: file link ‘cov.mve’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpq6NEGv/R.INSTALL2c6471d9b960/GenAlgo/man/maha.Rd:46: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GenAlgo.Rcheck/00install.out’ for details.
plot.rbga: no visible global function definition for ‘par’
plot.rbga: no visible global function definition for ‘hist’
plot.rbga: no visible global function definition for ‘lines’
rbga: no visible global function definition for ‘runif’
rbga: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm hist lines par runif
Consider adding
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
genmvnorm: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘genderdata’
t1p1: no visible global function definition for ‘var’
t1p1: no visible global function definition for ‘pt’
t1p2: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt var
Consider adding
  importFrom("stats", "pt", "var")
to your NAMESPACE file.
Rd file 'flexorhtest.Rd':
  \examples lines wider than 100 characters:
          plot(x,y, main="Location and Strong Order Restrictions",cex.axis=1.5, cex.lab=1.5, cex.main=1.5, cex=1.5)

These lines will be truncated in the PDF manual.
load.genelist: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
Rd file 'geneListPie-package.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

Rd file 'geneListProfile.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘RHugin’
Found the following significant warnings:
  Rd warning: /tmp/RtmpLnmybo/R.INSTALL6a6070707d0f/geneNetBP/man/fit-methods.Rd:60: file link ‘tabu’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLnmybo/R.INSTALL6a6070707d0f/geneNetBP/man/fit-methods.Rd:61: file link ‘gs’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLnmybo/R.INSTALL6a6070707d0f/geneNetBP/man/fit-methods.Rd:61: file link ‘iamb’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLnmybo/R.INSTALL6a6070707d0f/geneNetBP/man/fit-methods.Rd:61: file link ‘fast.iamb’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLnmybo/R.INSTALL6a6070707d0f/geneNetBP/man/fit-methods.Rd:61: file link ‘inter.iamb’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLnmybo/R.INSTALL6a6070707d0f/geneNetBP/man/fit-methods.Rd:62: file link ‘mmhc’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLnmybo/R.INSTALL6a6070707d0f/geneNetBP/man/fit-methods.Rd:77: file link ‘bn-class’ in package ‘bnlearn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geneNetBP.Rcheck/00install.out’ for details.
fit.dbn: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ForImp.Mahala: no visible global function definition for ‘combn’
ForImp.Mahala: no visible global function definition for ‘var’
ForImp.Mahala: no visible global function definition for ‘quantile’
ForImp.Mahala : <anonymous>: no visible global function definition for
  ‘var’
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for ‘var’
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
ForImp.PCA: no visible global function definition for ‘cov’
ForImp.PCA: no visible global function definition for ‘princomp’
ForImp.PCA: no visible global function definition for ‘combn’
ForImp.PCA: no visible global function definition for ‘quantile’
ForImp.PCA : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
Undefined global functions or variables:
  combn cov princomp quantile var
Consider adding
  importFrom("stats", "cov", "princomp", "quantile", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpDV2xdS/R.INSTALL6ab66c57190b/genie/man/hclust2.Rd:36: file link ‘genie’ in package ‘genieclust’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/genie.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘KernSmooth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KernSec: no visible global function definition for ‘na.omit’
KernSur: no visible global function definition for ‘na.fail’
KernSur: no visible global function definition for ‘na.omit’
bandwidthselect: no visible global function definition for ‘na.omit’
bandwidthselect: no visible global function definition for ‘dpik’
correlationselect: no visible global function definition for ‘cor’
nearest: no visible global function definition for ‘na.fail’
nearest: no visible global function definition for ‘na.omit’
per: no visible global function definition for ‘na.fail’
Undefined global functions or variables:
  cor dpik na.fail na.omit
Consider adding
  importFrom("stats", "cor", "na.fail", "na.omit")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘genotypeR.Rmd’
Found the following files/directories:
  ‘test.csv’ ‘test_temp_cross.csv’
Found the following significant warnings:
  Rd warning: /tmp/RtmpqWQK7p/R.INSTALL54107f105d9f/genridge/man/contourf.Rd:64: file link ‘contour.default’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqWQK7p/R.INSTALL54107f105d9f/genridge/man/contourf.Rd:66: file link ‘contour.default’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqWQK7p/R.INSTALL54107f105d9f/genridge/man/contourf.Rd:96: file link ‘contourplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqWQK7p/R.INSTALL54107f105d9f/genridge/man/plot3d.ridge.Rd:93: file link ‘wire3d’ in package ‘rgl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/genridge.Rcheck/00install.out’ for details.
splineAnalyze: no visible global function definition for ‘var’
splineAnalyze: no visible global function definition for ‘par’
splineAnalyze: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par var
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpDHT8rN/R.INSTALL2b6d74cd4d51/geoBayes/man/alik_cutoff.Rd:41: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDHT8rN/R.INSTALL2b6d74cd4d51/geoBayes/man/alik_inla.Rd:82: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDHT8rN/R.INSTALL2b6d74cd4d51/geoBayes/man/alik_optim.Rd:79: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDHT8rN/R.INSTALL2b6d74cd4d51/geoBayes/man/mcsglmm.Rd:124: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDHT8rN/R.INSTALL2b6d74cd4d51/geoBayes/man/mcsglmm_mala.Rd:127: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDHT8rN/R.INSTALL2b6d74cd4d51/geoBayes/man/mcstrga.Rd:123: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDHT8rN/R.INSTALL2b6d74cd4d51/geoBayes/man/mcstrga_mala.Rd:126: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDHT8rN/R.INSTALL2b6d74cd4d51/geoBayes/man/rsglmm.Rd:104: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDHT8rN/R.INSTALL2b6d74cd4d51/geoBayes/man/spcovariance.Rd:53: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geoBayes.Rcheck/00install.out’ for details.
PAEA : <anonymous>: no visible global function definition for
  ‘integrate’
PAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
PAEAAnalysis : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
PAEAAnalysis: no visible global function definition for ‘par’
PAEAAnalysis: no visible global function definition for ‘barplot’
chdirSig: no visible global function definition for ‘prcomp’
chdirSig: no visible global function definition for ‘rchisq’
chdirSig: no visible global function definition for ‘txtProgressBar’
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
chdirplots : <anonymous>: no visible global function definition for
  ‘par’
chdirplots : <anonymous>: no visible global function definition for
  ‘arrows’
chdirplots : <anonymous>: no visible global function definition for
  ‘barplot’
multigmtPAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘data’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘write.table’
Undefined global functions or variables:
  arrows barplot data integrate par prcomp rchisq setTxtProgressBar
  txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘PAEA_p_values-Cancer_Cell_Line_Encyclopedia.gmt.txt’
  ‘PAEA_p_values-ChEA.gmt.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpNyGCpb/R.INSTALL52301c63c8ce/geoknife/man/webprocess-class.Rd:17: file link ‘algorithm’ in package ‘geoknife’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNyGCpb/R.INSTALL52301c63c8ce/geoknife/man/webprocess-class.Rd:53: file link ‘algorithm’ in package ‘geoknife’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geoknife.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Rd file 'fujitopo.Rd':
  \examples lines wider than 100 characters:
     PLOC=list(LON=range(fujitopo$lon), x=range(fujitopo$lon), LAT=range(fujitopo$lat), y=range(fujitopo$lat))

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZ8Fuwu/R.INSTALL3a646de49520/GeomComb/man/comb_WA.Rd:74: file link ‘winsor.mean’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GeomComb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpA5NuOx/R.INSTALL6ed47520924d/geonetwork/man/geonetwork.Rd:18: file link ‘CRS’ in package ‘rgdal’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geonetwork.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6HwdDq/R.INSTALL78f2267bb97a/geoR/man/as.geodata.Rd:48: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6HwdDq/R.INSTALL78f2267bb97a/geoR/man/cov.spatial.Rd:166: file link ‘CovarianceFct’ in package ‘RandomFields’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6HwdDq/R.INSTALL78f2267bb97a/geoR/man/grf.Rd:90: file link ‘GaussRF’ in package ‘RandomFields’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6HwdDq/R.INSTALL78f2267bb97a/geoR/man/grf.Rd:113: file link ‘GaussRF’ in package ‘RandomFields’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6HwdDq/R.INSTALL78f2267bb97a/geoR/man/grf.Rd:183: file link ‘GaussRF’ in package ‘RandomFields’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geoR.Rcheck/00install.out’ for details.
geoscaleBox: no visible global function definition for ‘boxplot’
geoscaleBox: no visible global function definition for ‘par’
geoscaleBox: no visible global function definition for ‘text’
geoscaleBox: no visible global function definition for ‘segments’
geoscaleBox: no visible global function definition for ‘rect’
geoscaleBox: no visible global function definition for ‘rgb’
geoscaleBox: no visible global function definition for ‘polygon’
geoscaleBox: no visible global function definition for ‘points’
geoscaleBox: no visible global function definition for ‘axis’
geoscalePlot: no visible global function definition for ‘par’
geoscalePlot: no visible global function definition for ‘text’
geoscalePlot: no visible global function definition for ‘segments’
geoscalePlot: no visible global function definition for ‘rect’
geoscalePlot: no visible global function definition for ‘rgb’
geoscalePlot: no visible global function definition for ‘points’
geoscalePlot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis boxplot par points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "points", "polygon",
             "rect", "segments", "text")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpsBTc6p/R.INSTALL3423395e99be/geos/man/geos_read_wkt.Rd:56: file link ‘wkb_translate_wkt’ in package ‘wk’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geos.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Found the following significant warnings:
  Rd warning: /tmp/RtmpzcFDdI/R.INSTALL2fd047430d9f/geoTS/man/split_replace.Rd:70: file link ‘doParallel’ in package ‘doParallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geoTS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1d13JZ/R.INSTALL2d4b465887ca/geouy/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geouy.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCHDxj3/R.INSTALL58f3cbd68fd/geoviz/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geoviz.Rcheck/00install.out’ for details.
GESTr: no visible global function definition for ‘rnorm’
GESTr: no visible global function definition for ‘sd’
GESTr : <anonymous>: no visible global function definition for ‘pnorm’
TranSAM : magChange: no visible global function definition for ‘median’
TranSAM : dstat: no visible global function definition for ‘sd’
TranSAM: no visible binding for global variable ‘sd’
TranSAM: no visible global function definition for ‘quantile’
findReplicateGroups: no visible global function definition for ‘qnorm’
findReplicateGroups: no visible global function definition for ‘sd’
fitGMM : simulateData: no visible global function definition for
  ‘rnorm’
fitGMM : simulateData: no visible global function definition for ‘sd’
fitGMM: no visible global function definition for ‘median’
fitGMM: no visible global function definition for ‘ks.test’
fitRockeDurbin: no visible global function definition for ‘dist’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘median’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘mad’
fitRockeDurbin: no visible binding for global variable ‘sd’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘pnorm’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  dist ks.test mad median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "dist", "ks.test", "mad", "median", "pnorm",
             "qnorm", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Rd file 'TranSAM.Rd':
  \usage lines wider than 90 characters:
     TranSAM(x,samples1,samples2,minChange=0.2,var_filter=0.01,maxFDR=1,changeStep=0.1,scoreFun="magChange")
  \examples lines wider than 100 characters:
     selected.columns <- sort(c(sample(1:ncol(ABIdata),30),which(colnames(ABIdata) %in% c("GSM194513","GSM194514","GSM194515","GSM194516","G ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpKbdBQp/R.INSTALL30ef1c154992/getable/man/df2json.Rd:15: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/getable.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpW8UiEE/R.INSTALL4de040d95bf6/getlandsat/man/lsat_scenes.Rd:10: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpW8UiEE/R.INSTALL4de040d95bf6/getlandsat/man/lsat_scenes.Rd:16: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpW8UiEE/R.INSTALL4de040d95bf6/getlandsat/man/lsat_scenes.Rd:18: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/getlandsat.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘party’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘party’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gTree: no visible global function definition for ‘ctree’
gTree: no visible global function definition for ‘ctree_control’
guttmanErrors: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ctree ctree_control runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘multtest’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'gexmap.Rd':
  \usage lines wider than 90 characters:
     gexmap(genome = "homosapiens", scale = "", source = "", res = "", isGO = FALSE, isMAP = TRUE, lim_chi = 5, global_test_choice = 4, pcor ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpwiWuOH/R.INSTALL5b27175430bc/gfoRmula/man/gformula.Rd:148: file link ‘setDTthreads’ in package ‘data.table’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpwiWuOH/R.INSTALL5b27175430bc/gfoRmula/man/gformula_binary_eof.Rd:127: file link ‘setDTthreads’ in package ‘data.table’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpwiWuOH/R.INSTALL5b27175430bc/gfoRmula/man/gformula_continuous_eof.Rd:127: file link ‘setDTthreads’ in package ‘data.table’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpwiWuOH/R.INSTALL5b27175430bc/gfoRmula/man/gformula_survival.Rd:146: file link ‘setDTthreads’ in package ‘data.table’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gfoRmula.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCesw5L/R.INSTALL7ec04422f70f/GGally/man/ggally_cor.Rd:46: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GGally.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpcZvaMU/R.INSTALL2addb775117/ggalt/man/geom_xspline.Rd:187: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggalt.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpbksifl/R.INSTALL53632b24b439/ggChernoff/man/chernoffGrob.Rd:30: file link ‘grobTree’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggChernoff.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpY1WGfJ/R.INSTALL1b0c76ecd16d/ggdag/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggdag.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpuecWl4/R.INSTALL616c552d3dbf/ggedit/man/grapes-greater-than-grapes.Rd:127: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuecWl4/R.INSTALL616c552d3dbf/ggedit/man/grapes-greater-than-grapes.Rd:127: file link ‘%T>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuecWl4/R.INSTALL616c552d3dbf/ggedit/man/grapes-greater-than-grapes.Rd:127: file link ‘%$%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggedit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpx3Cpsy/R.INSTALL56724d75a1df/ggetho/man/stat_pop_etho.Rd:45: file link ‘mean_cl_boot’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpx3Cpsy/R.INSTALL56724d75a1df/ggetho/man/stat_pop_etho.Rd:103: file link ‘stat_smooth’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpx3Cpsy/R.INSTALL56724d75a1df/ggetho/man/time_scales.Rd:147: file link ‘scale_x_continuous’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggetho.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpruEOZg/R.INSTALL571a240bf829/ggfocus/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggfocus.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpt7sBVI/R.INSTALL5acb216759a1/gghalves/man/geom_half_violin.Rd:106: file link ‘bw.nrd’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gghalves.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2KAP8y/R.INSTALL3b6d4564feab/ggimage/man/reexports.Rd:15: file link ‘as.grob’ in package ‘ggplotify’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggimage.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘intro.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpGnYtpg/R.INSTALL5d4042fbcb09/ggmap/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggmap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUPAjWY/R.INSTALL5e3773ce9636/ggnormalviolin/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggnormalviolin.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpWo6DmV/R.INSTALL606f7fd5ddcb/ggnuplot/man/scale_x_gnuplot.Rd:22: file link ‘extended_breaks’ in package ‘scales’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggnuplot.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggOceanMapsData’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpjfiwxh/R.INSTALL60de2152e5e6/ggpage/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggpage.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIDF6Yn/R.INSTALL5f7a19197775/ggparty/man/geom_node_label.Rd:101: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggparty.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9rsgYy/R.INSTALL635c33d75077/ggplot.multistats/man/draw_key_hexagon.Rd:18: file link ‘polygonGrob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9rsgYy/R.INSTALL635c33d75077/ggplot.multistats/man/stat_summaries_hex.Rd:77: file link ‘stat_summary_hex’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggplot.multistats.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLv9zvy/R.INSTALL2bc62cd1c566/ggpmisc/man/geom_grob.Rd:62: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLv9zvy/R.INSTALL2bc62cd1c566/ggpmisc/man/geom_plot.Rd:63: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLv9zvy/R.INSTALL2bc62cd1c566/ggpmisc/man/geom_table.Rd:83: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLv9zvy/R.INSTALL2bc62cd1c566/ggpmisc/man/stat_dens1d_filter.Rd:81: file link ‘bw.nrd’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLv9zvy/R.INSTALL2bc62cd1c566/ggpmisc/man/stat_dens1d_labels.Rd:61: file link ‘bw.nrd’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLv9zvy/R.INSTALL2bc62cd1c566/ggpmisc/man/ttheme_gtdefault.Rd:116: file link ‘grid.table’ in package ‘gridExtra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggpmisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZk3j0G/R.INSTALL63ef706c3b16/ggpol/man/facet_share.Rd:47: file link ‘label_parsed’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZk3j0G/R.INSTALL63ef706c3b16/ggpol/man/facet_share.Rd:48: file link ‘label_value’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggpol.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpNbic8f/R.INSTALL646e6845b9c9/ggpolypath/man/geom_polypath.Rd:118: file link ‘polygonGrob’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggpolypath.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpsYrMeM/R.INSTALL66785ee86c21/ggquiver/man/reexports.Rd:14: file link ‘%>%’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggquiver.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIiK5hC/R.INSTALL426747cbc458/ggrepel/man/geom_text_repel.Rd:153: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIiK5hC/R.INSTALL426747cbc458/ggrepel/man/geom_text_repel.Rd:171: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIiK5hC/R.INSTALL426747cbc458/ggrepel/man/ggrepel-ggproto.Rd:16: file link ‘GeomLabel’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIiK5hC/R.INSTALL426747cbc458/ggrepel/man/ggrepel-ggproto.Rd:18: file link ‘GeomText’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggrepel.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ggroc: no visible global function definition for ‘ggplot’
ggroc: no visible global function definition for ‘aes’
ggroc: no visible global function definition for ‘geom_point’
ggroc: no visible global function definition for ‘geom_line’
ggroc: no visible global function definition for ‘theme’
ggroc: no visible global function definition for ‘element_text’
ggroc: no visible global function definition for ‘labs’
ggroc: no visible global function definition for ‘ggsave’
Undefined global functions or variables:
  aes element_text geom_line geom_point ggplot ggsave labs theme
Found the following files/directories:
  ‘roc.pdf’
Found the following significant warnings:
  Rd warning: /tmp/RtmpU88beX/R.INSTALL69f13d52ce7c/ggshadow/man/scale_brewer.Rd:52: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpU88beX/R.INSTALL69f13d52ce7c/ggshadow/man/scale_gradient.Rd:119: file link ‘scale_colour_gradient2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpU88beX/R.INSTALL69f13d52ce7c/ggshadow/man/scale_gradient.Rd:120: file link ‘scale_colour_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggshadow.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpERVRDq/R.INSTALL6a2c1d0e0f98/ggside/man/geom_xsidebar.Rd:122: file link ‘geom_col’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpERVRDq/R.INSTALL6a2c1d0e0f98/ggside/man/geom_xsidebar.Rd:124: file link ‘geom_col’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpERVRDq/R.INSTALL6a2c1d0e0f98/ggside/man/geom_xsidefreqpoly.Rd:81: file link ‘geom_freqpoly’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpERVRDq/R.INSTALL6a2c1d0e0f98/ggside/man/geom_xsideline.Rd:128: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpERVRDq/R.INSTALL6a2c1d0e0f98/ggside/man/ggside-ggproto-facets.Rd:64: file link ‘FacetNull’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpERVRDq/R.INSTALL6a2c1d0e0f98/ggside/man/ggside-ggproto-facets.Rd:65: file link ‘FacetGrid’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpERVRDq/R.INSTALL6a2c1d0e0f98/ggside/man/ggside-ggproto-facets.Rd:66: file link ‘FacetWrap’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggside.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpldIKhl/R.INSTALL4053a42640/ggstance/man/geom_linerangeh.Rd:109: file link ‘geom_pointrange’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpldIKhl/R.INSTALL4053a42640/ggstance/man/geom_linerangeh.Rd:110: file link ‘geom_errorbar’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpldIKhl/R.INSTALL4053a42640/ggstance/man/geom_linerangeh.Rd:111: file link ‘geom_crossbar’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpldIKhl/R.INSTALL4053a42640/ggstance/man/position-vertical.Rd:72: file link ‘position_fill’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpldIKhl/R.INSTALL4053a42640/ggstance/man/stat_binh.Rd:112: file link ‘stat_bin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpldIKhl/R.INSTALL4053a42640/ggstance/man/stat_boxploth.Rd:68: file link ‘stat_boxplot’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpldIKhl/R.INSTALL4053a42640/ggstance/man/stat_counth.Rd:68: file link ‘stat_count’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpldIKhl/R.INSTALL4053a42640/ggstance/man/stat_xdensity.Rd:88: file link ‘stat_ydensity’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggstance.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmphwCRRO/R.INSTALL6af85dcc3896/ggstar/man/scale_starshape_identity.Rd:110: file link ‘scale_shape_identity’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggstar.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /private/var/folders/67/ys78wlfd43zc4rzmvbtfthqh0000gn/T/RtmpjkG5XC/Rbuildbdf33a3b0c12/ggtern/man/geom_errorbarX.Rd:78: file link ‘geom_errorbar’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /private/var/folders/67/ys78wlfd43zc4rzmvbtfthqh0000gn/T/RtmpjkG5XC/Rbuildbdf33a3b0c12/ggtern/man/geom_label_viewport.Rd:106: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZFurgF/R.INSTALL6c90379e56bf/ggtern/man/scale_X_continuous.Rd:44: file link ‘extended_breaks’ in package ‘scales’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggtern.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpU9I0gY/R.INSTALL32341e85171/ggvis/man/ggvisControlOutput.Rd:16: file link ‘uiOutput’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggvis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIPjJ9i/R.INSTALL2db9332e25d5/ggvoronoi/man/fortify_voronoi.Rd:10: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIPjJ9i/R.INSTALL2db9332e25d5/ggvoronoi/man/ggvoronoi-package.Rd:9: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIPjJ9i/R.INSTALL2db9332e25d5/ggvoronoi/man/ggvoronoi-package.Rd:9: file link ‘sp’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIPjJ9i/R.INSTALL2db9332e25d5/ggvoronoi/man/ggvoronoi-package.Rd:9: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIPjJ9i/R.INSTALL2db9332e25d5/ggvoronoi/man/ggvoronoi-package.Rd:9: file link ‘gArea’ in package ‘rgeos’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIPjJ9i/R.INSTALL2db9332e25d5/ggvoronoi/man/voronoi_polygon.Rd:18: file link ‘StatVoronoi’ in package ‘ggvoronoi’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggvoronoi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbMNXbV/R.INSTALL544b6869aca1/ghibli/man/ghibli_palettes.Rd:20: file link ‘colour’ in package ‘prismatic’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ghibli.Rcheck/00install.out’ for details.
acovamcmc: no visible global function definition for ‘rnorm’
acovamcmc: no visible global function definition for ‘rgamma’
acovamcmc: no visible binding for global variable ‘quantile’
acovamcmc: no visible global function definition for ‘quantile’
acovamcmc: no visible global function definition for ‘var’
plot.acovamcmc: no visible global function definition for ‘dev.new’
plot.acovamcmc: no visible global function definition for ‘par’
plot.acovamcmc: no visible global function definition for ‘density’
plot.acovamcmc: no visible global function definition for ‘acf’
plot.acovamcmc: no visible global function definition for ‘contour’
plot.acovamcmc: no visible global function definition for ‘image’
plot.acovamcmc: no visible global function definition for ‘persp’
Undefined global functions or variables:
  acf contour density dev.new image par persp quantile rgamma rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘gibbs.met/R/firstlib.R’:
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

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

met_gaussian : one_transition: no visible global function definition
  for ‘rnorm’
met_gaussian : one_transition: no visible global function definition
  for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘mc_mvn_closemix.eps’ ‘mc_mvn_farmix_met.eps’ ‘mc_mvn_lowcor.eps’
Found the following significant warnings:
  Rd warning: /tmp/RtmpeBKwph/R.INSTALL592b299da60/Gifi/man/plot.homals.Rd:35: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeBKwph/R.INSTALL592b299da60/Gifi/man/plot.morals.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeBKwph/R.INSTALL592b299da60/Gifi/man/plot.princals.Rd:34: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Gifi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpRBwp9a/R.INSTALL6f2c41d6ebd0/giftwrap/man/temporary.Rd:20: file link ‘write_csv’ in package ‘readr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/giftwrap.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
choro.legend: no visible global function definition for ‘strwidth’
choro.legend: no visible global function definition for ‘legend’
choro.legend: no visible global function definition for ‘text’
jitter.points: no visible global function definition for ‘rnorm’
level.plot: no visible global function definition for ‘.filled.contour’
map.scale: no visible global function definition for ‘par’
map.scale: no visible global function definition for ‘rect’
map.scale: no visible global function definition for ‘lines’
map.scale: no visible global function definition for ‘text’
map.scale: no visible global function definition for ‘strheight’
north.arrow: no visible global function definition for ‘polygon’
north.arrow: no visible global function definition for ‘text’
north.arrow: no visible global function definition for ‘strheight’
poly.labels: no visible global function definition for ‘slot’
poly.labels : <anonymous>: no visible global function definition for
  ‘slot’
quantileCuts: no visible global function definition for ‘quantile’
sdCuts: no visible global function definition for ‘sd’
Undefined global functions or variables:
  .filled.contour legend lines par polygon quantile rect rnorm sd slot
  strheight strwidth text
Consider adding
  importFrom("graphics", ".filled.contour", "legend", "lines", "par",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("methods", "slot")
  importFrom("stats", "quantile", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/RtmpKhtj0S/R.INSTALL6f6a69da0797/git2r/man/git_time.Rd:23: file link ‘time zones’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKhtj0S/R.INSTALL6f6a69da0797/git2r/man/when.Rd:13: file link ‘time zones’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/git2r.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpseOEVl/R.INSTALL5ea67ef42051/githubinstall/man/reexports.Rd:14: file link ‘github_pull’ in package ‘devtools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/githubinstall.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘.gitlab-ci.yml’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3CCU6Z/R.INSTALL4c3046c52317/glancedata/man/plot_numerical_vars.Rd:33: file link ‘stat_qq_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3CCU6Z/R.INSTALL4c3046c52317/glancedata/man/plot_numerical_vars.Rd:34: file link ‘stat_qq’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/glancedata.Rcheck/00install.out’ for details.
fptcdf: no visible global function definition for ‘dnorm’
fptcdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘dnorm’
lba: no visible global function definition for ‘as.formula’
lba: no visible global function definition for ‘model.frame’
lba : logl: no visible global function definition for ‘head’
lba: no visible global function definition for ‘optim’
pmod: no visible global function definition for ‘model.frame’
pmod: no visible global function definition for ‘model.matrix’
rlba: no visible global function definition for ‘pnorm’
rlba: no visible global function definition for ‘rnorm’
rlba: no visible global function definition for ‘runif’
tablba: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula dnorm head model.frame model.matrix optim pnorm rnorm
  runif
Consider adding
  importFrom("stats", "as.formula", "dnorm", "model.frame",
             "model.matrix", "optim", "pnorm", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYLyBng/R.INSTALLa06690177ee/gld/man/fit.fkml.Rd:99: file link ‘summary.starship’ in package ‘gld’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYLyBng/R.INSTALLa06690177ee/gld/man/fit.fkml.moments.val.Rd:53: file link ‘gld’ in package ‘gld’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYLyBng/R.INSTALLa06690177ee/gld/man/starship.Rd:91: file link ‘summary.starship’ in package ‘gld’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYLyBng/R.INSTALLa06690177ee/gld/man/starship.Rd:104: file link ‘gld’ in package ‘gld’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gld.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpwtt1wG/R.INSTALL615a7aa2a42c/glmbb/man/glmbb.Rd:68: file link ‘binomial’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpwtt1wG/R.INSTALL615a7aa2a42c/glmbb/man/glmbb.Rd:68: file link ‘quasibinomial’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/glmbb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9trkoS/R.INSTALL5fc35defc82a/glmdisc/man/contr.ltfr.Rd:5: file link ‘contr.ltfr’ in package ‘caret’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9trkoS/R.INSTALL5fc35defc82a/glmdisc/man/contr.ltfr.Rd:13: file link ‘contr.ltfr’ in package ‘caret’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9trkoS/R.INSTALL5fc35defc82a/glmdisc/man/contr.ltfr.Rd:10: file link ‘contr.ltfr’ in package ‘caret’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/glmdisc.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpFXtFQF/R.INSTALL5c643826d836/glmmSeq/man/glmerApply.Rd:28: file link ‘glmerControl’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFXtFQF/R.INSTALL5c643826d836/glmmSeq/man/glmmGene.Rd:51: file link ‘glmerControl’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFXtFQF/R.INSTALL5c643826d836/glmmSeq/man/glmmSeq.Rd:50: file link ‘glmerControl’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFXtFQF/R.INSTALL5c643826d836/glmmSeq/man/modelPlot.Rd:66: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFXtFQF/R.INSTALL5c643826d836/glmmSeq/man/pairedPlot.Rd:94: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/glmmSeq.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘schlegel’
Found the following significant warnings:
  Rd warning: /tmp/RtmpGP1mEb/R.INSTALL461a5a32bc8c/glmx/man/glmx.control.Rd:47: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/glmx.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
.nPerms: no visible global function definition for ‘terms’
expr.dev.test: no visible global function definition for ‘terms’
expr.dev.test: no visible global function definition for ‘model.matrix’
expr.dev.test: no visible global function definition for ‘pchisq’
lancaster: no visible global function definition for ‘pgamma’
liptak: no visible global function definition for ‘pnorm’
summary.dev.test : ci: no visible global function definition for
  ‘qnorm’
varwiselogLik : <anonymous>: no visible global function definition for
  ‘deviance’
varwiselogLik.regression: no visible global function definition for
  ‘glm.fit’
Undefined global functions or variables:
  deviance glm.fit model.matrix pchisq pgamma pnorm qnorm terms
Consider adding
  importFrom("stats", "deviance", "glm.fit", "model.matrix", "pchisq",
             "pgamma", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
CreateFormula: no visible global function definition for ‘as.formula’
GeneratePvalues: no visible binding for global variable ‘binomial’
globalARTP: no visible binding for global variable ‘binomial’
globalFisher: no visible binding for global variable ‘binomial’
globalFisher: no visible global function definition for ‘pchisq’
globalSimes: no visible binding for global variable ‘binomial’
pvalFmla: no visible binding for global variable ‘binomial’
pvalFmla: no visible global function definition for ‘glm’
pvalFmla: no visible global function definition for ‘anova’
runPermut: no visible binding for global variable ‘binomial’
runPvalues: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  anova as.formula binomial glm pchisq
Consider adding
  importFrom("stats", "anova", "as.formula", "binomial", "glm", "pchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/RtmpViiPjI/R.INSTALL4edc27054914/glogis/man/glogisfit.Rd:63: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpViiPjI/R.INSTALL4edc27054914/glogis/man/glogisfit.Rd:91: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/glogis.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
ScoreTest: no visible global function definition for ‘pchisq’
Var1: no visible global function definition for ‘runif’
gLRT1: no visible global function definition for ‘pchisq’
gLRT2: no visible global function definition for ‘pchisq’
gLRT3: no visible global function definition for ‘pchisq’
gLRT4: no visible global function definition for ‘pf’
Undefined global functions or variables:
  pchisq pf runif
Consider adding
  importFrom("stats", "pchisq", "pf", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpTpJ7WY/R.INSTALL6c86477ed744/glue/man/glue_collapse.Rd:13: file link ‘NA_character_’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/glue.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpoFMtZE/R.INSTALL71c735ec78e4/gmailr/man/gm_auth.Rd:24: file link ‘gargle_oauth_email’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoFMtZE/R.INSTALL71c735ec78e4/gmailr/man/gm_auth.Rd:38: file link ‘gargle_oauth_cache’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoFMtZE/R.INSTALL71c735ec78e4/gmailr/man/gm_auth.Rd:42: file link ‘gargle_oob_default’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoFMtZE/R.INSTALL71c735ec78e4/gmailr/man/gm_auth_configure.Rd:33: file link ‘AuthState’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoFMtZE/R.INSTALL71c735ec78e4/gmailr/man/gm_token.Rd:10: file link ‘httr’ in package ‘httr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gmailr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmplTPZ7G/R.INSTALL6a9960e9fc11/GmAMisc/man/pointsInPolygons.Rd:96: file link ‘dbinom’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplTPZ7G/R.INSTALL6a9960e9fc11/GmAMisc/man/pointsInPolygons.Rd:96: file link ‘pbinom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GmAMisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmLvjxM/R.INSTALL7b993d5404cc/gMCP/man/entangled.Rd:43: file link ‘graphMCP-class’ in package ‘gMCP’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gMCP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbfLmcd/R.INSTALL475854490c7b/Gmedian/man/GmedianCov.Rd:22: file link ‘eigs_sym’ in package ‘RSpectra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Gmedian.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9T5gJD/R.INSTALL3e3952f248fc/gmGeostats/man/plot.logratioVariogramAnisotropy.Rd:28: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gmGeostats.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLli20M/R.INSTALL4dc71e8b5ae5/gmnl/man/AIC.gmnl.Rd:28: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLli20M/R.INSTALL4dc71e8b5ae5/gmnl/man/gmnl.Rd:81: file link ‘mlogit.data’ in package ‘mlogit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLli20M/R.INSTALL4dc71e8b5ae5/gmnl/man/gmnl.Rd:273: file link ‘mlogit.data’ in package ‘mlogit’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gmnl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4bvC2S/R.INSTALL3f44540a0ef9/GNAR/man/GNAR.Rd:5: file link ‘fiveNet’ in package ‘GNAR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4bvC2S/R.INSTALL3f44540a0ef9/GNAR/man/GNAR.Rd:5: file link ‘fiveVTS’ in package ‘GNAR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4bvC2S/R.INSTALL3f44540a0ef9/GNAR/man/GNARtoigraph.Rd:8: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4bvC2S/R.INSTALL3f44540a0ef9/GNAR/man/is.GNARnet.Rd:27: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GNAR.Rcheck/00install.out’ for details.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GANPA’ ‘WGCNA’
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  ‘GANPA’ ‘WGCNA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GANPA’ ‘WGCNA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GOGANPA: no visible global function definition for ‘GSE.Test.Main’
selectRho: no visible global function definition for
  ‘scaleFreeFitIndex’
Undefined global functions or variables:
  GSE.Test.Main scaleFreeFitIndex
Found the following files/directories:
  ‘GOGANPAResult.MeanAbs.MultiW.csv’ ‘GOGANPAResult.MeanAbs.NoW.csv’
  ‘GOGANPAResult.MeanAbs.OrigW.csv’
Found the following significant warnings:
  Rd warning: /tmp/RtmpWClKId/R.INSTALL40ae6c15073c/gogarch/man/unvech.Rd:39: file link ‘vec’ in package ‘fBasics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gogarch.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘fGarch’ ‘fastICA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
UprodR: no visible global function definition for ‘combn’
goinit: no visible global function definition for ‘as.formula’
ccor,GoGARCH : <anonymous>: no visible global function definition for
  ‘cov2cor’
ccor,Gopredict : <anonymous>: no visible global function definition for
  ‘cov2cor’
goest,Goestica: no visible global function definition for ‘fastICA’
goest,Goestml: no visible global function definition for ‘nlminb’
goest,Goestmm : <anonymous>: no visible global function definition for
  ‘combn’
goest,Goestnls: no visible global function definition for ‘optim’
show,Goinit: no visible global function definition for ‘head’
show,Gopredict: no visible global function definition for ‘head’
update,GoGARCH: no visible global function definition for
  ‘update.formula’
update,Goestica: no visible global function definition for
  ‘update.formula’
update,Goestml: no visible global function definition for
  ‘update.formula’
update,Goestmm: no visible global function definition for
  ‘update.formula’
update,Goestnls: no visible global function definition for
  ‘update.formula’
Undefined global functions or variables:
  as.formula combn cov2cor fastICA head nlminb optim update.formula
Consider adding
  importFrom("stats", "as.formula", "cov2cor", "nlminb", "optim",
             "update.formula")
  importFrom("utils", "combn", "head")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxlwyQP/R.INSTALL75c45a14561/googleCloudRunner/man/cr_jwt_create.Rd:32: file link ‘new_handle’ in package ‘curl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxlwyQP/R.INSTALL75c45a14561/googleCloudRunner/man/cr_jwt_create.Rd:36: file link ‘new_handle’ in package ‘curl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/googleCloudRunner.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpeTeyzn/R.INSTALL1cfd6ecf5dd9/googleCloudStorageR/man/gcs_upload.Rd:63: file link ‘write.csv’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeTeyzn/R.INSTALL1cfd6ecf5dd9/googleCloudStorageR/man/gcs_upload.Rd:64: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/googleCloudStorageR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpRZpuQz/R.INSTALL7ddd7e0ecc8f/googleComputeEngineR/man/as.cluster.gce_instance.Rd:28: file link ‘as.cluster’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRZpuQz/R.INSTALL7ddd7e0ecc8f/googleComputeEngineR/man/makeDockerClusterPSOCK.Rd:22: file link ‘makeClusterPSOCK’ in package ‘future’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/googleComputeEngineR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpB0HnMT/R.INSTALL4cdb7de9b35/googledrive/man/drive_auth.Rd:26: file link ‘gargle_oauth_email’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpB0HnMT/R.INSTALL4cdb7de9b35/googledrive/man/drive_auth.Rd:43: file link ‘gargle_oauth_cache’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpB0HnMT/R.INSTALL4cdb7de9b35/googledrive/man/drive_auth.Rd:47: file link ‘gargle_oob_default’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpB0HnMT/R.INSTALL4cdb7de9b35/googledrive/man/drive_auth_configure.Rd:27: file link ‘AuthState’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpB0HnMT/R.INSTALL4cdb7de9b35/googledrive/man/drive_token.Rd:10: file link ‘httr’ in package ‘httr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpB0HnMT/R.INSTALL4cdb7de9b35/googledrive/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpB0HnMT/R.INSTALL4cdb7de9b35/googledrive/man/request_generate.Rd:66: file link ‘request_build’ in package ‘gargle’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/googledrive.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpD4VuK6/R.INSTALL5c843ba9e731/googleLanguageR/man/gl_speech.Rd:37: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/googleLanguageR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpDWLobU/R.INSTALL19deb1b9f45/googlesheets4/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/googlesheets4.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/RtmpaA44jK/R.INSTALL648264b93bf0/GPareto/man/GPareto-package.Rd:180: file link ‘DiceKriging’ in package ‘DiceKriging’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaA44jK/R.INSTALL648264b93bf0/GPareto/man/GPareto-package.Rd:180: file link ‘DiceOptim’ in package ‘DiceOptim’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaA44jK/R.INSTALL648264b93bf0/GPareto/man/ParetoSetDensity.Rd:49: file link ‘ks’ in package ‘ks’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaA44jK/R.INSTALL648264b93bf0/GPareto/man/crit_optimizer.Rd:71: file link ‘pso’ in package ‘pso’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaA44jK/R.INSTALL648264b93bf0/GPareto/man/fastfun-class.Rd:48: file link ‘simulate’ in package ‘DiceKriging’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaA44jK/R.INSTALL648264b93bf0/GPareto/man/integration_design_optim.Rd:43: file link ‘KrigInv’ in package ‘KrigInv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaA44jK/R.INSTALL648264b93bf0/GPareto/man/plotGPareto.Rd:59: file link ‘simulate’ in package ‘DiceKriging’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaA44jK/R.INSTALL648264b93bf0/GPareto/man/plotSymDifRNP.Rd:18: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaA44jK/R.INSTALL648264b93bf0/GPareto/man/plot_uncertainty.Rd:40: file link ‘KrigInv’ in package ‘KrigInv’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GPareto.Rcheck/00install.out’ for details.
Random.Start: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
.r1: no visible global function definition for ‘cor’
.r2: no visible global function definition for ‘cor’
rgp: no visible global function definition for ‘runif’
rgp: no visible global function definition for ‘rexp’
Undefined global functions or variables:
  cor rexp runif
Consider adding
  importFrom("stats", "cor", "rexp", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0QtlDK/R.INSTALL781637c07ee6/gplots/man/reorder.Rd:56: file link ‘reorder’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gplots.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘geneA_GPprofile.pdf’ ‘geneA_abstr.png’ ‘geneA_gene.png’
  ‘geneA_reltr.png’ ‘geneB_abstr.png’ ‘geneB_gene.png’
  ‘geneB_reltr.png’ ‘geneC_abstr.png’ ‘geneC_gene.png’
  ‘geneC_reltr.png’ ‘testdb.sqlite’
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/cpt-update.Rd:52: file link ‘propagate’ in package ‘gRbase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/cpt-update.Rd:53: file link ‘triangulate’ in package ‘gRbase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/cpt-update.Rd:53: file link ‘rip’ in package ‘gRbase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/cpt-update.Rd:54: file link ‘junctionTree’ in package ‘gRbase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/cptable.Rd:104: file link ‘parray’ in package ‘gRbase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/grain_compile.Rd:51: file link ‘propagate’ in package ‘gRbase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/grain_compile.Rd:53: file link ‘triangulate’ in package ‘gRbase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/grain_compile.Rd:53: file link ‘rip’ in package ‘gRbase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/grain_compile.Rd:54: file link ‘junctionTree’ in package ‘gRbase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmph4yeq3/R.INSTALL2b487568a31e/gRain/man/grain_propagate.Rd:68: file link ‘compile’ in package ‘gRbase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gRain.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6bTLEg/R.INSTALL7a8a1ae851f/GRANBase/man/deltaDF.Rd:24: file link ‘anti_join’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GRANBase.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘mgcv’ ‘rgl’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
KL: no visible global function definition for ‘complete.cases’
MergeNodes: no visible global function definition for ‘colors’
cross.validate: no visible global function definition for ‘runif’
fit.APFA: no visible global function definition for ‘complete.cases’
fit.APFA: no visible global function definition for ‘aggregate’
select.beagle: no visible global function definition for ‘write.table’
select.beagle: no visible global function definition for ‘aggregate’
select.beagle: no visible global function definition for ‘colors’
simulateAPFA: no visible global function definition for ‘runif’
st: no visible global function definition for ‘colors’
Undefined global functions or variables:
  aggregate colors complete.cases runif write.table
Consider adding
  importFrom("grDevices", "colors")
  importFrom("stats", "aggregate", "complete.cases", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmrokNb/R.INSTALL7bb97d166845/graphhopper/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/graphhopper.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpB10t4J/R.INSTALL54633926d9dc/graphTweets/man/gt_collect.Rd:13: file link ‘tibble’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpB10t4J/R.INSTALL54633926d9dc/graphTweets/man/reexports.Rd:15: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpB10t4J/R.INSTALL54633926d9dc/graphTweets/man/reexports.Rd:17: file link ‘%<-%’ in package ‘zeallot’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/graphTweets.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘Matrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GrassmannOptim: no visible global function definition for ‘rnorm’
GrassmannOptim: no visible global function definition for ‘runif’
GrassmannOptim : <anonymous>: no visible global function definition for
  ‘expm’
GrassmannOptim : <anonymous>: no visible global function definition for
  ‘Matrix’
Undefined global functions or variables:
  Matrix expm rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following significant warnings:
  Rd warning: /tmp/Rtmpc4o8LO/R.INSTALL6bcb4aed4287/greport/man/survReport.Rd:44: file link ‘survplot.npsurv’ in package ‘rms’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpc4o8LO/R.INSTALL6bcb4aed4287/greport/man/survReport.Rd:48: file link ‘survplot.npsurv’ in package ‘rms’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/greport.Rcheck/00install.out’ for details.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
bestcut2: no visible global function definition for ‘pchisq’
cov.func: no visible global function definition for ‘rbinom’
cov.func: no visible global function definition for ‘cov’
cov.func: no visible global function definition for ‘pnorm’
cox.summary: no visible global function definition for ‘predict’
em.func: no visible global function definition for ‘quantile’
genSurvData: no visible global function definition for ‘rweibull’
greyzone.func: no visible global function definition for ‘points’
greyzone.func: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov pchisq pnorm points predict quantile rbinom rweibull
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "cov", "pchisq", "pnorm", "predict", "quantile",
             "rbinom", "rweibull")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
grid.graph: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/RtmpV0CYbY/R.INSTALL7ca4109d3ea6/gridSVG/man/gridsvg.Rd:55: file link ‘dev.off’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gridSVG.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpE6nSbc/R.INSTALL60c297746e6/GROAN/man/phenoRegressor.SVR.Rd:68: file link ‘best.svm’ in package ‘e1071’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE6nSbc/R.INSTALL60c297746e6/GROAN/man/phenoRegressor.SVR.Rd:172: file link ‘tune.svm’ in package ‘e1071’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE6nSbc/R.INSTALL60c297746e6/GROAN/man/phenoRegressor.SVR.Rd:172: file link ‘best.svm’ in package ‘e1071’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GROAN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZzKRRj/R.INSTALL48be1736929/groc/man/covRob-robust.Rd:42: file link ‘covMest’ in package ‘rrcov’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/groc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4pJqTh/R.INSTALL490d8a25e9e/gromovlab/man/gromovdist.Rd:76: file link ‘igraph-package’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gromovlab.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCYvCCw/R.INSTALL37a1c23b116/growth/man/elliptic.Rd:58: file link ‘dskewlaplace’ in package ‘rmutil’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCYvCCw/R.INSTALL37a1c23b116/growth/man/elliptic.Rd:464: file link ‘dpowexp’ in package ‘rmutil’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCYvCCw/R.INSTALL37a1c23b116/growth/man/elliptic.Rd:465: file link ‘dskewlaplace’ in package ‘rmutil’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/growth.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpB0t6lb/R.INSTALL1db4781a78c4/grpreg/man/auc.Rd:29: file link ‘survConcordance’ in package ‘survival’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/grpreg.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
PCgamma : <anonymous>: no visible global function definition for
  ‘prcomp’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘glm’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘update’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘pchisq’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘lm’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘anova’
PCgamma: no visible global function definition for ‘qgamma’
PCgamma: no visible global function definition for ‘pgamma’
RNAgamma : rnafunc: no visible global function definition for
  ‘model.matrix’
RNAgamma : rnafunc: no visible global function definition for
  ‘as.formula’
RNAgamma: no visible global function definition for ‘qgamma’
RNAgamma: no visible global function definition for ‘pgamma’
STTtoShapeParameter : f: no visible global function definition for
  ‘qgamma’
STTtoShapeParameter: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  anova as.formula glm lm model.matrix optimize pchisq pgamma prcomp
  qgamma update
Consider adding
  importFrom("stats", "anova", "as.formula", "glm", "lm", "model.matrix",
             "optimize", "pchisq", "pgamma", "prcomp", "qgamma",
             "update")
to your NAMESPACE file.
.gsa.assignGATKTableToEnvironment: no visible global function
  definition for ‘type.convert’
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
'library' or 'require' call to ‘impute’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GSA: no visible global function definition for ‘impute.knn’
Undefined global functions or variables:
  impute.knn
Rd file 'GSA.Rd':
  \usage lines wider than 90 characters:
     method=c("maxmean","mean","absmean"), resp.type=c("Quantitative","Two class unpaired","Survival","Multiclass", "Two class paired", "tCo ... [TRUNCATED]
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)
     #   GSA.obj<-GSA(x,y, genenames=genenames, genesets=geneset.obj$genesets,  resp.type="Two class unpaired", nperms=100)

Rd file 'GSA.func.Rd':
  \usage lines wider than 90 characters:
     s0 = NULL, s0.perc = NULL, minsize = 15, maxsize= 500, restand = TRUE, restand.basis=c("catalog","data")) 
  \examples lines wider than 100 characters:
     #   GSA.func.obj<-GSA.func(x,y, genenames=genenames, genesets=geneset.obj$genesets,  resp.type="Two class unpaired")

Rd file 'GSA.genescores.Rd':
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)

Rd file 'GSA.listsets.Rd':
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)

Rd file 'GSA.plot.Rd':
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)

These lines will be truncated in the PDF manual.
binding: no visible global function definition for ‘rnorm’
binding: no visible binding for global variable ‘var’
binding: no visible global function definition for ‘uniroot’
equivonly: no visible global function definition for ‘rnorm’
equivonly: no visible binding for global variable ‘var’
equivonly: no visible global function definition for ‘uniroot’
figureE: no visible global function definition for ‘rgb’
figureEF: no visible global function definition for ‘rgb’
nfix : f: no visible global function definition for ‘pnorm’
nfix : f: no visible global function definition for ‘qnorm’
nfix: no visible global function definition for ‘uniroot’
nonbinding: no visible global function definition for ‘rnorm’
nonbinding: no visible binding for global variable ‘var’
nonbinding: no visible global function definition for ‘uniroot’
oc: no visible global function definition for ‘rnorm’
oc: no visible global function definition for ‘var’
Undefined global functions or variables:
  pnorm qnorm rgb rnorm uniroot var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "uniroot", "var")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Introduction.Rmd’
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUkHsDR/R.INSTALL4a5f1107ee58/gsubfn/man/transform2.Rd:30: file link ‘within’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gsubfn.Rcheck/00install.out’ for details.
Rd file 'gtcorr.matrix.Rd':
  \usage lines wider than 90 characters:
     gtcorr.matrix(r, c, m = 1, p, sigma = 0, se = 1, sp = 1, r.prime, c.prime, arrangement = c("rectangular", "diagonal", "random"), model  ... [TRUNCATED]

Rd file 'gtcorr.matrix.user.Rd':
  \usage lines wider than 90 characters:
     gtcorr.matrix.user(clusters, p, sigma=0, se=1, sp=1, model = c("beta-binomial", "Madsen", "Morel-Neerchal"))

These lines will be truncated in the PDF manual.
gte: no visible global function definition for ‘model.extract’
gte: no visible global function definition for ‘model.matrix’
gte: no visible binding for global variable ‘sd’
gte: no visible global function definition for ‘dnorm’
plot.gte: no visible global function definition for ‘par’
plot.gte: no visible global function definition for ‘polygon’
plot.gte: no visible global function definition for ‘gray’
plot.gte: no visible global function definition for ‘lines’
plot.gte: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dnorm gray legend lines model.extract model.matrix par polygon sd
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "legend", "lines", "par", "polygon")
  importFrom("stats", "dnorm", "model.extract", "model.matrix", "sd")
to your NAMESPACE file.
Found the following possibly unsafe calls:
File ‘gtools/R/unByteCode.R’:
  unlockBinding(name, env = env)
Found the following significant warnings:
  Rd warning: /tmp/RtmpV6H43s/R.INSTALL1007209d9967/gt/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gt.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpC98dYw/R.INSTALL68fd74f7b003/Guerry/man/gfrance.Rd:20: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpC98dYw/R.INSTALL68fd74f7b003/Guerry/man/gfrance85.Rd:21: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Guerry.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘GuessCompx.Rmd’
Package vignette with placeholder title ‘Vignette Title’:
  ‘GUILDS.Rmd’
Found the following files/directories:
  ‘RRprof.out’
Found the following significant warnings:
  Rd warning: /tmp/RtmpMzwsi6/R.INSTALL674269f3733/gunit/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gunit.Rcheck/00install.out’ for details.
simCCCent : <anonymous>: no visible global function definition for
  ‘simulate.formula’
Undefined global functions or variables:
  simulate.formula
Non-standard file/directory found at top level:
  ‘TITEL’
calculate.threshold: no visible global function definition for ‘pchisq’
gwerAM: no visible global function definition for ‘rnorm’
gwerAM: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  pchisq quantile rnorm
Consider adding
  importFrom("stats", "pchisq", "quantile", "rnorm")
to your NAMESPACE file.
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘GWG/R/obese.R’:
  data(OB_above)
  data(OB_below)
File ‘GWG/R/overweight.R’:
  data(OW_above)
  data(OW_below)
See section ‘Good practice’ in ‘?data’.
'library' or 'require' calls to packages already attached by Depends:
  ‘fields’ ‘lars’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gwl.beta: no visible global function definition for ‘lars’
gwl.cv.err: no visible global function definition for ‘lars’
gwl.est: no visible global function definition for ‘lm’
gwr.bw.est: no visible global function definition for ‘lm’
gwr.est: no visible global function definition for ‘lm’
gwr.rsquare: no visible global function definition for ‘cor’
gwrr.est: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cor lars lm
Consider adding
  importFrom("stats", "cor", "lm")
to your NAMESPACE file.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
GxMestimator: no visible global function definition for ‘na.omit’
initialization_chol: no visible global function definition for ‘cov’
initialization_corr: no visible global function definition for ‘cov’
initialization_nlmain: no visible global function definition for
  ‘lm.fit’
print.summaryGxMclass: no visible global function definition for
  ‘pnorm’
print.summaryGxMclass: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  cov lm.fit na.omit pnorm printCoefmat
Consider adding
  importFrom("stats", "cov", "lm.fit", "na.omit", "pnorm",
             "printCoefmat")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpaXv3qR/R.INSTALL5043123e195e/h2o4gpu/man/reexports.Rd:22: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaXv3qR/R.INSTALL5043123e195e/h2o4gpu/man/reexports.Rd:24: file link ‘use_condaenv’ in package ‘reticulate’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaXv3qR/R.INSTALL5043123e195e/h2o4gpu/man/reexports.Rd:24: file link ‘use_virtualenv’ in package ‘reticulate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/h2o4gpu.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
hf.bt: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpemnXYO/R.INSTALL867728806ef/hackeRnews/man/to_datetime_origin.Rd:25: file link ‘as.POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hackeRnews.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpyfXryz/R.INSTALL9ae9e33d36/hacksaw/man/multi-assign.Rd:13: file link ‘%<-%’ in package ‘zeallot’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpyfXryz/R.INSTALL9ae9e33d36/hacksaw/man/multi-assign.Rd:15: file link ‘%->%’ in package ‘zeallot’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpyfXryz/R.INSTALL9ae9e33d36/hacksaw/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hacksaw.Rcheck/00install.out’ for details.
hsTableReader: no visible global function definition for ‘object.size’
hsWriteTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  object.size write.table
Consider adding
  importFrom("utils", "object.size", "write.table")
to your NAMESPACE file.
Rd file 'hsKeyValReader.Rd':
  \usage lines wider than 90 characters:
     hsKeyValReader(file = "", chunkSize = -1, skip = 0, sep = "\t",FUN = function(k, v) cat(paste(k, v, sep = ": "), sep = "\n"))

Rd file 'hsLineReader.Rd':
  \examples lines wider than 100 characters:
       str <- "Hello here are some\nlines of text\nto read in, chunkSize\nlines at a time.\nHow interesting.\nhuh?"

Rd file 'hsTableReader.Rd':
  \examples lines wider than 100 characters:
       str <- "key1\t3.9\nkey1\t8.9\nkey1\t1.2\nkey1\t3.9\nkey1\t8.9\nkey1\t1.2\nkey2\t9.9\nkey2\t10.1\nkey3\t1.0\nkey3\t3.4\nkey4\t9.4\n"
       hsTableReader(con,cols,chunkSize=5,FUN=reducerFullKeys,ignoreKey=FALSE,singleKey=FALSE,PFUN=reducerPartialKey)
       hsTableReader(con,cols,chunkSize=6,FUN=reducerKeyAtOnce,ignoreKey=FALSE,singleKey=TRUE,PFUN=reducerPartialKey)
       hsTableReader(con,cols,chunkSize=6,FUN=reducerManyCompleteKeys,ignoreKey=FALSE,singleKey=FALSE,PFUN=reducerPartialKey)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘datafile.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpyyiigF/R.INSTALLad26e19aca9/hagis/man/autoplot.hagis.complexities.Rd:26: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpyyiigF/R.INSTALLad26e19aca9/hagis/man/autoplot.hagis.gene.summary.Rd:26: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hagis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZzTJx0/R.INSTALLb0c78b2d596/haldensify/man/fit_haldensify.Rd:32: file link ‘cut_number’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZzTJx0/R.INSTALLb0c78b2d596/haldensify/man/format_long_hazards.Rd:32: file link ‘cut_number’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZzTJx0/R.INSTALLb0c78b2d596/haldensify/man/format_long_hazards.Rd:40: file link ‘cut.default’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZzTJx0/R.INSTALLb0c78b2d596/haldensify/man/format_long_hazards.Rd:41: file link ‘cut_number’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZzTJx0/R.INSTALLb0c78b2d596/haldensify/man/haldensify.Rd:33: file link ‘cut_number’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/haldensify.Rcheck/00install.out’ for details.
EMvar: no visible global function definition for ‘model.matrix’
RecodeHaplos: no visible global function definition for ‘na.omit’
RecodeHaplos: no visible global function definition for ‘tail’
anova.hapassoc: no visible global function definition for ‘pchisq’
handleMissings: no visible global function definition for ‘na.omit’
hapassoc: no visible global function definition for ‘binomial’
hapassoc: no visible global function definition for ‘formula’
hapassoc: no visible global function definition for ‘glm’
hapassoc : <anonymous>: no visible global function definition for ‘glm’
hapassoc: no visible global function definition for ‘model.frame’
hapassoc: no visible global function definition for ‘model.matrix’
hapassoc: no visible binding for global variable ‘contrasts’
hapassoc: no visible global function definition for ‘glm.control’
hapassoc : <anonymous>: no visible global function definition for
  ‘glm.control’
probY: no visible global function definition for ‘dbinom’
probY: no visible global function definition for ‘dpois’
probY: no visible global function definition for ‘dnorm’
probY: no visible global function definition for ‘dgamma’
summary.hapassoc: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  binomial contrasts dbinom dgamma dnorm dpois formula glm glm.control
  model.frame model.matrix na.omit pchisq tail
Consider adding
  importFrom("stats", "binomial", "contrasts", "dbinom", "dgamma",
             "dnorm", "dpois", "formula", "glm", "glm.control",
             "model.frame", "model.matrix", "na.omit", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
allele.marq: no visible global function definition for ‘na.omit’
depart.LDL: no visible global function definition for ‘aov’
freq.all: no visible global function definition for ‘na.omit’
hapim.LD.add: no visible global function definition for ‘optim’
hapim.LDL.add: no visible global function definition for ‘optim’
obj.haplomax.HS.add: no visible global function definition for ‘aov’
obj.haplomax.add: no visible global function definition for ‘aov’
vrais.LD.add: no visible global function definition for ‘dnorm’
vrais.LDL.add.pere: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  aov dnorm na.omit optim
Consider adding
  importFrom("stats", "aov", "dnorm", "na.omit", "optim")
to your NAMESPACE file.
AssignQTL : <anonymous>: no visible global function definition for
  ‘rgamma’
AssignSingleQTL: no visible global function definition for ‘rgamma’
ListQTL : <anonymous>: no visible global function definition for
  ‘rgamma’
SampleBaseHaplotype: no visible global function definition for ‘runif’
SampleHaplotype: no visible global function definition for ‘rpois’
SampleHaplotype: no visible global function definition for ‘runif’
SampleHaplotype: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom rgamma rpois runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rpois", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmplT6UIf/R.INSTALLc671ea71519/harrypotter/man/scale_hp.Rd:97: file link ‘scale_fill_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplT6UIf/R.INSTALLc671ea71519/harrypotter/man/scale_hp.Rd:97: file link ‘scale_color_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/harrypotter.Rcheck/00install.out’ for details.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘dev’
GNU make is a SystemRequirements.
extract_hazus_functions: no visible global function definition for
  ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
GNU make is a SystemRequirements.
detect.movement: no visible global function definition for ‘t.test’
generate.random.conf: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm t.test
Consider adding
  importFrom("stats", "rnorm", "t.test")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘examples’
Rd file 'fSAE.Rd':
  \examples lines wider than 100 characters:
     est.global <- fSAE(y0 ~ x + area2, data=d$sam, area=NULL, popdata=colSums(d$Xpop), method="synthetic")

Rd file 'plot.sae.Rd':
  \usage lines wider than 90 characters:
         main = switch(type, coef = "coefficients", raneff = "random effects", "SAE estimates"),

Rd file 'uweights.Rd':
  \examples lines wider than 100 characters:
     sae <- fSAE(y0 ~ x + area2, data=d$sam, area="area", popdata=d$Xpop, method="hybrid", keep.data=TRUE)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
PoincarePlot: no visible global function definition for ‘lines’
PoincarePlot: no visible global function definition for ‘lowess’
hctest: no visible global function definition for ‘cor.test’
rdplot: no visible global function definition for ‘lines’
rdplot: no visible global function definition for ‘lowess’
rdplot: no visible global function definition for ‘rgb’
simer: no visible global function definition for ‘runif’
simer: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cor.test lines lowess rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp85LLoa/R.INSTALLda34bf896b6/HDclassif/man/hdda.Rd:28: file link ‘getHDclassif.show’ in package ‘HDclassif’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp85LLoa/R.INSTALLda34bf896b6/HDclassif/man/hddc.Rd:40: file link ‘getHDclassif.show’ in package ‘HDclassif’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp85LLoa/R.INSTALLda34bf896b6/HDclassif/man/hddc.Rd:50: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/HDclassif.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZbTy40/R.INSTALLdd6143d8734/hdd/man/cash-.hdd.Rd:21: file link ‘getHdd_extract.cap’ in package ‘hdd’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZbTy40/R.INSTALLdd6143d8734/hdd/man/readfst.Rd:21: file link ‘read_fst’ in package ‘fst’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZbTy40/R.INSTALLdd6143d8734/hdd/man/txt2hdd.Rd:41: file link ‘cols_only’ in package ‘readr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hdd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpcq8gd1/R.INSTALL7405c77286a/HDMD/man/HDMD-package.Rd:44: file link ‘psych-package’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/HDMD.Rcheck/00install.out’ for details.
Promax.only: no visible global function definition for ‘lm.fit’
factor.pa.ginv: no visible binding for global variable ‘median’
factor.pa.ginv: no visible global function definition for ‘cor’
factor.pa.ginv: no visible global function definition for ‘varimax’
factor.pa.ginv: no visible global function definition for ‘pchisq’
pairwise.mahalanobis: no visible global function definition for ‘cor’
pairwise.mahalanobis: no visible global function definition for
  ‘mahalanobis’
Undefined global functions or variables:
  cor lm.fit mahalanobis median pchisq varimax
Consider adding
  importFrom("stats", "cor", "lm.fit", "mahalanobis", "median", "pchisq",
             "varimax")
to your NAMESPACE file.
Rd file 'AminoAcids.Rd':
  \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
       Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
       legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

Rd file 'FactorTransform.Rd':
  \usage lines wider than 90 characters:
     FactorTransform(Source, Search = AminoAcids, Replace = AAMetric.Atchley, Factor = 1, bycol = TRUE, SeqName = NULL,  alignment=FALSE, fi ... [TRUNCATED]

Rd file 'HDMD-package.Rd':
  \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
     plot(-1*AA54_lda_RawMetric1Centered[,1], -1*AA54_lda_RawMetric1Centered[,2], pch = grouping, xlab="Canonical Variate 1", ylab="Canonica ... [TRUNCATED]

Rd file 'NMI.Rd':
  \usage lines wider than 90 characters:
     NMI(Hx, Hy, Hxy, type = c("NULL", "marginal", "joint", "min.marginal", "max.marginal", "min.conditional", "max.conditional"))

Rd file 'factor.pa.ginv.Rd':
  \usage lines wider than 90 characters:
     factor.pa.ginv(r, nfactors = 1, residuals = FALSE, prerotate = FALSE, rotate = "varimax", m = 4, n.obs = NA, scores = c("none", "regres ... [TRUNCATED]
  \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
       Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
       legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYLAxui/R.INSTALLe6b59e76d14/hdnom/man/fit_mcp.Rd:18: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYLAxui/R.INSTALLe6b59e76d14/hdnom/man/fit_mnet.Rd:18: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYLAxui/R.INSTALLe6b59e76d14/hdnom/man/fit_mnet.Rd:20: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYLAxui/R.INSTALLe6b59e76d14/hdnom/man/fit_scad.Rd:18: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYLAxui/R.INSTALLe6b59e76d14/hdnom/man/fit_snet.Rd:18: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYLAxui/R.INSTALLe6b59e76d14/hdnom/man/fit_snet.Rd:20: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hdnom.Rcheck/00install.out’ for details.
coef.HDtweedie: no visible global function definition for ‘rbind2’
coef.cv.HDtweedie: no visible global function definition for ‘coef’
cv.tweediegrppath: no visible global function definition for ‘predict’
cv.tweediegrppath: no visible binding for global variable
  ‘weighted.mean’
cvcompute: no visible binding for global variable ‘weighted.mean’
error.bars: no visible global function definition for ‘segments’
lambda.interp: no visible global function definition for ‘approx’
plot.HDtweedie: no visible global function definition for ‘par’
plot.HDtweedie: no visible binding for global variable ‘plot.default’
plot.HDtweedie: no visible global function definition for ‘gray.colors’
plot.HDtweedie: no visible global function definition for ‘abline’
plot.cv.HDtweedie: no visible global function definition for ‘points’
plot.cv.HDtweedie: no visible global function definition for ‘axis’
plot.cv.HDtweedie: no visible global function definition for ‘abline’
predict.HDtweedie: no visible global function definition for ‘rbind2’
predict.HDtweedie: no visible global function definition for ‘cbind2’
predict.cv.HDtweedie: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  abline approx axis cbind2 coef gray.colors par plot.default points
  predict rbind2 segments weighted.mean
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "abline", "axis", "par", "plot.default",
             "points", "segments")
  importFrom("methods", "cbind2", "rbind2")
  importFrom("stats", "approx", "coef", "predict", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2nYxYv/R.INSTALLab63f528975/healthforum/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/healthforum.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpun5zdZ/R.INSTALL35f97cc6ee7c/heatmap3/man/heatmap3.Rd:105: file link ‘as.dendrogram’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/heatmap3.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpICTaFS/R.INSTALL3d757650303/heatmaply/man/heatmaply.Rd:185: file link ‘viridis’ in package ‘viridis’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpICTaFS/R.INSTALL3d757650303/heatmaply/man/heatmaply.Rd:186: file link ‘scale_fill_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpICTaFS/R.INSTALL3d757650303/heatmaply/man/heatmaply.Rd:319: file link ‘scale_fill_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpICTaFS/R.INSTALL3d757650303/heatmaply/man/heatmaply.Rd:384: file link ‘has_edgePar’ in package ‘dendextend’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/heatmaply.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZEMQq1/R.INSTALL372a7c6ec526/heddlr/man/export_template.Rd:19: file link ‘stdout’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/heddlr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘synbreed’
Package suggested but not available for checking: ‘glmmADMB’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/adjacent.Rd:35: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/adjacent.Rd:19: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/adjacent.Rd:43: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/assemble.Rd:48: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/enlarge.Rd:34: file link ‘gBuffer’ in package ‘rgeos’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/enlarge.Rd:18: file link ‘gBuffer’ in package ‘rgeos’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/plot.hero.Rd:33: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/plot.hero_bspline.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/prepare.matrix.Rd:40: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpsjc1cZ/R.INSTALL55d965f9af60/hero/man/spdiffpen.Rd:25: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hero.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpcYynnl/R.INSTALL6e4d25d33dcd/heuristicsmineR/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/heuristicsmineR.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘hexbin-classes.Rmd’
HubNetwork: no visible global function definition for ‘rbinom’
HubNetwork: no visible global function definition for ‘runif’
HubNetwork: no visible global function definition for ‘cov2cor’
binaryMCMC: no visible global function definition for ‘rbinom’
image.hbn: no visible global function definition for ‘col2rgb’
image.hbn: no visible global function definition for ‘rgb’
image.hbn: no visible global function definition for ‘dev.new’
image.hbn: no visible global function definition for ‘par’
image.hbn: no visible global function definition for ‘image’
image.hcov: no visible global function definition for ‘col2rgb’
image.hcov: no visible global function definition for ‘rgb’
image.hcov: no visible global function definition for ‘dev.new’
image.hcov: no visible global function definition for ‘par’
image.hcov: no visible global function definition for ‘image’
image.hglasso: no visible global function definition for ‘col2rgb’
image.hglasso: no visible global function definition for ‘rgb’
image.hglasso: no visible global function definition for ‘dev.new’
image.hglasso: no visible global function definition for ‘par’
image.hglasso: no visible global function definition for ‘image’
plot.hbn: no visible global function definition for ‘rgb’
plot.hcov: no visible global function definition for ‘rgb’
plot.hglasso: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpD2FOFR/R.INSTALL1210c1667ee/hgutils/man/compound-pipe.Rd:10: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpD2FOFR/R.INSTALL1210c1667ee/hgutils/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hgutils.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘HHG.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5OlAXT/Rbuild3dc162c6a94b/hhh4contacts/man/noroBE.Rd:37: file link ‘gUnaryUnion’ in package ‘rgeos’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hhh4contacts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmprTYE4m/R.INSTALL643a170a96be/hierarchicalSets/man/plot.HierarchicalSet.Rd:21: file link ‘trans’ in package ‘scales’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hierarchicalSets.Rcheck/00install.out’ for details.
':::' call which should be '::': ‘ggplot2:::guide_axis’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
banded: no visible global function definition for ‘toeplitz’
gpband: no visible global function definition for ‘toeplitz’
hierband.cv: no visible global function definition for ‘cov’
hierband.cv: no visible binding for global variable ‘sd’
subdiag.thresh: no visible global function definition for ‘uniroot’
subdiag.thresh: no visible global function definition for ‘toeplitz’
Undefined global functions or variables:
  cov sd toeplitz uniroot
Consider adding
  importFrom("stats", "cov", "sd", "toeplitz", "uniroot")
to your NAMESPACE file.
booties: no visible binding for global variable ‘sd’
booties: no visible binding for global variable ‘quantile’
hierDiversity: no visible global function definition for
  ‘txtProgressBar’
hierDiversity: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Unknown package ‘vegetarian’ in Rd xrefs
Package suggested but not available for checking: ‘XMLRPC’
calcPower: no visible global function definition for ‘pchisq’
calcPower: no visible global function definition for ‘qchisq’
delta2 : K1: no visible global function definition for ‘qnorm’
delta2: no visible global function definition for ‘qnorm’
delta2: no visible global function definition for ‘pnorm’
delta2: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm")
to your NAMESPACE file.
compute.contrasts: no visible binding for global variable ‘sd’
compute.contrasts: no visible global function definition for ‘cor’
compute.contrasts: no visible global function definition for ‘sd’
plot.hiertest: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cor legend sd
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘nnet’ ‘stats’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘nnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'HItest3.Rd':
  \examples lines wider than 100 characters:
                                                     # individuals will have nonzero contributions from each of the

Rd file 'spatial.AD.Rd':
  \examples lines wider than 100 characters:
     # simulate secondary contact by sorting aling the x dimension and assigning parental genotypes on each side of the centerline:
     # selection, inlcuding heterozygote disadvantage at locus 2 and a DM incompatibility between 3 and 4:
     G10 <- spatial.AD(minX,minY,maxX,maxY,XY,Genotypes,beta,sel,mid,h,DM,sigmac,R,M,gens=10,immigrants=TRUE)

Rd file 'spatial.HZ.Rd':
  \examples lines wider than 100 characters:
     # simulate secondary contact by sorting aling the x dimension and assigning parental genotypes on each side of the centerline:
     # selection, inlcuding heterozygote disadvantage at locus 2 and a DM incompatibility between 3 and 4:
     G10 <- spatial.HZ(minX,minY,maxX,maxY,XY,Genotypes,beta,sel,mid,h,DM,sigmad,sigmac,sigmam,R,M,gens=10,immigrants=TRUE)

Rd file 'thirdclass.Rd':
  \examples lines wider than 100 characters:
                                                     # individuals will have nonzero contributions from each of the 

These lines will be truncated in the PDF manual.
CLX.sim.Covtest: no visible global function definition for ‘cov’
CLX.sim.equalcov: no visible global function definition for ‘cov’
CLX.sim.unequalcov: no visible global function definition for ‘cov’
CLX.test.equalcov: no visible global function definition for ‘cov’
CLX.test.unequalcov: no visible global function definition for ‘cov’
ChenQin.sim: no visible global function definition for ‘pnorm’
ChenQin.test: no visible global function definition for ‘pnorm’
GCT.sim: no visible binding for global variable ‘var’
GCT.sim: no visible global function definition for ‘acf’
GCT.sim: no visible global function definition for ‘pnorm’
GCT.test: no visible binding for global variable ‘var’
GCT.test: no visible global function definition for ‘acf’
GCT.test: no visible global function definition for ‘pnorm’
GCT.test.missing: no visible binding for global variable ‘var’
GCT.test.missing: no visible global function definition for ‘acf’
GCT.test.missing: no visible global function definition for ‘pnorm’
SK.sim: no visible global function definition for ‘cov’
SK.sim: no visible global function definition for ‘pnorm’
SK.test: no visible global function definition for ‘cov’
SK.test: no visible global function definition for ‘pnorm’
build2popData : <anonymous>: no visible global function definition for
  ‘rnorm’
build2popData: no visible global function definition for ‘arima.sim’
build2popData_muYafunction : <anonymous>: no visible global function
  definition for ‘rnorm’
build2popData_muYafunction: no visible global function definition for
  ‘arima.sim’
innovate: no visible binding for global variable ‘rnorm’
rdblepareto: no visible global function definition for ‘runif’
rgammashift: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  acf arima.sim cov pnorm rgamma rnorm runif var
Consider adding
  importFrom("stats", "acf", "arima.sim", "cov", "pnorm", "rgamma",
             "rnorm", "runif", "var")
to your NAMESPACE file.
BenjaminiHochberg: no visible global function definition for ‘p.adjust’
CaoKosorok : CKfunc: no visible global function definition for ‘pnorm’
CaoKosorok : <anonymous>: no visible global function definition for
  ‘pnorm’
StoreyTibshirani: no visible global function definition for
  ‘smooth.spline’
plotI_Lines: no visible global function definition for ‘par’
plotI_Lines: no visible global function definition for ‘lines’
plotI_Lines: no visible global function definition for ‘legend’
plotI_Points: no visible global function definition for ‘points’
plotI_Points: no visible global function definition for ‘legend’
tStatistic : <anonymous>: no visible global function definition for
  ‘t.test’
venn2: no visible global function definition for ‘plot.new’
venn3: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  legend lines p.adjust par plot.new pnorm points smooth.spline t.test
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot.new", "points")
  importFrom("stats", "p.adjust", "pnorm", "smooth.spline", "t.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
occupancy: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
data_simu: no visible global function definition for ‘runif’
data_simu: no visible global function definition for ‘rbinom’
data_simu: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rbinom rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
overlay.sim: no visible global function definition for ‘points’
plotDistr: no visible global function definition for ‘dev.hold’
plotDistr: no visible global function definition for ‘dev.flush’
plotDistr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  dev.flush dev.hold points segments
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold")
  importFrom("graphics", "points", "segments")
to your NAMESPACE file.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘hiPOD/R/predictPoolNCP.R’:
  data(ncp.pool.pred)
See section ‘Good practice’ in ‘?data’.
Found the following files/directories:
  ‘hiPOD_examples’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8mLfG0/R.INSTALLbfa5c8cf1ce/hipread/man/callback.Rd:102: file link ‘ChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8mLfG0/R.INSTALLbfa5c8cf1ce/hipread/man/callback.Rd:140: file link ‘ChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8mLfG0/R.INSTALLbfa5c8cf1ce/hipread/man/callback.Rd:140: file link ‘HipChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8mLfG0/R.INSTALLbfa5c8cf1ce/hipread/man/callback.Rd:205: file link ‘ChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8mLfG0/R.INSTALLbfa5c8cf1ce/hipread/man/callback.Rd:205: file link ‘HipChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8mLfG0/R.INSTALLbfa5c8cf1ce/hipread/man/callback.Rd:279: file link ‘ChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8mLfG0/R.INSTALLbfa5c8cf1ce/hipread/man/callback.Rd:279: file link ‘HipChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8mLfG0/R.INSTALLbfa5c8cf1ce/hipread/man/hipread_long_yield.Rd:164: file link ‘HipYield’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8mLfG0/R.INSTALLbfa5c8cf1ce/hipread/man/hipread_long_yield.Rd:208: file link ‘HipYield’ in package ‘hipread’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hipread.Rcheck/00install.out’ for details.
arms: no visible global function definition for ‘rnorm’
rballunif: no visible global function definition for ‘rnorm’
rballunif: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpjtCIcJ/R.INSTALL614d7f8c865c/HistData/man/SnowMap.Rd:153: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjtCIcJ/R.INSTALL614d7f8c865c/HistData/man/SnowMap.Rd:156: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjtCIcJ/R.INSTALL614d7f8c865c/HistData/man/SnowMap.Rd:190: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/HistData.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXyCNuj/R.INSTALL767641182b7c/HistogramTools/man/histogram-message.Rd:33: file link ‘RProtoBuf’ in package ‘RProtoBuf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXyCNuj/R.INSTALL767641182b7c/HistogramTools/man/informationloss.Rd:43: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXyCNuj/R.INSTALL767641182b7c/HistogramTools/man/message-histogram.Rd:30: file link ‘RProtoBuf’ in package ‘RProtoBuf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXyCNuj/R.INSTALL767641182b7c/HistogramTools/man/plot.Rd:49: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXyCNuj/R.INSTALL767641182b7c/HistogramTools/man/plothist.Rd:31: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXyCNuj/R.INSTALL767641182b7c/HistogramTools/man/plothist.Rd:34: file link ‘plot.histogram’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXyCNuj/R.INSTALL767641182b7c/HistogramTools/man/plothist.Rd:42: file link ‘plot.histogram’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXyCNuj/R.INSTALL767641182b7c/HistogramTools/man/quantiles.Rd:34: file link ‘wtd.quantile’ in package ‘Hmisc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/HistogramTools.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘FGN’
Found the following significant warnings:
  Rd warning: /tmp/RtmpcUNdPP/R.INSTALL776b19f07f5b/HLMdiag/man/pull_resid.lmerMod.Rd:52: file link ‘hlm_resid’ in package ‘HLMdiag’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/HLMdiag.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmDrr8F/R.INSTALLa5b29d5e29d/Hmisc/man/popower.Rd:136: file link ‘scale_fill_brewer’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmDrr8F/R.INSTALLa5b29d5e29d/Hmisc/man/rcspline.plot.Rd:131: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmDrr8F/R.INSTALLa5b29d5e29d/Hmisc/man/summaryS.Rd:24: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmDrr8F/R.INSTALLa5b29d5e29d/Hmisc/man/transcan.Rd:261: file link ‘lm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Hmisc.Rcheck/00install.out’ for details.
baumwelchcont: no visible global function definition for ‘dnorm’
hmmcontSimul: no visible global function definition for ‘rnorm’
hmmcontSimul: no visible global function definition for ‘rbinom’
plot.ContObservHMM: no visible global function definition for ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘dnorm’
statesDistributionsPlot: no visible global function definition for ‘sd’
statesDistributionsPlot: no visible global function definition for
  ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘legend’
summary.ContObservHMM: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm legend lines rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘HMM2est.image’
Malformed Description field: should contain one or more complete sentences.
dishonestCasino: no visible global function definition for ‘axis’
dishonestCasino: no visible global function definition for ‘text’
dishonestCasino: no visible global function definition for ‘rect’
dishonestCasino: no visible global function definition for ‘rgb’
dishonestCasino: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis points rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "points", "rect", "text")
to your NAMESPACE file.
Package suggested but not available for checking: ‘glmmADMB’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/cond.object.Rd:85: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/cond.rsm.Rd:135: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/marg.object.Rd:88: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/nlreg.Rd:133: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/nlreg.contours.object.Rd:18: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/nlreg.profile.objects.Rd:20: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/plot.nlreg.contours.Rd:7: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/plot.nlreg.diag.Rd:12: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/plot.nlreg.profiles.Rd:104: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2gB54l/R.INSTALL5a84231b708b/hoa/man/profile.nlreg.Rd:104: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hoa.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1nIxfu/R.INSTALL55df7bddeb70/Holidays/man/Holidays-package.Rd:12: file link ‘registerHolidays’ in package ‘TimeWarp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1nIxfu/R.INSTALL55df7bddeb70/Holidays/man/Holidays-package.Rd:29: file link ‘registerHolidays’ in package ‘TimeWarp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1nIxfu/R.INSTALL55df7bddeb70/Holidays/man/Holidays-package.Rd:29: file link ‘allHolidays’ in package ‘TimeWarp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Holidays.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpAtthDF/R.INSTALL144657646dca/homals/man/plot.homals.Rd:38: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/homals.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpF7f9S9/R.INSTALL17815308640f/homologene/man/reexports.Rd:16: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpF7f9S9/R.INSTALL17815308640f/homologene/man/reexports.Rd:16: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpF7f9S9/R.INSTALL17815308640f/homologene/man/reexports.Rd:16: file link ‘%$%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/homologene.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZuTqNi/Rbuild181a4751942f/hopit/man/hopit.Rd:40: file link ‘na.omit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZuTqNi/Rbuild181a4751942f/hopit/man/hopit.Rd:41: file link ‘na.exclude’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZuTqNi/Rbuild181a4751942f/hopit/man/hopit.Rd:42: file link ‘na.pass’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hopit.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘ALB_msk_alt.grd’ ‘ALB_msk_alt.gri’ ‘ALB_msk_alt.vrt’
hornpa: no visible global function definition for ‘rnorm’
hornpa: no visible global function definition for ‘cor’
hornpa: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cor quantile rnorm
Consider adding
  importFrom("stats", "cor", "quantile", "rnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘NUL’
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
hpbayes.plot: no visible global function definition for ‘par’
hpbayes.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘par’
postpri.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘segments’
postpri.plot: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot par points segments
Consider adding
  importFrom("graphics", "boxplot", "par", "points", "segments")
to your NAMESPACE file.
ApproxC: no visible global function definition for ‘convolve’
DMC: no visible global function definition for ‘median’
DMC: no visible global function definition for ‘ecdf’
ToSWF: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  convolve ecdf median write.table
Consider adding
  importFrom("stats", "convolve", "ecdf", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘output.swf’
bracket: no visible global function definition for ‘segments’
Undefined global functions or variables:
  segments
Consider adding
  importFrom("graphics", "segments")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpEJElvk/R.INSTALL40ff340c3259/hrbrthemes/man/gg_check.Rd:12: file link ‘dictionary’ in package ‘hunspell’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEJElvk/R.INSTALL40ff340c3259/hrbrthemes/man/theme_ipsum_es.Rd:60: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEJElvk/R.INSTALL40ff340c3259/hrbrthemes/man/theme_ipsum_ps.Rd:59: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEJElvk/R.INSTALL40ff340c3259/hrbrthemes/man/theme_ipsum_pub.Rd:60: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEJElvk/R.INSTALL40ff340c3259/hrbrthemes/man/theme_ipsum_rc.Rd:124: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEJElvk/R.INSTALL40ff340c3259/hrbrthemes/man/theme_ipsum_tw.Rd:60: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEJElvk/R.INSTALL40ff340c3259/hrbrthemes/man/theme_tinyhand.Rd:57: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hrbrthemes.Rcheck/00install.out’ for details.
hsicCCA: no visible global function definition for ‘median’
hsicCCA: no visible global function definition for ‘dist’
hsicCCAfunc: no visible global function definition for ‘rnorm’
hsicCCAfunc: no visible global function definition for ‘runif’
hsicCCAfunc: no visible global function definition for ‘optim’
ktaCCA: no visible global function definition for ‘median’
ktaCCA: no visible global function definition for ‘dist’
ktaCCAfunc: no visible global function definition for ‘rnorm’
ktaCCAfunc: no visible global function definition for ‘runif’
ktaCCAfunc: no visible global function definition for ‘optim’
Undefined global functions or variables:
  dist median optim rnorm runif
Consider adding
  importFrom("stats", "dist", "median", "optim", "rnorm", "runif")
to your NAMESPACE file.
Rd file 'hsicCCA.Rd':
  \usage lines wider than 90 characters:
     hsicCCA(x, y, M, sigmax = NULL, sigmay = NULL, numrepeat = 5, numiter = 100, reltolstop = 1e-04)

Rd file 'ktaCCA.Rd':
  \usage lines wider than 90 characters:
     ktaCCA(x, y, M, sigmax = NULL, sigmay = NULL, numrepeat = 5, numiter = 100, reltolstop = 1e-04)

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
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.
get.d: no visible global function definition for ‘dgeom’
get.d: no visible global function definition for ‘dnbinom’
get.d: no visible global function definition for ‘dpois’
get.pdf: no visible global function definition for ‘dnorm’
get.pdf: no visible global function definition for ‘dpois’
get.pdf: no visible global function definition for ‘dmvnorm’
hsmm: no visible global function definition for ‘uniroot’
hsmm.sim: no visible global function definition for ‘rbinom’
hsmm.sim: no visible global function definition for ‘rnorm’
hsmm.sim: no visible global function definition for ‘rpois’
hsmm.sim: no visible global function definition for ‘rmvnorm’
loggeom.update: no visible global function definition for ‘plogis’
rmt: no visible global function definition for ‘rt’
rmt: no visible global function definition for ‘rnorm’
rmt: no visible global function definition for ‘rchisq’
rvm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dgeom dmvnorm dnbinom dnorm dpois plogis rbinom rchisq rmvnorm rnorm
  rpois rt runif uniroot
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dnorm", "dpois", "plogis",
             "rbinom", "rchisq", "rnorm", "rpois", "rt", "runif",
             "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0U6VZo/R.INSTALL116b10784e05/HTLR/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/HTLR.Rcheck/00install.out’ for details.
BasicHTML: no visible global function definition for ‘png’
BasicHTML: no visible global function definition for ‘dev.list’
BasicHTML: no visible global function definition for ‘dev.off’
FramedHTML: no visible global function definition for ‘graphics.off’
Undefined global functions or variables:
  dev.list dev.off graphics.off png
Consider adding
  importFrom("grDevices", "dev.list", "dev.off", "graphics.off", "png")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpRq8SZ2/R.INSTALL3ecf201e5bb1/htmlwidgets/man/createWidget.Rd:25: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRq8SZ2/R.INSTALL3ecf201e5bb1/htmlwidgets/man/onStaticRenderComplete.Rd:15: file link ‘tags’ in package ‘htmltools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRq8SZ2/R.INSTALL3ecf201e5bb1/htmlwidgets/man/prependContent.Rd:15: file link ‘tags’ in package ‘htmltools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/htmlwidgets.Rcheck/00install.out’ for details.
getToHost: no visible global function definition for ‘make.socket’
getToHost: no visible global function definition for ‘write.socket’
getToHost: no visible global function definition for ‘read.socket’
getToHost: no visible global function definition for ‘close.socket’
postToHost: no visible global function definition for ‘runif’
simplePostToHost: no visible global function definition for
  ‘make.socket’
simplePostToHost: no visible global function definition for
  ‘write.socket’
simplePostToHost: no visible global function definition for
  ‘read.socket’
simplePostToHost: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket make.socket read.socket runif write.socket
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "close.socket", "make.socket", "read.socket",
             "write.socket")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘testthat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6mRq9k/R.INSTALL67e5acd47cb/humanize/man/reexports.Rd:22: file link ‘is.date’ in package ‘assertthat’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6mRq9k/R.INSTALL67e5acd47cb/humanize/man/reexports.Rd:22: file link ‘is.count’ in package ‘assertthat’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6mRq9k/R.INSTALL67e5acd47cb/humanize/man/reexports.Rd:24: file link ‘today’ in package ‘lubridate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/humanize.Rcheck/00install.out’ for details.
Calculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "points", "polygon", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: ‘hurricaneexposuredata’
Malformed Title field: should not end in a period.
HWEImportSamp: no visible global function definition for ‘dnorm’
HWEImportSamp: no visible global function definition for ‘rnorm’
HWEmodelsMLE: no visible global function definition for ‘optim’
HWEsimdat: no visible global function definition for ‘rmultinom’
LambdaOptim: no visible global function definition for ‘rnorm’
LambdaOptim : LambdaPriorChoice: no visible global function definition
  for ‘quantile’
LambdaOptim: no visible global function definition for ‘optim’
SinglefPrior: no visible global function definition for ‘rnorm’
SinglefReject: no visible global function definition for ‘runif’
TriangNormHWE: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  dnorm optim pbeta quantile rmultinom rnorm runif
Consider adding
  importFrom("stats", "dnorm", "optim", "pbeta", "quantile", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
HW.plain: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
getHwriterVersion: no visible global function definition for
  ‘sessionInfo’
hmapRowCol: no visible global function definition for ‘na.omit’
hwriteImage: no visible global function definition for ‘dev.print’
hwriteImage: no visible binding for global variable ‘png’
showExample: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL dev.print na.omit png sessionInfo
Consider adding
  importFrom("grDevices", "dev.print", "png")
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "sessionInfo")
to your NAMESPACE file.
Checking should be performed on sources prepared by ‘R CMD build’.
Package in Depends field not imported from: ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
hybridMC: no visible global function definition for ‘txtProgressBar’
hybridMC : pbFun: no visible global function definition for
  ‘setTxtProgressBar’
hybridMC: no visible global function definition for ‘mcmc’
Undefined global functions or variables:
  mcmc setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Rd file 'hybridMC.Rd':
  \usage lines wider than 90 characters:
     hybridMC(y.start, n.samp=1, logDens, dLogDens, epsilon, LFsteps, compWeights=NULL, MPwidth=1, MPweights=NULL, progress=0 ,...)

These lines will be truncated in the PDF manual.
ARPIEM2012.Lmom.sample: no visible global function definition for ‘var’
ARPIEM2012.freq: no visible binding for global variable ‘quantile’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_camp: no visible global
  function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_reg_moltiplicativo: no
  visible global function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_camp: no visible
  global function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_reg_additivo: no
  visible global function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments :
  ARPIEM2012.sim.LCV_reg_moltiplicativo.LCA_reg_additivo: no visible
  global function definition for ‘rnorm’
Undefined global functions or variables:
  quantile rnorm var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9mcdNa/R.INSTALL207e34abd840/hydroGOF/man/ggof.Rd:103: file link ‘drawTimeAxis’ in package ‘hydroTSM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9mcdNa/R.INSTALL207e34abd840/hydroGOF/man/plot2.Rd:53: file link ‘drawTimeAxis’ in package ‘hydroTSM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9mcdNa/R.INSTALL207e34abd840/hydroGOF/man/plotbands.Rd:83: file link ‘drawTimeAxis’ in package ‘hydroTSM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hydroGOF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpWGSlFh/Rbuild5732259baca3/HyperG/man/aaHyperG-package.Rd:33: file link ‘igraph.plotting’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWGSlFh/Rbuild5732259baca3/HyperG/man/aaHyperG-package.Rd:87: file link ‘igraph-package’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqptlxr/R.INSTALL145e3d1914f6/HyperG/man/clique_hypergraph.Rd:38: file link ‘max_cliques’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqptlxr/R.INSTALL145e3d1914f6/HyperG/man/degree.Rd:50: file link ‘degree.distribution’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqptlxr/R.INSTALL145e3d1914f6/HyperG/man/delete.edges.Rd:34: file link ‘delete.vertices’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqptlxr/R.INSTALL145e3d1914f6/HyperG/man/delete.edges.Rd:35: file link ‘delete.edges’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqptlxr/R.INSTALL145e3d1914f6/HyperG/man/is.connected.Rd:29: file link ‘is.connected’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqptlxr/R.INSTALL145e3d1914f6/HyperG/man/is.hypertree.Rd:39: file link ‘line_graph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqptlxr/R.INSTALL145e3d1914f6/HyperG/man/line.graph.Rd:41: file link ‘line_graph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqptlxr/R.INSTALL145e3d1914f6/HyperG/man/plot.hypergraph.Rd:52: file link ‘igraph.plotting’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/HyperG.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘R.utils’ ‘ape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
requiprobable: no visible global function definition for ‘extract’
requiprobable : make.tree: no visible global function definition for
  ‘extract’
requiprobable : make.tree: no visible global function definition for
  ‘runif’
rgenetree: no visible global function definition for ‘dbinom’
rgenetree: no visible global function definition for ‘dnbinom’
rgenetree: no visible global function definition for ‘runif’
rgenetree: no visible global function definition for ‘rbinom’
rgenetree: no visible global function definition for ‘rnbinom’
Undefined global functions or variables:
  dbinom dnbinom extract rbinom rnbinom runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "rbinom", "rnbinom", "runif")
to your NAMESPACE file.
Rd file 'requiprobable.Rd':
  \examples lines wider than 100 characters:
     for (i in 1:10) unlabeled[[i]]$tip.label<-sample(c("A1","A2","B1","B2","B3","C1","C2","C3","C4","C5"))

Rd file 'rgenetree.Rd':
  \examples lines wider than 100 characters:
     ##Now lets start with 3 genes, set the number of genes at each tip of spec and vary mu between the branches of spec 

These lines will be truncated in the PDF manual.
conint: no visible global function definition for ‘sd’
findroot: no visible global function definition for ‘integrate’
hypothesis: no visible global function definition for ‘sd’
hypothesis: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate sd
Consider adding
  importFrom("stats", "integrate", "sd")
to your NAMESPACE file.
Rd file 'conint.Rd':
  \usage lines wider than 90 characters:
     conint(TrnX = NULL, TrnY = NULL, m, n1, n2, s1, s2, side = "both", alpha = 0.95, method = "n")

Rd file 'hypothesis-package.Rd':
  \examples lines wider than 100 characters:
     hypothesis(TrnX=c(3,4,5),TrnY=c(4,5,6),m,u0=4,3,3,s1=NULL,s2=NULL,sigma1=NULL,sigma2=NULL,alpha=0.05,method="n",H0="u=u0",p)

Rd file 'hypothesis.Rd':
  \usage lines wider than 90 characters:
     hypothesis(TrnX = NULL, TrnY = NULL, m, u0, n1, n2, s1 = NULL, s2 = NULL, sigma1 = NULL, sigma2 = NULL, alpha = 0.05, method = "n", H0  ... [TRUNCATED]
  \examples lines wider than 100 characters:
      hypothesis(TrnX=c(3,4,5),TrnY=c(4,5,6),m,u0=4,3,3,s1=NULL,s2=NULL,sigma1=NULL,sigma2=NULL,alpha=0.05,method="n",H0="u=u0",p)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpojFOU0/R.INSTALL7489e74cb8f/hypr/man/cmat.Rd:41: file link ‘as.fractions’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpojFOU0/R.INSTALL7489e74cb8f/hypr/man/cmat.Rd:56: file link ‘C’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpojFOU0/R.INSTALL7489e74cb8f/hypr/man/conversions.Rd:37: file link ‘as.fractions’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpojFOU0/R.INSTALL7489e74cb8f/hypr/man/hmat.Rd:21: file link ‘as.fractions’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpojFOU0/R.INSTALL7489e74cb8f/hypr/man/hypr.Rd:25: file link ‘C’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpojFOU0/R.INSTALL7489e74cb8f/hypr/man/hypr.Rd:71: file link ‘C’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpojFOU0/R.INSTALL7489e74cb8f/hypr/man/hypr.Rd:71: file link ‘contr.hypothesis’ in package ‘hypr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hypr.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘MCMCpack’ ‘coda’ ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmpeVMjoS/R.INSTALL7cd850bf2889/i2dash/man/grapes-greater-than-grapes.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeVMjoS/R.INSTALL7cd850bf2889/i2dash/man/grapes-less-than-greater-than-grapes.Rd:10: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/i2dash.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘vignette-IAbin.Rmd’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IalsaSynthesis)
  > 
  > test_check("IalsaSynthesis")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-extract.R:5:1): (code run outside of `test_that()`) ─────────────
  Error: 'inst' is not an exported object from 'namespace:devtools'
  Backtrace:
      █
   1. ├─base::file.path(devtools::inst(name = "IalsaSynthesis"), "test_data/2015-portland/b1_female_ae_muscle_fluid_grip_trailsb.out") test-extract.R:5:0
   2. └─devtools::inst
   3.   └─base::getExportedValue(pkg, name)
  ── Error (test-validate.R:7:3): validate_filename_output -good ─────────────────
  Error: 'inst' is not an exported object from 'namespace:devtools'
  Backtrace:
      █
   1. ├─base::file.path(devtools::inst(name = "IalsaSynthesis"), "test_data/2015-portland") test-validate.R:7:2
   2. └─devtools::inst
   3.   └─base::getExportedValue(pkg, name)
  ── Error (test-validate.R:19:3): validate_filename_output -missing ─────────────
  Error: 'inst' is not an exported object from 'namespace:devtools'
  Backtrace:
      █
   1. ├─base::file.path(devtools::inst(name = "IalsaSynthesis"), "test_data/2015-portland") test-validate.R:19:2
   2. └─devtools::inst
   3.   └─base::getExportedValue(pkg, name)
  ── Error (test-validate.R:28:3): validate_filename_output -bad extension ───────
  Error: 'inst' is not an exported object from 'namespace:devtools'
  Backtrace:
      █
   1. ├─base::file.path(devtools::inst(name = "IalsaSynthesis"), "test_data/2015-portland") test-validate.R:28:2
   2. └─devtools::inst
   3.   └─base::getExportedValue(pkg, name)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘AIC.txt’ ‘AICc.txt’ ‘IAS.pdf’ ‘IAS2.pdf’ ‘IAS3.pdf’
  ‘P.microlepis-AIC.txt’ ‘P.microlepis-AICc.txt’ ‘P.microlepis-IAS.pdf’
  ‘P.microlepis-IAS2.pdf’ ‘P.microlepis-IAS3.pdf’
ibdhap.barplot: no visible global function definition for ‘rect’
ibdhap.compare.loci: no visible global function definition for ‘hist’
ibdhap.compare.segs: no visible global function definition for ‘tail’
ibdhap.make.calls: no visible global function definition for
  ‘count.fields’
ibdhap.make.calls: no visible global function definition for
  ‘read.table’
ibdhap.make.true: no visible global function definition for
  ‘read.table’
ibdhap.names: no visible global function definition for ‘count.fields’
ibdhap.names: no visible global function definition for ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  count.fields hist read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
CreateVoronoi: no visible global function definition for ‘slot’
CreateVoronoi : <anonymous>: no visible global function definition for
  ‘slot’
CreateVoronoi: no visible global function definition for ‘chull’
ExtractIMFi2D: no visible global function definition for ‘par’
LocatedAtBoundary: no visible global function definition for
  ‘txtProgressBar’
LocatedAtBoundary: no visible global function definition for
  ‘setTxtProgressBar’
PlotFit: no visible global function definition for ‘par’
iBEEMD: no visible global function definition for ‘is’
iBEEMD: no visible global function definition for ‘sd’
iBEEMD: no visible global function definition for ‘txtProgressBar’
iBEEMD: no visible global function definition for ‘rnorm’
iBEEMD: no visible global function definition for ‘setTxtProgressBar’
iBEEMD: no visible global function definition for ‘terrain.colors’
rbfcreate: no visible global function definition for ‘is’
rbfcreate : rbfAssemble: no visible global function definition for
  ‘dist’
rbfinterp: no visible global function definition for ‘is’
rbfinterp: no visible global function definition for ‘dist’
Undefined global functions or variables:
  chull dist is par rnorm sd setTxtProgressBar slot terrain.colors
  txtProgressBar
Consider adding
  importFrom("grDevices", "chull", "terrain.colors")
  importFrom("graphics", "par")
  importFrom("methods", "is", "slot")
  importFrom("stats", "dist", "rnorm", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘SparkR’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6HKET4/R.INSTALL211b4e03de26/ibmdbR/man/idadf.Rd:55: file link ‘sqlUpdate’ in package ‘RODBC’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6HKET4/R.INSTALL211b4e03de26/ibmdbR/man/idadf.Rd:62: file link ‘sqlUpdate’ in package ‘RODBC’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ibmdbR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpB1LE2t/R.INSTALL6fb41ce0bb22/IBMPopSim/man/weibull.Rd:15: file link ‘dweibull’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IBMPopSim.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘ibmsunburst.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpofMiwm/R.INSTALL7c687b2c4bf5/Iboot/man/Iboot-package.Rd:37: file link ‘stats’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Iboot.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Iboot: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
..placeOrder: no visible global function definition for ‘str’
.reqMktData.vignette: no visible global function definition for
  ‘flush.console’
e_portfolio_value: no visible global function definition for ‘str’
print.eventPortfolioValue: no visible global function definition for
  ‘str’
print.twsContract: no visible global function definition for ‘str’
print.twsContractDetails: no visible global function definition for
  ‘str’
print.twsOrder: no visible global function definition for ‘str’
print.twsOrderState: no visible global function definition for ‘str’
print.twsScannerSubscription: no visible global function definition for
  ‘str’
reqAccountUpdates: no visible binding for global variable ‘timestamp’
reqContractDetails: no visible binding for global variable ‘timestamp’
reqHistoricalData: no visible global function definition for
  ‘flush.console’
reqHistoricalData: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  flush.console str timestamp write.table
Consider adding
  importFrom("utils", "flush.console", "str", "timestamp", "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Rd file 'curveConcent.Rd':
  \examples lines wider than 100 characters:
     curveConcent(x=hhbudgets[, "transporte"], y=hhbudgets[,"ingreso"], w=hhbudgets[,"factor"], col="red", xlab="Ranking by income")
     curveConcent(x=hhbudgets[, "mantenimiento"], y=hhbudgets[,"ingreso"], w=hhbudgets[,"factor"], col="blue", add=TRUE)
     curveConcent(x=hhbudgets[, "publico"], y=hhbudgets[,"ingreso"], w=hhbudgets[,"factor"], col="green", add=TRUE)
     legend("topleft", legend = c("All transport", "Private: Maintenance and repair", "Public transport"), col=c("red", "blue", "green"), lt ... [TRUNCATED]

Rd file 'decompAtkinson.Rd':
  \examples lines wider than 100 characters:
     summary(decompAtkinson(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], decomp="DP", ELMO=FALSE))
     summary(decompAtkinson(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], decomp="DP", epsilon=0.25))

Rd file 'decompGEI.Rd':
  \examples lines wider than 100 characters:
     summary(decompGEI(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], alpha=1.5))

Rd file 'decompSGini.Rd':
  \examples lines wider than 100 characters:
     decompSGini(x=hhbudgets[,"transporte"], z=hhbudgets[,"estructura"], w=hhbudgets[,"factor"], decomp="YL", ELMO=FALSE)
     summary(decompSGini(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], param=1.5))

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'hts.Rd':
  \examples lines wider than 100 characters:
                   measure="mpi384_measure.txt",control="mpi384_control.txt",dilution="mpi384_dilution.txt",

Rd file 'ic50.Rd':
  \examples lines wider than 100 characters:
                    measure="mpi384_measure.txt",control="mpi384_control.txt",dilution="mpi384_dilution.txt",

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘.last384_control.txt’ ‘.last384_dilution.txt’ ‘.last384_measure.txt’
  ‘.last96_control.txt’ ‘.last96_dilution.txt’ ‘.last96_measure.txt’
  ‘HCC2429_1.txt’ ‘HCC2429_2.txt’ ‘HCC2429_results’ ‘NSCLC_results’
  ‘NSCLC_screen’ ‘mpi384_control.txt’ ‘mpi384_dilution.txt’
  ‘mpi384_measure.txt’
ICA: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpd2kcn8/R.INSTALL21937e84458e/ICAOD/man/student.Rd:10: file link ‘dmt’ in package ‘mnormt’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpd2kcn8/R.INSTALL21937e84458e/ICAOD/man/student.Rd:12: file link ‘dmt’ in package ‘mnormt’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpd2kcn8/R.INSTALL21937e84458e/ICAOD/man/student.Rd:14: file link ‘dmt’ in package ‘mnormt’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ICAOD.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
ICCbare: no visible global function definition for ‘na.omit’
ICCbare: no visible global function definition for ‘formula’
ICCbare: no visible global function definition for ‘replications’
ICCbare: no visible global function definition for ‘aggregate’
ICCbare: no visible global function definition for ‘anova’
ICCbare: no visible global function definition for ‘aov’
ICCbareF: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘na.omit’
ICCest: no visible global function definition for ‘anova’
ICCest: no visible global function definition for ‘aov’
ICCest: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘qf’
ICCest: no visible global function definition for ‘qnorm’
Nest: no visible global function definition for ‘qnorm’
effort : CIW: no visible global function definition for ‘qf’
effort: no visible global function definition for ‘axis’
effort: no visible global function definition for ‘lines’
effort: no visible global function definition for ‘legend’
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: ‘icd’
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘KernSmooth’ which was already attached by Depends.
  Please remove these calls from your code.
bickde: no visible global function definition for ‘optimize’
iclocpoly: no visible global function definition for ‘approx’
iclocpoly: no visible global function definition for ‘sd’
iclocpoly: no visible global function definition for ‘dnorm’
iclocpoly: no visible global function definition for ‘pnorm’
iclocpoly: no visible global function definition for ‘var’
inmost: no visible global function definition for ‘stack’
Undefined global functions or variables:
  approx dnorm optimize pnorm sd stack var
Consider adding
  importFrom("stats", "approx", "dnorm", "optimize", "pnorm", "sd",
             "var")
  importFrom("utils", "stack")
to your NAMESPACE file.
Rd file 'ickde.Rd':
  \usage lines wider than 90 characters:
     ickde(I, h, f, m, n.iterations = 10, x1, xm, right.limit = 10000,kernel="gaussian", old=TRUE)

These lines will be truncated in the PDF manual.
INCAncinner : dian: no visible global function definition for ‘cutree’
INCAncinner : bestela: no visible global function definition for
  ‘cutree’
center: no visible global function definition for ‘var’
dbhatta: no visible global function definition for ‘as.dist’
dcor: no visible global function definition for ‘cor’
dcor: no visible global function definition for ‘as.dist’
dgower: no visible global function definition for ‘as.dist’
dmahal: no visible global function definition for ‘as.dist’
dproc2: no visible global function definition for ‘as.dist’
plot.incaix: no visible global function definition for ‘barplot’
plot.incanc: no visible global function definition for ‘lines’
plot.incanc: no visible global function definition for ‘legend’
selectioncluster : dian: no visible global function definition for
  ‘cutree’
selectioncluster : bestela: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  as.dist barplot cor cutree legend lines var
Consider adding
  importFrom("graphics", "barplot", "legend", "lines")
  importFrom("stats", "as.dist", "cor", "cutree", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'lattice', 'caTools', 'gdata', 'gtools', 'gplots', 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘caTools’ ‘gdata’ ‘gplots’ ‘gtools’ ‘lattice’ ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGmLh6f/R.INSTALL64ca5b11e131/icosa/man/heatMapLegend.Rd:54: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGmLh6f/R.INSTALL64ca5b11e131/icosa/man/heatMapLegend.Rd:48: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/icosa.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpa5F6nw/R.INSTALL1c6e6b562bc8/ICSOutlier/man/comp.simu.test.Rd:24: file link ‘clusterSetRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa5F6nw/R.INSTALL1c6e6b562bc8/ICSOutlier/man/dist.simu.test.Rd:24: file link ‘clusterSetRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa5F6nw/R.INSTALL1c6e6b562bc8/ICSOutlier/man/ics.outlier.Rd:37: file link ‘clusterSetRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ICSOutlier.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpoVvk1C/R.INSTALL226d4559acf8/ICSShiny/man/ICSShiny.Rd:30: file link ‘clusterSetRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ICSShiny.Rcheck/00install.out’ for details.
PH.ICsurv.EM: no visible global function definition for ‘quantile’
PH.ICsurv.EM: no visible global function definition for ‘optim’
fast.PH.ICsurv.EM: no visible global function definition for ‘quantile’
fast.PH.ICsurv.EM: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim quantile
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9btOpM/R.INSTALL7f105d271b1e/idar/man/SF.Rd:25: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9btOpM/R.INSTALL7f105d271b1e/idar/man/fdis.Rd:16: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9btOpM/R.INSTALL7f105d271b1e/idar/man/midar.Rd:34: file link ‘multifocalsimulator’ in package ‘idar’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9btOpM/R.INSTALL7f105d271b1e/idar/man/pisar.Rd:71: file link ‘multifocalsimulator’ in package ‘idar’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/idar.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

idbg.interact: no visible global function definition for
  ‘capture.output’
idbg.interact: no visible global function definition for ‘timestamp’
idbg.print_breakpoints: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output timestamp
Consider adding
  importFrom("utils", "capture.output", "timestamp")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
Non-standard file/directory found at top level:
  ‘README.Idcoefs2b1.txt’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpf5UQtZ/R.INSTALL65a860cd046c/IDF/man/IDF.agg.Rd:36: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpf5UQtZ/R.INSTALL65a860cd046c/IDF/man/dgev.d.Rd:25: file link ‘dgev’ in package ‘evd’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpf5UQtZ/R.INSTALL65a860cd046c/IDF/man/pgev.d.Rd:24: file link ‘pgev’ in package ‘evd’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpf5UQtZ/R.INSTALL65a860cd046c/IDF/man/qgev.d.Rd:24: file link ‘qgev’ in package ‘evd’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IDF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8Hw7pj/R.INSTALL6fbffd76189/IDPmisc/man/longtsPlot.Rd:95: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IDPmisc.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
comp.uri: no visible global function definition for ‘quantile’
est.IDR: no visible global function definition for ‘ecdf’
get.pseudo.mix: no visible global function definition for ‘pnorm’
get.uri.2d: no visible global function definition for ‘smooth.spline’
get.uri.2d: no visible global function definition for ‘predict’
Undefined global functions or variables:
  ecdf pnorm predict quantile smooth.spline
Consider adding
  importFrom("stats", "ecdf", "pnorm", "predict", "quantile",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘XML’ ‘vegan’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘ie2miscdata’
ROC_plot: no visible global function definition for ‘pdf’
ROC_plot: no visible global function definition for ‘par’
ROC_plot: no visible global function definition for ‘dev.off’
Ymean_compare: no visible binding for global variable ‘sd’
Ymean_compare: no visible global function definition for ‘pdf’
Ymean_compare: no visible global function definition for ‘par’
Ymean_compare: no visible global function definition for ‘dev.off’
data_simulation: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
mcmc_trace_plot: no visible global function definition for ‘pdf’
mcmc_trace_plot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par pdf rnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "rnorm", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘Demo_Gibbs_result.RData’ ‘Demo_traceplot.pdf’ ‘RMSE_demo.RData’
  ‘RMSE_plot.pdf’ ‘ROC_plot.pdf’ ‘ROC_result.RData’ ‘demo_data.RData’
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

ifa.em: no visible global function definition for ‘runif’
ifa.init.pca: no visible global function definition for ‘var’
ifa.init.pca: no visible global function definition for ‘cor’
ifa.init.pca: no visible global function definition for ‘runif’
ifa.init.random: no visible global function definition for ‘runif’
ifa.init.random: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor runif var
Consider adding
  importFrom("stats", "cor", "runif", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘IFCdata’
Found the following significant warnings:
  Rd warning: /tmp/RtmpcDqCJw/R.INSTALL12df52d1d058/ifultools/man/ACVStoPACS.Rd:44: file link ‘ar.yw’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpcDqCJw/R.INSTALL12df52d1d058/ifultools/man/scaleData.Rd:28: file link ‘exp’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpcDqCJw/R.INSTALL12df52d1d058/ifultools/man/variance.Rd:33: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ifultools.Rcheck/00install.out’ for details.
Found the following assignments to the global environment:
File ‘IgorR/R/ReadIgorBinary.R’:
  assign(WaveName, rval, envir = .GlobalEnv)
Found the following significant warnings:
  Rd warning: /tmp/RtmpmwWhyG/R.INSTALL401540ea05be/igraph/man/cluster_leading_eigen.Rd:120: file link ‘as.dendrogram’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmwWhyG/R.INSTALL401540ea05be/igraph/man/plot.common.Rd:13: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmwWhyG/R.INSTALL401540ea05be/igraph/man/plot.common.Rd:184: file link ‘tkfont.create’ in package ‘tcltk’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmwWhyG/R.INSTALL401540ea05be/igraph/man/plot.common.Rd:186: file link ‘tkfont.create’ in package ‘tcltk’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmwWhyG/R.INSTALL401540ea05be/igraph/man/plot.common.Rd:217: file link ‘tkfont.create’ in package ‘tcltk’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/igraph.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1WQYlW/R.INSTALL720d404e1240/ilc/man/plot_dd.Rd:31: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ilc.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘fit.mod6.ps’ ‘res.mod6d.ps’
Found the following significant warnings:
  Rd warning: /tmp/RtmpLIo5HF/R.INSTALL684619e176e3/imager/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/imager.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/G_moments.Rd:26: file link ‘Rmpfr’ in package ‘Rmpfr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/G_moments.Rd:38: file link ‘Rmpfr’ in package ‘Rmpfr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/G_moments.Rd:66: file link ‘Rmpfr’ in package ‘Rmpfr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/G_priorDensity.Rd:36: file link ‘Rmpfr’ in package ‘Rmpfr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/G_priorDensity.Rd:61: file link ‘Rmpfr’ in package ‘Rmpfr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/Zsimilarity.Rd:19: file link ‘mcclust’ in package ‘mcclust’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/Zsimilarity.Rd:15: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/Zsimilarity.Rd:27: file link ‘mcclust’ in package ‘mcclust’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/Zsimilarity.Rd:57: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKV81w3/R.INSTALL211b3dc7fa91/IMIFA/man/get_IMIFA_results.Rd:67: file link ‘mcclust’ in package ‘mcclust’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IMIFA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: C:/Users/sunpn563/AppData/Local/Temp/RtmpGkWkg1/Rbuild26fc48a06982/immer/man/immer-package.Rd:100: file link ‘tam.mml.mfr’ in package ‘TAM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/immer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpWGI84a/R.INSTALL1ffa78738067/impimp/man/impimp.Rd:41: file link ‘print.data.frame’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/impimp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPfc7Af/R.INSTALL2b3e52151d6b/implyr/man/src_impala.Rd:16: file link ‘dbConnect,OdbcDriver-method’ in package ‘odbc’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPfc7Af/R.INSTALL2b3e52151d6b/implyr/man/src_impala.Rd:17: file link ‘dbConnect,JDBCDriver-method’ in package ‘RJDBC’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/implyr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpAUAHRH/R.INSTALL29c3a7c380e/ImportExport/man/spss_import.Rd:24: file link ‘read_sav’ in package ‘haven’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAUAHRH/R.INSTALL29c3a7c380e/ImportExport/man/spss_import.Rd:35: file link ‘read_sav’ in package ‘haven’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpAUAHRH/R.INSTALL29c3a7c380e/ImportExport/man/spss_import.Rd:41: file link ‘read_sav’ in package ‘haven’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ImportExport.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpHYpGF0/R.INSTALL217727a0f7f6/imptree/man/node_imptree.Rd:19: file link ‘as.integer’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHYpGF0/R.INSTALL217727a0f7f6/imptree/man/print.imptree.Rd:15: file link ‘getOption’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/imptree.Rcheck/00install.out’ for details.
generate.ExpressionData: no visible global function definition for
  ‘rnorm’
impute.MinDet: no visible binding for global variable ‘quantile’
impute.MinProb: no visible binding for global variable ‘quantile’
impute.MinProb: no visible binding for global variable ‘sd’
impute.MinProb: no visible global function definition for ‘median’
impute.MinProb: no visible global function definition for ‘rnorm’
impute.QRILC: no visible global function definition for ‘qnorm’
impute.QRILC: no visible global function definition for ‘quantile’
impute.QRILC: no visible global function definition for ‘lm’
insertMVs: no visible global function definition for ‘rnorm’
model.Selector: no visible global function definition for ‘qnorm’
model.Selector: no visible global function definition for ‘quantile’
model.Selector: no visible global function definition for ‘lm’
model.Selector: no visible global function definition for ‘ecdf’
model.Selector: no visible global function definition for ‘pnorm’
pep2prot: no visible binding for global variable ‘median’
Undefined global functions or variables:
  ecdf lm median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "ecdf", "lm", "median", "pnorm", "qnorm",
             "quantile", "rnorm", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
impute.mdr: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Rd file 'impute.mdr.Rd':
  \usage lines wider than 90 characters:
     impute.mdr(dataset, colresp, cs, combi, cv.fold = 10, na.method = 0, max_iter = 30, randomize = FALSE)

These lines will be truncated in the PDF manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
heal_data: no visible global function definition for ‘optimum_k’
heal_data: no visible global function definition for ‘optimum_w’
heal_data: no visible global function definition for ‘pred_for_w’
Undefined global functions or variables:
  optimum_k optimum_w pred_for_w
Found the following significant warnings:
  Rd warning: /tmp/Rtmpcr2mgd/R.INSTALL6e4b17643fa5/imputeR/man/CubistR.Rd:29: file link ‘cubist’ in package ‘Cubist’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpcr2mgd/R.INSTALL6e4b17643fa5/imputeR/man/pcrR.Rd:28: file link ‘pcr’ in package ‘pls’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpcr2mgd/R.INSTALL6e4b17643fa5/imputeR/man/plsR.Rd:28: file link ‘plsr’ in package ‘pls’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/imputeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3TyrPm/R.INSTALL7a57586271db/INCATome/man/INCATome.Rd:19: file link ‘eBayes’ in package ‘limma’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/INCATome.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
IDM.bootCI: no visible global function definition for ‘cov’
IDM.bootCI: no visible global function definition for ‘cor’
IDM.bootCI: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cor cov quantile
Consider adding
  importFrom("stats", "cor", "cov", "quantile")
to your NAMESPACE file.
Rd file 'IDM.bootCI.Rd':
  \examples lines wider than 100 characters:
     #a built-in dataset fish is used. This data gives sizes of 53 female stickleback measured at the age of 17, 45, 80, and 115 days.
     #figure showing first two trajectories and percentages of variations accounted for by each trajectory.
     barplot(out$Percent.trajectory,ylim=c(0,105),las=1,names.arg=c("1","2","3","4"), ylab="Percentage of variation",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]
     plot(age,out$Trajectories97.5CI[,1],type="l",lty=2,ylim=c(-1,1),las=1,ylab="Trajectory value",xlab="Age (days)",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]
     plot(age,out$Trajectories97.5CI[,2],type="l",lty=2,ylim=c(-1,1),las=1,ylab="Trajectory value",xlab="Age (days)",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]

Rd file 'p.function.Rd':
  \examples lines wider than 100 characters:
     temp2b=(-1)^i*factorial(j)/(factorial(i)*factorial(j-i))*factorial(2*j-2*i)/(factorial(j)*factorial(2*j-2*i-j))*x^(j-2*i)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpQ3bYWQ/R.INSTALL18363fae514f/inference/man/transform.inference.Rd:17: file link ‘exp’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/inference.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘sandwich’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
infer,coxph: no visible global function definition for ‘coef’
infer,coxph: no visible global function definition for ‘vcov’
infer,coxph: no visible global function definition for ‘sandwich’
infer,coxph: no visible global function definition for ‘pnorm’
infer,coxph: no visible global function definition for ‘qnorm’
infer,gee: no visible global function definition for ‘coef’
infer,gee: no visible global function definition for ‘pnorm’
infer,gee: no visible global function definition for ‘qnorm’
infer,glm: no visible global function definition for ‘coef’
infer,glm: no visible global function definition for ‘sandwich’
infer,glm: no visible global function definition for ‘vcov’
infer,glm: no visible global function definition for ‘pnorm’
infer,glm: no visible global function definition for ‘qnorm’
infer,lm: no visible global function definition for ‘coef’
infer,lm: no visible global function definition for ‘sandwich’
infer,lm: no visible global function definition for ‘vcov’
infer,lm: no visible global function definition for ‘pnorm’
infer,lm: no visible global function definition for ‘qnorm’
infer,lme: no visible global function definition for ‘coef’
infer,lme: no visible global function definition for ‘fixed.effects’
infer,lme: no visible global function definition for ‘vcov’
infer,lme: no visible global function definition for ‘pnorm’
infer,lme: no visible global function definition for ‘qnorm’
infer,mer: no visible global function definition for ‘coef’
infer,mer: no visible global function definition for ‘vcov’
infer,mer: no visible global function definition for ‘pnorm’
infer,mer: no visible global function definition for ‘qnorm’
infer,mer: no visible binding for global variable ‘fm1’
Undefined global functions or variables:
  coef fixed.effects fm1 pnorm qnorm sandwich vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "vcov")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
contrib: no visible global function definition for ‘aggregate’
est.expDeath : surv_p: no visible global function definition for
  ‘survfit’
est.expDeath : surv_p: no visible global function definition for
  ‘approx’
function1: no visible global function definition for ‘coxph.detail’
inference.SMR: no visible global function definition for ‘qnorm’
var.expDeath : surv_p: no visible global function definition for
  ‘survfit’
var.expDeath : surv_p: no visible global function definition for
  ‘approx’
Undefined global functions or variables:
  aggregate approx coxph.detail qnorm survfit
Consider adding
  importFrom("stats", "aggregate", "approx", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpfRLuq2/R.INSTALL2cbb6c295c7/infix/man/except.Rd:28: file link ‘tryCatch’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfRLuq2/R.INSTALL2cbb6c295c7/infix/man/funlogic.Rd:25: file link ‘Negate’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfRLuq2/R.INSTALL2cbb6c295c7/infix/man/nomatch.Rd:16: file link ‘%in%’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfRLuq2/R.INSTALL2cbb6c295c7/infix/man/pipes.Rd:27: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfRLuq2/R.INSTALL2cbb6c295c7/infix/man/pipes.Rd:27: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfRLuq2/R.INSTALL2cbb6c295c7/infix/man/pipes.Rd:27: file link ‘%$%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfRLuq2/R.INSTALL2cbb6c295c7/infix/man/pipes.Rd:27: file link ‘%T>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/infix.Rcheck/00install.out’ for details.
BugReports field should be the URL of a single webpage
gen.intercepts: no visible global function definition for ‘contr.SAS’
Undefined global functions or variables:
  contr.SAS
Consider adding
  importFrom("stats", "contr.SAS")
to your NAMESPACE file.
entropy: no visible global function definition for ‘na.omit’
interinformation: no visible global function definition for ‘na.omit’
multiinformation: no visible global function definition for ‘na.omit’
mutinformation: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
Malformed Description field: should contain one or more complete sentences.
getInfra: no visible global function definition for ‘txtProgressBar’
getInfra: no visible global function definition for ‘download.file’
getInfra: no visible global function definition for ‘setTxtProgressBar’
getInfra : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "download.file", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  ‘bingFileContents.txt’ ‘japanInfraBing.png’
Found the following significant warnings:
  Rd warning: /tmp/RtmplVokCI/R.INSTALL7d2555fe0a65/Infusion/man/plot.SLik.Rd:30: file link ‘filled.mapMM’ in package ‘spaMM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplVokCI/R.INSTALL7d2555fe0a65/Infusion/man/plot.SLik.Rd:33: file link ‘filled.mapMM’ in package ‘spaMM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplVokCI/R.INSTALL7d2555fe0a65/Infusion/man/plot.SLik.Rd:56: file link ‘filled.mapMM’ in package ‘spaMM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Infusion.Rcheck/00install.out’ for details.
Unexported object imported by a ':::' call: ‘ltm:::crf.GPCM’
  See the note in ?`:::` about the use of this operator.
Jeffreys: no visible global function definition for ‘integrate’
Jeffreys: no visible global function definition for ‘splinefun’
count.rows: no visible global function definition for ‘tail’
count.rows: no visible global function definition for ‘head’
cprobs : <anonymous>: no visible global function definition for
  ‘plogis’
inf.func.ltm : f: no visible global function definition for ‘plogis’
iota: no visible global function definition for ‘integrate’
iota: no visible global function definition for ‘optimize’
iota: no visible global function definition for ‘pchisq’
iota.c : rirm: no visible global function definition for ‘coef’
iota.c: no visible global function definition for ‘integrate’
iota.c: no visible global function definition for ‘sd’
iota.u: no visible global function definition for ‘integrate’
iprobs : <anonymous>: no visible global function definition for
  ‘plogis’
logL.ltm : logL: no visible global function definition for ‘dbinom’
logL.ltm : logL: no visible global function definition for ‘plogis’
logL.ltm : logL : <anonymous>: no visible global function definition
  for ‘plogis’
rJeffreys : Jpinv.min: no visible global function definition for
  ‘integrate’
rJeffreys : Jpinv: no visible global function definition for ‘nlminb’
rJeffreys : Jpinv: no visible global function definition for ‘qnorm’
rJeffreys: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef dbinom head integrate nlminb optimize pchisq plogis qnorm runif
  sd splinefun tail
Consider adding
  importFrom("stats", "coef", "dbinom", "integrate", "nlminb",
             "optimize", "pchisq", "plogis", "qnorm", "runif", "sd",
             "splinefun")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Rd file 'Jeffreys.Rd':
  \usage lines wider than 90 characters:
     Jeffreys(ltm.obj = NULL, inf.mat = NULL, inf.func = NULL, return = "prior", spl.method = "natural", range.int = c(-Inf, Inf))

Rd file 'iota.Rd':
  \usage lines wider than 90 characters:
     iota(ltm.obj, logL.fun, fscore.obj = NULL, data = NULL, prior = NULL, theta0 = NULL, range.int = c(-Inf, Inf), range.theta = c(-10, 10) ... [TRUNCATED]

Rd file 'iota.c.Rd':
  \usage lines wider than 90 characters:
     iota.c(ltm.obj, M = NULL, prior = NULL, logL.fun = NULL, rirm = NULL, range.int = c(-Inf, Inf))

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/conversion.Rd:47: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/conversion.Rd:48: file link ‘as.character.DNAbin’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/conversion.Rd:49: file link ‘as.character.AAbin’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/conversion.Rd:50: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/conversion.Rd:51: file link ‘as.DNAbin’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/conversion.Rd:51: file link ‘as.AAbin’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/manipulate.Rd:62: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/rc.Rd:21: file link ‘complement’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/rc.Rd:21: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/rc.Rd:23: file link ‘seqinr’ in package ‘seqinr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Rh3zw/R.INSTALL7ed77108f6bc/insect/man/read.Rd:89: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/insect.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘spcosa’
Unknown package ‘spcosa’ in Rd xrefs
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
Found the following significant warnings:
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/cat_plot.Rd:54: file link ‘merMod’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/cat_plot.Rd:189: file link ‘geom_errorbar’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/cat_plot.Rd:249: file link ‘scale_colour_brewer’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/cat_plot.Rd:288: file link ‘effects’ in package ‘effects’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/interact_plot.Rd:51: file link ‘merMod’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/plot.sim_margins.Rd:12: file link ‘plot_coefs’ in package ‘jtools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/plot.sim_slopes.Rd:12: file link ‘plot_coefs’ in package ‘jtools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/probe_interaction.Rd:11: file link ‘merMod’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/sim_margins.Rd:30: file link ‘merMod’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4W3eN/R.INSTALL6ddc51b7d867/interactions/man/sim_slopes.Rd:35: file link ‘merMod’ in package ‘lme4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/interactions.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
ClearBottomMenuPlot: no visible global function definition for ‘rect’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertX’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertX’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘polygon’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertX’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertY’
InteractiveIGraph : keybd: no visible global function definition for
  ‘par’
PlotRegionGeneral: no visible global function definition for ‘polygon’
plot.InteractiveIGraph: no visible global function definition for ‘par’
plot.Menu: no visible global function definition for ‘par’
plot.Menu: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘strwidth’
plot.MenuItem: no visible binding for global variable ‘strheight’
plot.MenuItem: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘text’
plot.MenuLine: no visible binding for global variable ‘rect’
Undefined global functions or variables:
  grconvertX grconvertY par polygon rect strheight strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "polygon",
             "rect", "strheight", "strwidth", "text")
to your NAMESPACE file.
Rd file 'InteractiveIGraph.Rd':
  \examples lines wider than 100 characters:
     # this is an 'InteractiveIGraph' object, up till now there is not much difference. Just some extra attributes.

Rd file 'MenuAddItems.Rd':
  \examples lines wider than 100 characters:
       Item = list(list(label=msg, RegionParams=list(XBufCof = 0, YBufCof=0.2), RecParams=list(lwd = NA, border=NA), TextParams=list(cex=0.8 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
interact: no visible global function definition for ‘cor’
standardize.matrix: no visible binding for global variable ‘var’
standardize.matrix: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor sd var
Consider adding
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
HH: no visible global function definition for ‘var’
HH: no visible global function definition for ‘qnorm’
exactCI: no visible global function definition for ‘quantile’
sample.n: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  qnorm quantile rbinom var
Consider adding
  importFrom("stats", "qnorm", "quantile", "rbinom", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSAINdQ/R.INSTALL50e16dd029c8/intergraph/man/as.matrix.igraph.Rd:41: file link ‘get.adjacency’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSAINdQ/R.INSTALL50e16dd029c8/intergraph/man/as.matrix.igraph.Rd:41: file link ‘get.edgelist’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSAINdQ/R.INSTALL50e16dd029c8/intergraph/man/as.matrix.igraph.Rd:52: file link ‘get.adjacency’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSAINdQ/R.INSTALL50e16dd029c8/intergraph/man/as.matrix.igraph.Rd:53: file link ‘get.edgelist’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSAINdQ/R.INSTALL50e16dd029c8/intergraph/man/asDF.Rd:65: file link ‘get.edgelist’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSAINdQ/R.INSTALL50e16dd029c8/intergraph/man/asIgraph.Rd:43: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSAINdQ/R.INSTALL50e16dd029c8/intergraph/man/asIgraph.Rd:95: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSAINdQ/R.INSTALL50e16dd029c8/intergraph/man/asNetwork.Rd:40: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSAINdQ/R.INSTALL50e16dd029c8/intergraph/man/asNetwork.Rd:69: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/intergraph.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘chron’ ‘date’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Mo.Th.Ra.: no visible global function definition for ‘aggregate’
daily_mean: no visible global function definition for ‘aggregate’
date.time: no visible global function definition for ‘chron’
date.time: no visible global function definition for ‘years’
date.time: no visible global function definition for ‘days’
date.time: no visible global function definition for ‘hours’
par_calibration: no visible global function definition for ‘date.mdy’
par_calibration: no visible global function definition for ‘as.date’
par_calibration: no visible global function definition for ‘aggregate’
plot_meas_sim: no visible global function definition for ‘as.date’
plot_meas_sim: no visible global function definition for ‘date.mdy’
plot_meas_sim: no visible global function definition for ‘par’
plot_meas_sim: no visible global function definition for ‘legend’
shape_calibration: no visible global function definition for ‘date.mdy’
shape_calibration: no visible global function definition for ‘as.date’
shape_calibration: no visible global function definition for
  ‘aggregate’
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par years
Consider adding
  importFrom("graphics", "legend", "par")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnGMNGA/R.INSTALL7c56200f72/interval/man/ictest.Rd:87: file link ‘permTS’ in package ‘perm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnGMNGA/R.INSTALL7c56200f72/interval/man/ictest.Rd:131: file link ‘permTS’ in package ‘perm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnGMNGA/R.INSTALL7c56200f72/interval/man/methodRuleIC1.Rd:21: file link ‘permTS’ in package ‘perm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/interval.Rcheck/00install.out’ for details.
interventionEffects: no visible binding for global variable ‘sd’
interventionEffects: no visible global function definition for ‘pt’
interventionEffects: no visible global function definition for ‘sd’
interventionalInference: no visible global function definition for ‘sd’
interventionalInferenceAdvanced: no visible global function definition
  for ‘sd’
linesROC: no visible global function definition for ‘segments’
plotMaxML: no visible global function definition for ‘segments’
Undefined global functions or variables:
  pt sd segments
Consider adding
  importFrom("graphics", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘maxLik’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘maxLik’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ILik : rbern: no visible global function definition for ‘runif’
ILik : q: no visible global function definition for ‘dnorm’
ILik : SlambdaG: no visible global function definition for ‘rnorm’
ILik : Pi_hat: no visible global function definition for ‘rnorm’
ILik : q: no visible global function definition for ‘dgamma’
ILik : SlambdaG: no visible global function definition for ‘rgamma’
ILik : Pi_hat: no visible global function definition for ‘rgamma’
ILik: no visible global function definition for ‘maxLik’
ILik: no visible global function definition for ‘coef’
ILik: no visible global function definition for ‘hessian’
Undefined global functions or variables:
  coef dgamma dnorm hessian maxLik rgamma rnorm runif
Consider adding
  importFrom("stats", "coef", "dgamma", "dnorm", "rgamma", "rnorm",
             "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpoFvQ35/R.INSTALL25ea4ed0bd5d/intRvals/man/intervalpdf.Rd:65: file link ‘dgamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoFvQ35/R.INSTALL25ea4ed0bd5d/intRvals/man/intervalpdf.Rd:71: file link ‘dnorm’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/intRvals.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnJP5Q8/R.INSTALL1d645ab14da4/intsurv/man/cox_cure.Rd:93: file link ‘model.matrix.default’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnJP5Q8/R.INSTALL1d645ab14da4/intsurv/man/cox_cure_net.Rd:113: file link ‘model.matrix.default’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnJP5Q8/R.INSTALL1d645ab14da4/intsurv/man/iCoxph.Rd:33: file link ‘na.omit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnJP5Q8/R.INSTALL1d645ab14da4/intsurv/man/iCoxph.Rd:34: file link ‘na.exclude’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnJP5Q8/R.INSTALL1d645ab14da4/intsurv/man/iCoxph.Rd:35: file link ‘na.pass’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnJP5Q8/R.INSTALL1d645ab14da4/intsurv/man/iCoxph.Rd:41: file link ‘model.matrix.default’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/intsurv.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘intubate.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpVvAZRV/R.INSTALL1dd8513c3933/invctr/man/is.wholenumber.Rd:21: file link ‘is.integer’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/invctr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCYk4eC/R.INSTALL7b701dec5720/investr/man/plotFit.Rd:133: file link ‘plotfit’ in package ‘nlstools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/investr.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
f.B: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘dnorm’
f.grovest3 : f.est: no visible global function definition for ‘survfit’
f.grovest3 : f.est: no visible global function definition for ‘lines’
f.grovest3: no visible global function definition for ‘model.frame’
f.grovest3: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.frame’
invGauss: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.matrix’
predict.invGauss: no visible global function definition for
  ‘model.frame’
predict.invGauss: no visible global function definition for
  ‘model.extract’
predict.invGauss: no visible global function definition for
  ‘model.matrix’
predict.invGauss: no visible binding for global variable ‘formula’
predict.invGauss: no visible binding for global variable ‘data’
summary.invGauss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  data dnorm formula lines model.extract model.frame model.matrix pnorm
  survfit
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "dnorm", "formula", "model.extract", "model.frame",
             "model.matrix", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpAzXGxQ/R.INSTALL3d1863a98f63/invLT/man/ivLT.plot.Rd:19: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/invLT.Rcheck/00install.out’ for details.
flowsRandom: no visible global function definition for ‘dmultinom’
readBed: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dmultinom read.table
Consider adding
  importFrom("stats", "dmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘version’
Found the following significant warnings:
  Rd warning: /tmp/RtmpuWhXcv/R.INSTALL5494094b50b/ips/man/descendants.Rd:12: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuWhXcv/R.INSTALL5494094b50b/ips/man/fixNodes.Rd:24: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuWhXcv/R.INSTALL5494094b50b/ips/man/forceEqualTipHeights.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuWhXcv/R.INSTALL5494094b50b/ips/man/forceEqualTipHeights.Rd:16: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuWhXcv/R.INSTALL5494094b50b/ips/man/oi.Rd:15: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ips.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpJAEYg7/R.INSTALL7dbc23140a7d/IRdisplay/man/display-images.Rd:22: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJAEYg7/R.INSTALL7dbc23140a7d/IRdisplay/man/display-textual.Rd:28: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IRdisplay.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpP0OW0A/R.INSTALL6c3ff59fbbb/irr/man/bhapkar.Rd:37: file link ‘stuart.maxwell.mh’ in package ‘irr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/irr.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘irtoys-vignette.Rmd’
Malformed Description field: should contain one or more complete sentences.
dendrify: no visible binding for global variable ‘item’
dendrify: no visible binding for global variable ‘node’
dendrify: no visible binding for global variable ‘value’
exogenize: no visible binding for global variable ‘item’
Undefined global functions or variables:
  item node value
isbf: no visible global function definition for ‘var’
isbf: no visible global function definition for ‘qnorm’
isbfReg: no visible global function definition for ‘var’
isbfReg: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
residualplot: no visible global function definition for ‘predict’
residualplot: no visible global function definition for ‘rstandard’
residualplot: no visible global function definition for
  ‘complete.cases’
residualplot: no visible global function definition for ‘points’
residualplot: no visible global function definition for ‘lines’
residualplot: no visible global function definition for ‘smooth.spline’
residualplot: no visible global function definition for ‘sd’
residualplot: no visible global function definition for ‘rgb’
residualplot: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  complete.cases lines points polygon predict rgb rstandard sd
  smooth.spline
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "points", "polygon")
  importFrom("stats", "complete.cases", "predict", "rstandard", "sd",
             "smooth.spline")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
C.cal: no visible global function definition for ‘as.stepfun’
bandwidth.choose.cv: no visible global function definition for ‘isoreg’
g.density: no visible global function definition for ‘as.stepfun’
g.density: no visible global function definition for ‘dnorm’
h.density: no visible global function definition for ‘dnorm’
iso.bt.unit: no visible global function definition for ‘quantile’
iso.bt.unit.sub: no visible global function definition for ‘isoreg’
iso.bt.unit.sub: no visible global function definition for ‘as.stepfun’
iso.bt.wald.unit: no visible global function definition for ‘var’
iso.ci: no visible global function definition for ‘isoreg’
iso.ci.transform.unit: no visible global function definition for
  ‘as.stepfun’
Undefined global functions or variables:
  as.stepfun dnorm isoreg quantile var
Consider adding
  importFrom("stats", "as.stepfun", "dnorm", "isoreg", "quantile", "var")
to your NAMESPACE file.
ACO : bordacircular: no visible global function definition for
  ‘medianCircular’
Undefined global functions or variables:
  medianCircular
'library' or 'require' call to ‘proxy’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
isopam : core: no visible global function definition for ‘dist’
isopam : core: no visible global function definition for ‘write.table’
isopam : core: no visible global function definition for ‘as.dist’
isopam : core: no visible global function definition for
  ‘txtProgressBar’
isopam : core: no visible global function definition for
  ‘setTxtProgressBar’
isopam : core: no visible global function definition for ‘aggregate’
isopam: no visible binding for global variable ‘var’
isopam: no visible global function definition for ‘na.omit’
isopam: no visible global function definition for ‘write.table’
isopam: no visible global function definition for ‘bmp’
isopam: no visible global function definition for ‘dev.off’
isotab: no visible global function definition for ‘aggregate’
isotab : fshtest: no visible global function definition for ‘dhyper’
isotab : fshtest : pnhyper: no visible global function definition for
  ‘phyper’
Undefined global functions or variables:
  aggregate as.dist bmp dev.off dhyper dist na.omit phyper
  setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.off")
  importFrom("stats", "aggregate", "as.dist", "dhyper", "dist",
             "na.omit", "phyper", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmphoq3OC/R.INSTALL7fa4c372e30/isoreader/man/iso_parse_file_info.Rd:31: file link ‘as.character’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmphoq3OC/R.INSTALL7fa4c372e30/isoreader/man/iso_read_continuous_flow.Rd:44: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmphoq3OC/R.INSTALL7fa4c372e30/isoreader/man/iso_read_dual_inlet.Rd:47: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmphoq3OC/R.INSTALL7fa4c372e30/isoreader/man/iso_read_files.Rd:46: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmphoq3OC/R.INSTALL7fa4c372e30/isoreader/man/iso_read_scan.Rd:41: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/isoreader.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSaBYDO/R.INSTALL2ac12ae0e030/IsoriX/man/getelev.Rd:39: file link ‘tools’ in package ‘tools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IsoriX.Rcheck/00install.out’ for details.
Running examples in ‘iSubGen-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write.scaling.factors
> ### Title: Write scaling factors to file
> ### Aliases: write.scaling.factors
> 
> ### ** Examples
> 
> 
> # load the aberration profiles for three data types 
> example.molecular.data.dir <- paste0(path.package('iSubGen'),'/exdata/');
> molecular.data <- list();
> for(i in c('cna','snv','methy')) {
+   molecular.data[[i]] <- load.molecular.aberration.data(
+     paste0(example.molecular.data.dir,i,'_profiles.txt'),
+     patients = c(paste0('EP00',1:9), paste0('EP0',10:30))
+     );
+   }
> 
> # calculate scaling factors for all three data types
> scaling.factors <- calculate.scaling(molecular.data);
> 
> # save the scaling factors to file
> write.scaling.factors(scaling.factors, example.molecular.data.dir);
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/iSubGen/exdata/cna_gene_recenter.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: write.scaling.factors -> write.table -> file
Execution halted
Found the following files/directories:
  ‘RMTplot.pdf’
Depends: includes the non-default packages:
  'partitions', 'VGAM', 'MASS', 'ape', 'apTreeshape', 'geiger',
  'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘MASS’ ‘VGAM’ ‘apTreeshape’ ‘ape’ ‘geiger’ ‘gtools’ ‘partitions’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmplQEjAd/R.INSTALL5910390faafb/itertools2/man/imap.Rd:24: file link ‘Map’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplQEjAd/R.INSTALL5910390faafb/itertools2/man/istarmap.Rd:27: file link ‘Map’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/itertools2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpR4JF3P/R.INSTALL35f77672748d/itertools/man/iRNGStream.Rd:19: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpR4JF3P/R.INSTALL35f77672748d/itertools/man/iRNGStream.Rd:19: file link ‘nextRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpR4JF3P/R.INSTALL35f77672748d/itertools/man/iRNGStream.Rd:20: file link ‘nextRNGSubStream’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/itertools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpWMbJ1u/R.INSTALL2c19a8a95d/itsadug/man/fvisgam.Rd:235: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWMbJ1u/R.INSTALL2c19a8a95d/itsadug/man/gamtabs.Rd:19: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWMbJ1u/R.INSTALL2c19a8a95d/itsadug/man/info.Rd:24: file link ‘R.version’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWMbJ1u/R.INSTALL2c19a8a95d/itsadug/man/itsadug.Rd:10: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWMbJ1u/R.INSTALL2c19a8a95d/itsadug/man/pvisgam.Rd:214: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWMbJ1u/R.INSTALL2c19a8a95d/itsadug/man/resid_gam.Rd:98: file link ‘resid’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/itsadug.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘Matching’ ‘R2jags’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bpsm: no visible global function definition for ‘glm’
bpsm: no visible global function definition for ‘binomial’
bpsm: no visible global function definition for ‘Match’
bpsm: no visible global function definition for ‘cov’
bpsm: no visible global function definition for ‘vcov’
bpsm : inits: no visible global function definition for ‘runif’
bpsm: no visible global function definition for ‘jags’
bpsr: no visible global function definition for ‘glm’
bpsr: no visible global function definition for ‘binomial’
bpsr: no visible global function definition for ‘lm’
bpsr : inits: no visible global function definition for ‘runif’
bpsr: no visible global function definition for ‘jags’
modelpsm: no visible binding for global variable ‘D’
modelpsr: no visible binding for global variable ‘D’
Undefined global functions or variables:
  D Match binomial cov glm jags lm runif vcov
Consider adding
  importFrom("stats", "D", "binomial", "cov", "glm", "lm", "runif",
             "vcov")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpfeF8cb/R.INSTALL5b2039f256af/iva/man/mra.Rd:69: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfeF8cb/R.INSTALL5b2039f256af/iva/man/mra.Rd:71: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfeF8cb/R.INSTALL5b2039f256af/iva/man/mra.Rd:71: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/iva.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gurobi’
Malformed Description field: should contain one or more complete sentences.
ivFixed.formula: no visible global function definition for
  ‘model.matrix’
ivFixed.formula: no visible global function definition for
  ‘model.response’
summary.ivFixed: no visible global function definition for ‘coef’
summary.ivFixed: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Package suggested but not available for checking: ‘locClass’
Package suggested but not available for checking: ‘gurobi’
Malformed Title field: should not end in a period.
ARsensitivity.ci: no visible global function definition for ‘residuals’
ARsensitivity.ci: no visible global function definition for ‘lm’
ARsensitivity.ci: no visible global function definition for ‘qf’
ARsensitivity.ci: no visible global function definition for ‘fitted’
ARsensitivity.power: no visible global function definition for ‘qf’
ARsensitivity.power: no visible global function definition for ‘pf’
ARsensitivity.size: no visible global function definition for ‘qf’
ARsensitivity.size: no visible global function definition for ‘pf’
anderson.rubin.ci: no visible global function definition for ‘qf’
anderson.rubin.ci: no visible global function definition for ‘fitted’
anderson.rubin.ci: no visible global function definition for ‘lm’
power.iv: no visible global function definition for ‘qf’
power.iv: no visible global function definition for ‘pf’
Undefined global functions or variables:
  fitted lm pf qf residuals
Consider adding
  importFrom("stats", "fitted", "lm", "pf", "qf", "residuals")
to your NAMESPACE file.
hausman: no visible global function definition for ‘pchisq’
ivbe: no visible global function definition for ‘cor’
ivbe: no visible global function definition for ‘pt’
ivfixed: no visible global function definition for ‘cor’
ivfixed: no visible global function definition for ‘pt’
ivpan.formula: no visible global function definition for ‘model.matrix’
ivpan.formula: no visible global function definition for
  ‘model.response’
ivrandom: no visible global function definition for ‘cor’
ivrandom: no visible global function definition for ‘pt’
summary.ivpan: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response", "pchisq",
             "printCoefmat", "pt")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis lines plot.new plot.window rect
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpmx0S4o/R.INSTALL6502ea84482/jack/man/ESF.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmx0S4o/R.INSTALL6502ea84482/jack/man/Jack.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmx0S4o/R.INSTALL6502ea84482/jack/man/MSF.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmx0S4o/R.INSTALL6502ea84482/jack/man/Schur.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmx0S4o/R.INSTALL6502ea84482/jack/man/Zonal.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmx0S4o/R.INSTALL6502ea84482/jack/man/ZonalQ.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jack.Rcheck/00install.out’ for details.
boxplot.james: no visible global function definition for ‘mtext’
getBestSolutionValues.james : <anonymous>: no visible global function
  definition for ‘tail’
isMinimizing: no visible global function definition for ‘head’
isMinimizing: no visible global function definition for ‘tail’
mergeJAMES.james: no visible global function definition for ‘glob2rx’
plotConvergence.james : <anonymous> : <anonymous>: no visible global
  function definition for ‘tail’
plotConvergence.james: no visible global function definition for ‘tail’
plotConvergence.james: no visible global function definition for ‘head’
plotConvergence.james : <anonymous>: no visible global function
  definition for ‘tail’
plotConvergence.james: no visible global function definition for
  ‘matplot’
plotConvergence.james: no visible global function definition for
  ‘mtext’
summary.james: no visible global function definition for ‘sd’
summary.james: no visible global function definition for ‘median’
summary.james: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR glob2rx head matplot median mtext sd tail
Consider adding
  importFrom("graphics", "matplot", "mtext")
  importFrom("stats", "IQR", "median", "sd")
  importFrom("utils", "glob2rx", "head", "tail")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘gtools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

make_template: no visible global function definition for ‘invalid’
Undefined global functions or variables:
  invalid
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYkjGHT/R.INSTALL464b211521e8/jcolors/man/jcolors_contin.Rd:20: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYkjGHT/R.INSTALL464b211521e8/jcolors/man/jcolors_contin.Rd:21: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jcolors.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2hmrPb/R.INSTALL471531389eb8/jetset/man/jmap.Rd:31: file link ‘org.Hs.egSYMBOL2EG’ in package ‘org.Hs.eg.db’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jetset.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUxrG0z/R.INSTALL63915849a822/jipApprox/man/is.wholenumber.Rd:19: file link ‘is.integer’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jipApprox.Rcheck/00install.out’ for details.
powerLongSurv: no visible global function definition for ‘qnorm’
powerLongSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
JBTest: no visible global function definition for ‘pchisq’
generateSignificance: no visible global function definition for ‘pnorm’
packages: no visible global function definition for ‘install.packages’
shift: no visible global function definition for ‘tail’
shift: no visible global function definition for ‘head’
splitBy: no visible global function definition for ‘head’
Undefined global functions or variables:
  head install.packages pchisq pnorm tail
Consider adding
  importFrom("stats", "pchisq", "pnorm")
  importFrom("utils", "head", "install.packages", "tail")
to your NAMESPACE file.
RE.ADT: no visible global function definition for ‘sd’
RE.ADT: no visible global function definition for ‘pnorm’
RE.Johnson: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm sd
Consider adding
  importFrom("stats", "pnorm", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3sORhT/R.INSTALL490871bb72ab/joineRmeta/man/jointmeta2.Rd:58: file link ‘forest’ in package ‘meta’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/joineRmeta.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7vVMJ3/R.INSTALL4b1b6fc647e9/joineRML/man/bootSE.Rd:129: file link ‘tryCatch’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7vVMJ3/R.INSTALL4b1b6fc647e9/joineRML/man/fixef.mjoint.Rd:74: file link ‘fixef’ in package ‘nlme’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7vVMJ3/R.INSTALL4b1b6fc647e9/joineRML/man/pbc2.Rd:62: file link ‘pbc2’ in package ‘JM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7vVMJ3/R.INSTALL4b1b6fc647e9/joineRML/man/ranef.mjoint.Rd:56: file link ‘ranef’ in package ‘nlme’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7vVMJ3/R.INSTALL4b1b6fc647e9/joineRML/man/vcov.mjoint.Rd:86: file link ‘cov2cor’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/joineRML.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLCbuAb/R.INSTALL55f750454aa/joineR/man/lines.jointdata.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLCbuAb/R.INSTALL55f750454aa/joineR/man/plot.jointdata.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLCbuAb/R.INSTALL55f750454aa/joineR/man/plot.jointdata.Rd:29: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLCbuAb/R.INSTALL55f750454aa/joineR/man/points.jointdata.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLCbuAb/R.INSTALL55f750454aa/joineR/man/points.jointdata.Rd:20: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/joineR.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  'MRCE', 'remMap'
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
binteg: no visible global function definition for ‘contourLines’
binteg: no visible global function definition for ‘approx’
binteg: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘rect’
plot1: no visible global function definition for ‘axis’
plot1: no visible global function definition for ‘contour’
plot1: no visible global function definition for ‘contourLines’
plot1: no visible binding for global variable ‘approx’
plot1: no visible global function definition for ‘lines’
plot1: no visible global function definition for ‘text’
plot2: no visible global function definition for ‘abline’
plot2: no visible global function definition for ‘lines’
plot2: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par rect text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmprqY2rT/R.INSTALL68cd75045b55/josaplay/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/josaplay.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2qFmNo/R.INSTALL3ec74c92f672/jose/man/jwt_encode.Rd:36: file link ‘read_pubkey’ in package ‘openssl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jose.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpkWxIZA/R.INSTALL193b3b819838/jpmesh/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jpmesh.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/tidyeval.Rd:24: file link ‘syms’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/tidyeval.Rd:26: file link ‘expr’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/tidyeval.Rd:26: file link ‘quo’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/tidyeval.Rd:29: file link ‘exprs’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/tidyeval.Rd:30: file link ‘quos’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/tidyeval.Rd:32: file link ‘enexpr’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/tidyeval.Rd:32: file link ‘enquo’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/tidyeval.Rd:36: file link ‘enexprs’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXglSlB/R.INSTALLd8111e42e9f/JSmediation/man/tidyeval.Rd:36: file link ‘enquos’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/JSmediation.Rcheck/00install.out’ for details.
sonarCSV: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbBZ1T6/R.INSTALL1991355f2ca5/jsonld/man/jsonld.Rd:44: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jsonld.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLYEALY/R.INSTALL84e2fdfcfaf/jstable/man/geeglm.display.Rd:32: file link ‘data.table-package’ in package ‘data.table’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jstable.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSQmuC6/R.INSTALLbd35494f9f7/jstor/man/jst_get_chapters.Rd:30: file link ‘unnest’ in package ‘tidyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSQmuC6/R.INSTALLbd35494f9f7/jstor/man/jst_get_ngram.Rd:21: file link ‘read_tsv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSQmuC6/R.INSTALLbd35494f9f7/jstor/man/jst_import.Rd:76: file link ‘write_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSQmuC6/R.INSTALLbd35494f9f7/jstor/man/jst_import.Rd:92: file link ‘write_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSQmuC6/R.INSTALLbd35494f9f7/jstor/man/jst_re_import.Rd:27: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jstor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpoNpxT5/R.INSTALLc8c6d554f77/jsTreeR/man/jstree.Rd:36: file link ‘jstreeOutput’ in package ‘jsTreeR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoNpxT5/R.INSTALLc8c6d554f77/jsTreeR/man/jstree.Rd:42: file link ‘jstreeOutput’ in package ‘jsTreeR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoNpxT5/R.INSTALLc8c6d554f77/jsTreeR/man/jstree.Rd:86: file link ‘jstreeOutput’ in package ‘jsTreeR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoNpxT5/R.INSTALLc8c6d554f77/jsTreeR/man/jstree.Rd:122: file link ‘jstreeOutput’ in package ‘jsTreeR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jsTreeR.Rcheck/00install.out’ for details.
qtls: no visible global function definition for ‘quantile’
qtls: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm quantile
Consider adding
  importFrom("stats", "pnorm", "quantile")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘jumptest.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpunetxt/R.INSTALL11bc2a3fdb63/kableExtra/man/kbl.Rd:70: file link ‘opts_current’ in package ‘knitr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kableExtra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpBnvJxi/R.INSTALLde71b7837c4/kangar00/man/pathway-class.Rd:114: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpBnvJxi/R.INSTALLde71b7837c4/kangar00/man/pathway-class.Rd:122: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpBnvJxi/R.INSTALLde71b7837c4/kangar00/man/pathway-class.Rd:83: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpBnvJxi/R.INSTALLde71b7837c4/kangar00/man/read_geno-character-method.Rd:21: file link ‘read.big.matrix’ in package ‘bigmemory’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpBnvJxi/R.INSTALLde71b7837c4/kangar00/man/read_geno-character-method.Rd:29: file link ‘read.big.matrix’ in package ‘bigmemory’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kangar00.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpqVtkfc/R.INSTALL925d95d109/kantorovich/man/kantorovich_glpk.Rd:29: file link ‘Rglpk_solve_LP’ in package ‘Rglpk’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqVtkfc/R.INSTALL925d95d109/kantorovich/man/kantorovich_glpk.Rd:31: file link ‘Rglpk_solve_LP’ in package ‘Rglpk’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kantorovich.Rcheck/00install.out’ for details.
expression_up : <anonymous>: no visible global function definition for
  ‘quantile’
expression_up : <anonymous>: no visible global function definition for
  ‘IQR’
expression_up : <anonymous>: no visible global function definition for
  ‘median’
expression_up : <anonymous>: no visible global function definition for
  ‘sd’
plot_up: no visible global function definition for ‘text’
Undefined global functions or variables:
  IQR median quantile sd text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "IQR", "median", "quantile", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘my.Mobius.set.func.csv’ ‘my.card.set.func.csv’ ‘my.set.func.csv’
Malformed Title field: should not end in a period.
KappaV: no visible global function definition for ‘over’
KappaV: no visible global function definition for ‘layout’
KappaV: no visible global function definition for ‘terrain.colors’
KappaV: no visible global function definition for ‘as’
Undefined global functions or variables:
  as layout over terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "layout")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/RtmpdOQ8cu/R.INSTALL4e8a410db51b/kaps/man/km.curve.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kaps.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
Malformed Description field: should contain one or more complete sentences.
ikcirt.fun.mss.eta: no visible global function definition for ‘var’
ikcirt.fun.mss.eta: no visible global function definition for ‘pnorm’
ikcirt.fun.mss.lambda: no visible global function definition for ‘var’
ikcirt.fun.mss.lambda: no visible global function definition for
  ‘pnorm’
ikcirt.fun.mss.mu: no visible global function definition for ‘pnorm’
kcirt.fitEE: no visible binding for global variable ‘sd’
kcirt.fitEE: no visible global function definition for ‘var’
kcirt.fitEE: no visible global function definition for ‘cor’
kcirt.fitMSS: no visible global function definition for ‘var’
kcirt.fitMSS: no visible global function definition for ‘pnorm’
kcirt.fitMSS: no visible global function definition for ‘sfInit’
kcirt.fitMSS: no visible global function definition for ‘sfExport’
kcirt.fitMSS: no visible global function definition for ‘rnorm’
kcirt.fitMSS: no visible global function definition for
  ‘txtProgressBar’
kcirt.fitMSS: no visible global function definition for ‘sfIsRunning’
kcirt.fitMSS: no visible global function definition for ‘sfStop’
kcirt.fitMSS: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor pnorm rnorm sd sfExport sfInit sfIsRunning sfStop txtProgressBar
  var
Consider adding
  importFrom("stats", "cor", "pnorm", "rnorm", "sd", "var")
  importFrom("utils", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpzBnIAb/R.INSTALLa8a6abca478/kdecopula/man/dkdecop.Rd:29: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzBnIAb/R.INSTALLa8a6abca478/kdecopula/man/dkdecop.Rd:82: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzBnIAb/R.INSTALLa8a6abca478/kdecopula/man/kdecop.Rd:163: file link ‘pkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzBnIAb/R.INSTALLa8a6abca478/kdecopula/man/kdecop.Rd:164: file link ‘rkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzBnIAb/R.INSTALLa8a6abca478/kdecopula/man/kdecopula.Rd:20: file link ‘pkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzBnIAb/R.INSTALLa8a6abca478/kdecopula/man/kdecopula.Rd:21: file link ‘rkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzBnIAb/R.INSTALLa8a6abca478/kdecopula/man/logLik.kdecopula.Rd:38: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzBnIAb/R.INSTALLa8a6abca478/kdecopula/man/plot.kdecopula.Rd:60: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kdecopula.Rcheck/00install.out’ for details.
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for ‘cophenetic’
bw.nn : <anonymous>: no visible global function definition for
  ‘quantile’
dist.diss: no visible binding for global variable ‘median’
dist.diss: no visible global function definition for ‘dist’
hist.kdetrees: no visible binding for global variable ‘density’
kdetrees : cutoff: no visible global function definition for ‘quantile’
kdetrees.complete: no visible global function definition for ‘hist’
kdetrees.complete: no visible global function definition for
  ‘write.csv’
plot.kdetrees: no visible binding for global variable ‘density’
Undefined global functions or variables:
  cophenetic density dist hist median quantile write.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7i0uTJ/R.INSTALL307c496f07dd/kdevine/man/dkde1d.Rd:29: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7i0uTJ/R.INSTALL307c496f07dd/kdevine/man/dkdevinecop.Rd:28: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7i0uTJ/R.INSTALL307c496f07dd/kdevine/man/dkdevinecop.Rd:59: file link ‘rkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7i0uTJ/R.INSTALL307c496f07dd/kdevine/man/dkdevinecop.Rd:60: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7i0uTJ/R.INSTALL307c496f07dd/kdevine/man/kdevine-package.Rd:17: file link ‘kdecopula-package’ in package ‘kdecopula’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kdevine.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpQ1azwc/R.INSTALL755218b45e92/kedd/man/h.bcv.Rd:105: file link ‘bw.bcv’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpQ1azwc/R.INSTALL755218b45e92/kedd/man/h.ucv.Rd:122: file link ‘bw.ucv’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpQ1azwc/R.INSTALL755218b45e92/kedd/man/kernel.fun.Rd:71: file link ‘D’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kedd.Rcheck/00install.out’ for details.
SeasonalMannKendall: no visible global function definition for ‘is.ts’
SeasonalMannKendall: no visible global function definition for
  ‘frequency’
SeasonalMannKendall: no visible global function definition for ‘cycle’
SeasonalMannKendall: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cycle frequency is.ts pnorm
Consider adding
  importFrom("stats", "cycle", "frequency", "is.ts", "pnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpL9MOpt/R.INSTALL674858671beb/keras/man/multi-assign.Rd:10: file link ‘%<-%’ in package ‘zeallot’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpL9MOpt/R.INSTALL674858671beb/keras/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/keras.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Checking should be performed on sources prepared by ‘R CMD build’.
Packages in Depends field not imported from:
  ‘chron’ ‘date’ ‘evir’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ALbw: no visible global function definition for ‘sd’
ALbw: no visible global function definition for ‘quantile’
CVbw: no visible global function definition for ‘quantile’
PBbw: no visible global function definition for ‘sd’
PBbw: no visible global function definition for ‘IQR’
kernel_function: no visible global function definition for ‘dnorm’
kernel_function_distribution: no visible global function definition for
  ‘pnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  IQR approx dnorm pnorm quantile sd
Consider adding
  importFrom("stats", "IQR", "approx", "dnorm", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYgKqFK/R.INSTALLe711fd844da/kergp/man/covQualNested.Rd:96: file link ‘contr.helmert’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYgKqFK/R.INSTALLe711fd844da/kergp/man/covQualNested.Rd:97: file link ‘contr.treatment’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kergp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZYiZ4b/R.INSTALL333f57e5cdc/kernelboot/man/kernelboot-class.Rd:40: file link ‘.Random.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZYiZ4b/R.INSTALL333f57e5cdc/kernelboot/man/kernelboot.Rd:34: file link ‘bw.nrd0’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZYiZ4b/R.INSTALL333f57e5cdc/kernelboot/man/kernelboot.Rd:157: file link ‘runif’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZYiZ4b/R.INSTALL333f57e5cdc/kernelboot/man/kernelboot.Rd:157: file link ‘rnorm’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kernelboot.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8R9bcn/R.INSTALL50711c9ef30c/keyholder/man/keyed-df-one-tbl.Rd:60: file link ‘transmute’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8R9bcn/R.INSTALL50711c9ef30c/keyholder/man/keyed-df-two-tbl.Rd:29: file link ‘join’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8R9bcn/R.INSTALL50711c9ef30c/keyholder/man/keyed-df-two-tbl.Rd:26: file link ‘join’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8R9bcn/R.INSTALL50711c9ef30c/keyholder/man/reexports.Rd:15: file link ‘%>%’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8R9bcn/R.INSTALL50711c9ef30c/keyholder/man/rename-keys-scoped.Rd:29: file link ‘rename_all’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/keyholder.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpRikZKS/R.INSTALL512448747ca5/keyplayer/man/fragment.Rd:85: file link ‘shortest.paths’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRikZKS/R.INSTALL512448747ca5/keyplayer/man/mreach.closeness.Rd:97: file link ‘shortest.paths’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRikZKS/R.INSTALL512448747ca5/keyplayer/man/mreach.degree.Rd:83: file link ‘shortest.paths’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/keyplayer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmprMzHfF/R.INSTALL77fa6a6043f3/KFKSDS/man/KF.Rd:31: file link ‘KS.deriv’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprMzHfF/R.INSTALL77fa6a6043f3/KFKSDS/man/KF.Rd:93: file link ‘KS.deriv’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprMzHfF/R.INSTALL77fa6a6043f3/KFKSDS/man/KS.Rd:32: file link ‘KF.deriv’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprMzHfF/R.INSTALL77fa6a6043f3/KFKSDS/man/KS.Rd:32: file link ‘KF.deriv.C’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprMzHfF/R.INSTALL77fa6a6043f3/KFKSDS/man/KS.Rd:70: file link ‘KSDS’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprMzHfF/R.INSTALL77fa6a6043f3/KFKSDS/man/predict-stsmSS.Rd:34: file link ‘predict.StructTS’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/KFKSDS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpEhlEJh/R.INSTALLd207eda7373/KFPCA/man/SparsePlot.Rd:14: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/KFPCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpBKXrfb/R.INSTALL36805e5d032b/kgrams/man/language_model.Rd:57: file link ‘kgrams’ in package ‘kgrams’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmps9GUou/Rbuild259f16a6893e/kgrams/man/perplexity.Rd:83: file link ‘kgrams’ in package ‘kgrams’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmps9GUou/Rbuild259f16a6893e/kgrams/man/smoothers.Rd:17: file link ‘kgrams’ in package ‘kgrams’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kgrams.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmps4BXkF/R.INSTALL12e127b6eb7c/kimisc/man/seconds.to.hms-deprecated.Rd:29: file link ‘strftime’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kimisc.Rcheck/00install.out’ for details.
kissmigDummyS: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpcTG158/R.INSTALL4c4c63415a95/kknn/man/kknn.Rd:70: file link ‘simulation’ in package ‘kknn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpcTG158/R.INSTALL4c4c63415a95/kknn/man/train.kknn.Rd:62: file link ‘simulation’ in package ‘kknn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kknn.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘rkward’
Found the following significant warnings:
  Rd warning: /tmp/RtmpNL2r9w/R.INSTALL321378565724/klausuR/man/klausur.Rd:170: file link ‘psychometric’ in package ‘psychometric’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNL2r9w/R.INSTALL321378565724/klausuR/man/klausur.Rd:74: file link ‘plot’ in package ‘klausuR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNL2r9w/R.INSTALL321378565724/klausuR/man/klausur.Rd:261: file link ‘plot’ in package ‘klausuR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNL2r9w/R.INSTALL321378565724/klausuR/man/klausur.Rd:261: file link ‘psychometric’ in package ‘psychometric’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNL2r9w/R.INSTALL321378565724/klausuR/man/klausur.report.Rd:41: file link ‘plot’ in package ‘klausuR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/klausuR.Rcheck/00install.out’ for details.
distrct.analysis : <anonymous> : <anonymous>: no visible global
  function definition for ‘cor’
grand.table: no visible global function definition for ‘write.csv2’
grand.table: no visible global function definition for ‘write.csv’
klausur: no visible global function definition for ‘sd’
klausur: no visible global function definition for ‘na.omit’
klausur.gen.marks : suggestion : <anonymous>: no visible global
  function definition for ‘qnorm’
klausur.mufo: no visible global function definition for ‘sd’
klausur.report: no visible global function definition for ‘dev.off’
klausur.report : tabellenbau: no visible global function definition for
  ‘capture.output’
plot,klausuR-missing: no visible global function definition for
  ‘na.omit’
plot,klausuR-missing: no visible global function definition for ‘sd’
plot,klausuR-missing : <anonymous>: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  capture.output cor dev.off dnorm na.omit qnorm sd write.csv
  write.csv2
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "cor", "dnorm", "na.omit", "qnorm", "sd")
  importFrom("utils", "capture.output", "write.csv", "write.csv2")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘km.ci/R/epband.fun.R’:
  data(critical.value.nair.90, critical.value.nair.95, critical.value.nair.99)
File ‘km.ci/R/hall.wellner.fun.R’:
  data(critical.value.hall.90, critical.value.hall.95, critical.value.hall.99)
See section ‘Good practice’ in ‘?data’.
dscore: no visible global function definition for ‘glm’
dscore: no visible binding for global variable ‘binomial’
dscore: no visible global function definition for ‘pnorm’
pearson.group: no visible global function definition for ‘cor’
spearman.group: no visible global function definition for ‘cor’
sscore: no visible global function definition for ‘glm’
sscore: no visible binding for global variable ‘binomial’
sscore: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binomial cor glm pnorm
Consider adding
  importFrom("stats", "binomial", "cor", "glm", "pnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxYTbYR/R.INSTALL2f9d286df6c1/kmer/man/cluster.Rd:57: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxYTbYR/R.INSTALL2f9d286df6c1/kmer/man/kcount.Rd:58: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxYTbYR/R.INSTALL2f9d286df6c1/kmer/man/kdistance.Rd:57: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxYTbYR/R.INSTALL2f9d286df6c1/kmer/man/mbed.Rd:84: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxYTbYR/R.INSTALL2f9d286df6c1/kmer/man/otu.Rd:77: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kmer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXePc3M/R.INSTALL62a62d2318d/kml3d/man/kml3d-package.Rd:107: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXePc3M/R.INSTALL62a62d2318d/kml3d/man/plot3d.Rd:51: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXePc3M/R.INSTALL62a62d2318d/kml3d/man/plot3dPdf.Rd:56: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXePc3M/R.INSTALL62a62d2318d/kml3d/man/plotMean3d.Rd:48: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXePc3M/R.INSTALL62a62d2318d/kml3d/man/plotTraj3d.Rd:48: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kml3d.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘cld1.Rdata’ ‘main.tex’ ‘myCld.Rdata’ ‘myCld3d.Rdata’ ‘scene.asy’
Found the following files/directories:
  ‘cld1.Rdata’ ‘ld.Rdata’ ‘myCld.Rdata’
C_zero : <anonymous>: no visible global function definition for ‘runif’
get_extra_centroid_index: no visible global function definition for
  ‘head’
get_within_cluster_ss: no visible global function definition for
  ‘aggregate’
kmod: no visible global function definition for ‘head’
kmod: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head runif tail
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGeepoq/R.INSTALL32d824698ba2/knitcitations/man/citep.Rd:17: file link ‘Citep’ in package ‘RefManageR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGeepoq/R.INSTALL32d824698ba2/knitcitations/man/citep.Rd:47: file link ‘Citep’ in package ‘RefManageR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGeepoq/R.INSTALL32d824698ba2/knitcitations/man/citet.Rd:17: file link ‘Citet’ in package ‘RefManageR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGeepoq/R.INSTALL32d824698ba2/knitcitations/man/citet.Rd:47: file link ‘Citep’ in package ‘RefManageR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/knitcitations.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Killed after ’
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘rbeta’
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘runif’
calculate.power : <anonymous>: no visible binding for global variable
  ‘quantile’
generate.benchmark.data: no visible global function definition for
  ‘runif’
generate.benchmark.data: no visible global function definition for
  ‘rnorm’
generate.benchmark.data: no visible global function definition for
  ‘rbinom’
generate.patchwork.copula: no visible global function definition for
  ‘rbeta’
generate.patchwork.copula: no visible global function definition for
  ‘runif’
novelTest.chisq: no visible global function definition for ‘pchisq’
novelTest.chisq4nn: no visible global function definition for ‘pchisq’
optimise.copula.mi : <anonymous>: no visible global function definition
  for ‘optimize’
power.plot: no visible global function definition for ‘axis’
power.plot : <anonymous>: no visible global function definition for
  ‘points’
power.plot: no visible global function definition for ‘legend’
roc.plot: no visible global function definition for ‘colorRampPalette’
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for ‘runif’
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq points quantile rbeta
  rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUi6cAp/R.INSTALL331a5ad0926/knockoff/man/stat.stability_selection.Rd:39: file link ‘lars.lasso’ in package ‘stabs’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/knockoff.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘Completeness.RData’ ‘Estimators.RData’ ‘Inf.txt’ ‘List of
  species.RData’ ‘Observed richness.RData’ ‘Records.RData’
  ‘Slope.RData’ ‘Standard error of the estimators.RData’
Found the following significant warnings:
  Rd warning: /tmp/Rtmplit5AF/R.INSTALL104c43f08984/kntnr/man/kntn_unnest.Rd:14: file link ‘unnest’ in package ‘tidyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/kntnr.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
Found the following significant warnings:
  Rd warning: /tmp/RtmpyMQzRM/R.INSTALL93a23f55114/krige/man/as.mcmc.krige.Rd:66: file link ‘as.mcmc’ in package ‘coda’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/krige.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
image.kriging: no visible global function definition for ‘heat.colors’
image.kriging: no visible global function definition for ‘image’
kriging: no visible global function definition for ‘lm’
plot.kriging: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve heat.colors image lm
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image")
  importFrom("stats", "lm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2v3qJh/R.INSTALLa9819e79f37/krippendorffsalpha/man/krippendorffs.alpha.Rd:22: file link ‘pblapply’ in package ‘pbapply’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/krippendorffsalpha.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
kselection: no visible global function definition for ‘txtProgressBar’
kselection: no visible global function definition for
  ‘setTxtProgressBar’
plot.Kselection: no visible global function definition for ‘lines’
plot.Kselection: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  ‘DF7.bas’ ‘DF7.dat’ ‘DF7.rel’ ‘DF7.spc’ ‘DF7.struct’
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘XML’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
auc: no visible global function definition for ‘approx’
kulife.colors: no visible global function definition for ‘palette’
rootonorm: no visible global function definition for ‘sd’
rootonorm: no visible global function definition for ‘hist’
rootonorm: no visible global function definition for ‘pnorm’
rootonorm: no visible global function definition for ‘dnorm’
rootonorm: no visible global function definition for ‘rect’
rootonorm: no visible global function definition for ‘lines’
rootonorm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approx dnorm hist lines palette pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘mydata.xml’ ‘swarms.pdf’
Found the following files/directories:
  ‘m.kvh’ ‘test.kvh’
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘readme.txt’
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  ‘dim’ to ‘dims’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5m8IeB/R.INSTALL16db442f3a7b/labdsv/man/dga.Rd:28: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5m8IeB/R.INSTALL16db442f3a7b/labdsv/man/homoteneity.Rd:15: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5m8IeB/R.INSTALL16db442f3a7b/labdsv/man/importance.Rd:17: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/labdsv.Rcheck/00install.out’ for details.
Found the following hidden files and directories:
  .Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  MIT
Found the following significant warnings:
  Rd warning: /tmp/RtmpxedeyL/R.INSTALL184f12f3b236/labelmachine/man/lapplI.Rd:42: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxedeyL/R.INSTALL184f12f3b236/labelmachine/man/lapplI.Rd:48: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxedeyL/R.INSTALL184f12f3b236/labelmachine/man/lapplI.Rd:50: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxedeyL/R.INSTALL184f12f3b236/labelmachine/man/lapplI.Rd:18: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxedeyL/R.INSTALL184f12f3b236/labelmachine/man/lapplI.Rd:23: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxedeyL/R.INSTALL184f12f3b236/labelmachine/man/named_lapply.Rd:13: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxedeyL/R.INSTALL184f12f3b236/labelmachine/man/named_lapply.Rd:18: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/labelmachine.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘labelrank.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpfY4O2O/R.INSTALL16596a77c32a/LabRS/man/expchart.Rd:28: file link ‘dev.copy’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfY4O2O/R.INSTALL16596a77c32a/LabRS/man/expchart.Rd:11: file link ‘dev.copy’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfY4O2O/R.INSTALL16596a77c32a/LabRS/man/expchart.Rd:22: file link ‘dev.copy’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfY4O2O/R.INSTALL16596a77c32a/LabRS/man/percent.Rd:12: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfY4O2O/R.INSTALL16596a77c32a/LabRS/man/percent.Rd:14: file link ‘prop.table’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfY4O2O/R.INSTALL16596a77c32a/LabRS/man/tabcont.Rd:14: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfY4O2O/R.INSTALL16596a77c32a/LabRS/man/tabcont.Rd:16: file link ‘prop.table’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfY4O2O/R.INSTALL16596a77c32a/LabRS/man/tabfreq.Rd:12: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LabRS.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1VD9zy/R.INSTALL57d7566014d8/labsimplex/man/plot.smplx.Rd:35: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1VD9zy/R.INSTALL57d7566014d8/labsimplex/man/plotSimplexResponse.Rd:13: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1VD9zy/R.INSTALL57d7566014d8/labsimplex/man/prspctv.Rd:51: file link ‘graphical parameters’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/labsimplex.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXq9WXl/R.INSTALLfde27700677/lacunaritycovariance/man/gblemp.Rd:45: file link ‘roll_sum’ in package ‘RcppRoll’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXq9WXl/R.INSTALLfde27700677/lacunaritycovariance/man/rbdd.Rd:33: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXq9WXl/R.INSTALLfde27700677/lacunaritycovariance/man/rbdr.Rd:22: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXq9WXl/R.INSTALLfde27700677/lacunaritycovariance/man/rblnd.Rd:21: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXq9WXl/R.INSTALLfde27700677/lacunaritycovariance/man/rbpto.Rd:43: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lacunaritycovariance.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
LDuncan.aov : prob: no visible global function definition for ‘qtukey’
LDuncan.aov: no visible global function definition for ‘qtukey’
LScottKnott.aov : sk: no visible global function definition for
  ‘pchisq’
LScottKnott.aov: no visible global function definition for ‘read.table’
LTukey.aov: no visible global function definition for ‘qtukey’
Undefined global functions or variables:
  pchisq qtukey read.table
Consider adding
  importFrom("stats", "pchisq", "qtukey")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXd7M5G/R.INSTALL1162107dc18b/LAGOSNE/man/classifications.Rd:135: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXd7M5G/R.INSTALL1162107dc18b/LAGOSNE/man/conn.Rd:303: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXd7M5G/R.INSTALL1162107dc18b/LAGOSNE/man/lake_info.Rd:18: file link ‘agrepl’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXd7M5G/R.INSTALL1162107dc18b/LAGOSNE/man/lakes_limno.Rd:39: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXd7M5G/R.INSTALL1162107dc18b/LAGOSNE/man/locus.Rd:49: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXd7M5G/R.INSTALL1162107dc18b/LAGOSNE/man/lulc.Rd:109: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LAGOSNE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpWYqk5G/R.INSTALL62da7146ad0d/laGP/man/optim.auglag.Rd:255: file link ‘optim.step.tgp’ in package ‘tgp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/laGP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYqoow3/Rbuild5a5373a5f226/lagsarlmtree/man/lagsarlmtree.Rd:36: file link ‘lagsarlm’ in package ‘spdep’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYqoow3/Rbuild5a5373a5f226/lagsarlmtree/man/lagsarlmtree.Rd:94: file link ‘lagsarlm’ in package ‘spdep’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lagsarlmtree.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  ‘GPArotation’ ‘mice’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
angoff: no visible global function definition for ‘cov2cor’
angoff: no visible global function definition for ‘runif’
cov.lambda4: no visible global function definition for ‘cov2cor’
cov.lambda4: no visible global function definition for ‘median’
guttman: no visible global function definition for ‘cov2cor’
impute.cov: no visible global function definition for ‘cov’
impute.cov: no visible global function definition for ‘complete’
impute.cov: no visible global function definition for ‘mice’
kristof: no visible global function definition for ‘cov2cor’
kristof: no visible global function definition for ‘runif’
lambda1: no visible global function definition for ‘cov2cor’
lambda2: no visible global function definition for ‘cov2cor’
lambda3: no visible global function definition for ‘cov2cor’
lambda3: no visible binding for global variable ‘sd’
lambda5: no visible global function definition for ‘cov2cor’
lambda6: no visible global function definition for ‘cov2cor’
omega.tot: no visible global function definition for ‘cov2cor’
omega.tot: no visible global function definition for ‘factanal’
quant.lambda4: no visible global function definition for ‘cov2cor’
quant.lambda4: no visible global function definition for ‘runif’
quant.lambda4: no visible global function definition for ‘quantile’
raju: no visible global function definition for ‘cov2cor’
raju: no visible global function definition for ‘runif’
user.lambda4: no visible global function definition for ‘runif’
user.lambda4: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  complete cov cov2cor factanal median mice quantile runif sd
Consider adding
  importFrom("stats", "cov", "cov2cor", "factanal", "median", "quantile",
             "runif", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpqIWMHz/R.INSTALLf77199a40d3/LambertW/man/W.Rd:54: file link ‘lambertW0’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqIWMHz/R.INSTALLf77199a40d3/LambertW/man/W.Rd:55: file link ‘lambertWm1’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqIWMHz/R.INSTALLf77199a40d3/LambertW/man/W.Rd:38: file link ‘lambertW0’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqIWMHz/R.INSTALLf77199a40d3/LambertW/man/W.Rd:38: file link ‘lambertWm1’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqIWMHz/R.INSTALLf77199a40d3/LambertW/man/W.Rd:112: file link ‘lambertW0’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqIWMHz/R.INSTALLf77199a40d3/LambertW/man/W.Rd:112: file link ‘lambertWm1’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqIWMHz/R.INSTALLf77199a40d3/LambertW/man/p_m1.Rd:58: file link ‘pgeom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LambertW.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
getGO: no visible global function definition for ‘new’
getGO: no visible global function definition for ‘getGeneric’
graph.kd: no visible global function definition for ‘as’
Undefined global functions or variables:
  as getGeneric new
Consider adding
  importFrom("methods", "as", "getGeneric", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Kern.FUN: no visible global function definition for ‘dnorm’
Prob.Covariate.ShortEvent: no visible global function definition for
  ‘bw.nrd’
optimize.mse.BW: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  bw.nrd dnorm optimize
Consider adding
  importFrom("stats", "bw.nrd", "dnorm", "optimize")
to your NAMESPACE file.
Found the following files/directories:
  ‘example.llo’
betabreaker: no visible global function definition for ‘predict’
coef.lars: no visible global function definition for ‘predict’
cv.lars: no visible global function definition for ‘predict’
cv.lars: no visible binding for global variable ‘var’
error.bars: no visible global function definition for ‘segments’
plot.lars: no visible global function definition for ‘matplot’
plot.lars: no visible global function definition for ‘title’
plot.lars: no visible global function definition for ‘abline’
plot.lars: no visible global function definition for ‘axis’
predict.lars: no visible global function definition for ‘approx’
Undefined global functions or variables:
  abline approx axis matplot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
Rd file 'cv.lars.Rd':
  \usage lines wider than 90 characters:
         trace = FALSE, plot.it = TRUE, se = TRUE,type = c("lasso", "lar", "forward.stagewise", "stepwise"),

Rd file 'lars.Rd':
  \usage lines wider than 90 characters:
         trace = FALSE, normalize = TRUE, intercept = TRUE, Gram, eps = .Machine$double.eps, max.steps, use.Gram = TRUE)

Rd file 'plot.lars.Rd':
  \usage lines wider than 90 characters:
     plot(x, xvar= c("norm", "df", "arc.length", "step"), breaks = TRUE, plottype = c("coefficients", 

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘covTest’
glassoscore: no visible global function definition for ‘var’
glassoscore: no visible global function definition for ‘pchisq’
lassoscore: no visible global function definition for ‘txtProgressBar’
lassoscore: no visible global function definition for
  ‘setTxtProgressBar’
lassoscore: no visible global function definition for ‘pchisq’
plot.glassoscore: no visible global function definition for ‘legend’
plot.lassoscore: no visible global function definition for ‘legend’
plot.mbscore: no visible global function definition for ‘legend’
qqpval: no visible global function definition for ‘ppoints’
qqpval: no visible global function definition for ‘qbeta’
qqpval: no visible global function definition for ‘points’
qqpval: no visible global function definition for ‘abline’
qqpval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline legend pchisq points polygon ppoints qbeta setTxtProgressBar
  txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Rd file 'lassoshooting.Rd':
  \usage lines wider than 90 characters:
     lassoshooting(X=NULL, y=NULL, lambda, XtX=NULL, Xty=NULL, thr=1.0e-6, maxit=1e4, nopenalize=NULL, penaltyweight=NULL, trace=0, ...)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpDvZQRy/R.INSTALL7556628e8361/latentnet/man/ergmm-terms.Rd:427: file link ‘terms-ergm’ in package ‘ergm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDvZQRy/R.INSTALL7556628e8361/latentnet/man/gof.ergmm.Rd:43: file link ‘plot.gof’ in package ‘ergm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDvZQRy/R.INSTALL7556628e8361/latentnet/man/gof.ergmm.Rd:93: file link ‘plot.gof’ in package ‘ergm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDvZQRy/R.INSTALL7556628e8361/latentnet/man/mcmc.diagnostics.ergmm.Rd:71: file link ‘plot.mcmc.list’ in package ‘coda’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDvZQRy/R.INSTALL7556628e8361/latentnet/man/simulate.ergmm.Rd:70: file link ‘print.network’ in package ‘network’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/latentnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUx81q8/R.INSTALL5a67653a4f5b/Laterality/man/Laterality-package.Rd:41: file link ‘ade4-package’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUx81q8/R.INSTALL5a67653a4f5b/Laterality/man/laterAFCM.Rd:70: file link ‘ade4-package’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUx81q8/R.INSTALL5a67653a4f5b/Laterality/man/laterAFCM.Rd:70: file link ‘acm.disjonctif’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUx81q8/R.INSTALL5a67653a4f5b/Laterality/man/laterAFCM.Rd:70: file link ‘acm.burt’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUx81q8/R.INSTALL5a67653a4f5b/Laterality/man/lvisAFCM.Rd:114: file link ‘ade4-package’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUx81q8/R.INSTALL5a67653a4f5b/Laterality/man/lvisAFCM.Rd:114: file link ‘acm.disjonctif’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUx81q8/R.INSTALL5a67653a4f5b/Laterality/man/lvisAFCM.Rd:114: file link ‘acm.burt’ in package ‘ade4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Laterality.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIih6Dt/R.INSTALL796a6c365ce6/latrend/man/interface-funFEM.Rd:66: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIih6Dt/R.INSTALL796a6c365ce6/latrend/man/interface-mixAK.Rd:69: file link ‘GLMM_MCMC’ in package ‘mixAK’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIih6Dt/R.INSTALL796a6c365ce6/latrend/man/lcApproxModel-class.Rd:36: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/latrend.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbYuein/R.INSTALL123f71c8398c/latte/man/reexports.Rd:14: file link ‘edit_r_environ’ in package ‘usethis’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/latte.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGXUni2/R.INSTALL3c20298e5c4c/lavaan/man/getCov.Rd:39: file link ‘cov2cor’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGXUni2/R.INSTALL3c20298e5c4c/lavaan/man/lavaan-class.Rd:127: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lavaan.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'gof', 'lava.tobit'
Found the following significant warnings:
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/brunner.munzel.test.Rd:70: file link ‘pwilcox’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/laplace.test.Rd:50: file link ‘plaplace’ in package ‘VGAM’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/lorenz.curve.Rd:48: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/nig.parameter.Rd:59: file link ‘rnig’ in package ‘fBasics’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/rqq.Rd:51: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/rqq.Rd:99: file link ‘qqplot’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/rqq.Rd:99: file link ‘qqline’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lawstat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpQvc4f8/R.INSTALL145a397c5813/lax/man/plot.retlev.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lax.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
plotcorr.lba.3d: warning in pch3d(colcoordi[, dim], pch = pch.budget,
  col = col.budget, ...): partial argument match of ‘col’ to ‘color’
lbfgs: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  hasArg
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0WdlsL/R.INSTALL5cdc6afbca31/lcc/man/lccPlot.Rd:50: file link ‘marrangeGrob’ in package ‘gridExtra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lcc.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
cclcda.default: no visible global function definition for ‘as.formula’
cclcda.default: no visible global function definition for ‘chisq.test’
cclcda.formula: no visible global function definition for ‘model.frame’
cclcda2.default: no visible global function definition for ‘runif’
cclcda2.default: no visible global function definition for ‘chisq.test’
cclcda2.formula: no visible global function definition for
  ‘model.frame’
lcda.default: no visible global function definition for ‘as.formula’
lcda.formula: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  as.formula chisq.test model.frame runif
Consider adding
  importFrom("stats", "as.formula", "chisq.test", "model.frame", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
Found the following significant warnings:
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.lconnect.Rd:20: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.lconnect.Rd:12: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.lconnect.Rd:13: file link ‘plot.sf’ in package ‘sf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.lconnect.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.lconnect.Rd:26: file link ‘plot.sf’ in package ‘sf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.pimp.Rd:21: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.pimp.Rd:12: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.pimp.Rd:13: file link ‘plot.sf’ in package ‘sf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.pimp.Rd:28: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXx35F/R.INSTALL3a0a5266b417/lconnect/man/plot.pimp.Rd:28: file link ‘plot.sf’ in package ‘sf’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lconnect.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘fitted.pdf’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8brZQf/R.INSTALL14767e9400d5/ldaPrototype/man/LDAPrototype.Rd:54: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8brZQf/R.INSTALL14767e9400d5/ldaPrototype/man/LDARep.Rd:34: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8brZQf/R.INSTALL14767e9400d5/ldaPrototype/man/cosineTopics.Rd:26: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8brZQf/R.INSTALL14767e9400d5/ldaPrototype/man/dendTopics.Rd:56: file link ‘labels.hclust’ in package ‘dendextend’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8brZQf/R.INSTALL14767e9400d5/ldaPrototype/man/getPrototype.Rd:102: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8brZQf/R.INSTALL14767e9400d5/ldaPrototype/man/jaccardTopics.Rd:48: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8brZQf/R.INSTALL14767e9400d5/ldaPrototype/man/jsTopics.Rd:30: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8brZQf/R.INSTALL14767e9400d5/ldaPrototype/man/rboTopics.Rd:33: file link ‘availableCores’ in package ‘future’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ldaPrototype.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/Arun2010.Rd:10: file link ‘LDA’ in package ‘topicmodels’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/Arun2010.Rd:12: file link ‘DocumentTermMatrix’ in package ‘tm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/Arun2010.Rd:14: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/CaoJuan2009.Rd:10: file link ‘LDA’ in package ‘topicmodels’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/Deveaud2014.Rd:10: file link ‘LDA’ in package ‘topicmodels’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/FindTopicsNumber.Rd:20: file link ‘DocumentTermMatrix’ in package ‘tm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/FindTopicsNumber.Rd:22: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/FindTopicsNumber.Rd:29: file link ‘LDA’ in package ‘topicmodels’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/FindTopicsNumber.Rd:40: file link ‘LDA’ in package ‘topicmodels’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjPhWjP/R.INSTALL5d47413ed809/ldatuning/man/Griffiths2004.Rd:10: file link ‘LDA’ in package ‘topicmodels’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ldatuning.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘LDOD.Rproj’
multistart : <anonymous>: no visible global function definition for
  ‘runif’
plot.FreD.x: no visible global function definition for ‘modifyList’
plot.FreD.x: no visible global function definition for ‘abline’
plot.FreD.x: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline modifyList points runif
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "runif")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
ARConfIntEst: no visible global function definition for ‘sd’
PTLinkFunc: no visible global function definition for ‘pnorm’
PTLinkFunc: no visible global function definition for ‘qnorm’
PTMultiPeriodPD: no visible global function definition for ‘uniroot’
PTOnePeriodPD : f: no visible global function definition for ‘pbinom’
PTOnePeriodPD: no visible global function definition for ‘uniroot’
QMMGetRLogitPD: no visible global function definition for ‘ecdf’
QMMPDlinkFunc: no visible global function definition for ‘qnorm’
QMMPlot: no visible global function definition for ‘lines’
QMMPlot: no visible global function definition for ‘legend’
VDBCalibratePD: no visible global function definition for ‘ecdf’
VDBGetK: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  ecdf legend lines pbinom pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
core: no visible global function definition for ‘cov’
lad: no visible global function definition for ‘cov’
lad : InitialMatrix: no visible global function definition for ‘cov’
pfc : onepfc: no visible global function definition for ‘as.formula’
pfc : onepfc: no visible global function definition for ‘lm’
pfc: no visible global function definition for ‘cov’
pfc : aniso: no visible global function definition for ‘cov’
plot.lad: no visible global function definition for ‘lines’
plot.lad: no visible global function definition for ‘lowess’
plot.lad: no visible global function definition for ‘title’
plot.lad: no visible global function definition for ‘par’
plot.lad: no visible global function definition for ‘legend’
plot.pfc: no visible global function definition for ‘lines’
plot.pfc: no visible global function definition for ‘lowess’
plot.pfc: no visible global function definition for ‘title’
plot.pfc: no visible global function definition for ‘par’
plot.pfc: no visible global function definition for ‘legend’
screen.pfc : unipfc: no visible global function definition for
  ‘as.formula’
screen.pfc : unipfc: no visible global function definition for ‘lm’
screen.pfc : unipfc: no visible global function definition for ‘pf’
structure.test: no visible global function definition for ‘pchisq’
summary.core : lrtest: no visible global function definition for
  ‘pchisq’
summary.lad : lrtest: no visible global function definition for
  ‘pchisq’
summary.pfc : lrtest: no visible global function definition for
  ‘pchisq’
summary.pfc : r2: no visible global function definition for ‘lm’
Undefined global functions or variables:
  as.formula cov legend lines lm lowess par pchisq pf title
Consider adding
  importFrom("graphics", "legend", "lines", "par", "title")
  importFrom("stats", "as.formula", "cov", "lm", "lowess", "pchisq",
             "pf")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnK0dNu/R.INSTALL45e91ca25bed/leafem/man/addGeoRaster.Rd:37: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnK0dNu/R.INSTALL45e91ca25bed/leafem/man/addGeotiff.Rd:39: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnK0dNu/R.INSTALL45e91ca25bed/leafem/man/addStaticLabels.Rd:29: file link ‘addLabelOnlyMarkers’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnK0dNu/R.INSTALL45e91ca25bed/leafem/man/addStaticLabels.Rd:23: file link ‘labelOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnK0dNu/R.INSTALL45e91ca25bed/leafem/man/addStaticLabels.Rd:63: file link ‘addLabelOnlyMarkers’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnK0dNu/R.INSTALL45e91ca25bed/leafem/man/addTileFolder.Rd:32: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnK0dNu/R.INSTALL45e91ca25bed/leafem/man/colorOptions.Rd:11: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/leafem.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpuq8nyI/R.INSTALL161613cc44de/leaflegend/man/addLeafLegends.Rd:109: file link ‘addControl’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpuq8nyI/R.INSTALL161613cc44de/leaflegend/man/addLeafLegends.Rd:116: file link ‘addControl’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpuq8nyI/R.INSTALL161613cc44de/leaflegend/man/addLegendImage.Rd:36: file link ‘addControl’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpuq8nyI/R.INSTALL161613cc44de/leaflegend/man/addLegendImage.Rd:39: file link ‘addControl’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpuq8nyI/R.INSTALL161613cc44de/leaflegend/man/addLegendSize.Rd:56: file link ‘addControl’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpuq8nyI/R.INSTALL161613cc44de/leaflegend/man/addLegendSize.Rd:59: file link ‘addControl’ in package ‘leaflet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/leaflegend.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUdOWzU/R.INSTALL17636810764c/leafletCN/man/leafletCN-imports.Rd:8: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/leafletCN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpvogrIt/R.INSTALL16977a057606/leaflet.esri/man/addEsriBasemapLayer.Rd:21: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvogrIt/R.INSTALL16977a057606/leaflet.esri/man/addEsriDynamicMapLayer.Rd:24: file link ‘popupOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvogrIt/R.INSTALL16977a057606/leaflet.esri/man/addEsriFeatureLayer.Rd:47: file link ‘markerClusterOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvogrIt/R.INSTALL16977a057606/leaflet.esri/man/addEsriFeatureLayer.Rd:91: file link ‘highlightOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvogrIt/R.INSTALL16977a057606/leaflet.esri/man/addEsriImageMapLayer.Rd:24: file link ‘popupOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvogrIt/R.INSTALL16977a057606/leaflet.esri/man/tiledMapLayerOptions.Rd:21: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/leaflet.esri.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpMP8OhN/R.INSTALL1a614a316b81/leaflet.extras/man/TileCaching.Rd:13: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMP8OhN/R.INSTALL1a614a316b81/leaflet.extras/man/TileCaching.Rd:13: file link ‘addTiles’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMP8OhN/R.INSTALL1a614a316b81/leaflet.extras/man/addGeodesicPolylines.Rd:67: file link ‘pathOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMP8OhN/R.INSTALL1a614a316b81/leaflet.extras/man/omnivore.Rd:197: file link ‘addGeoJSON’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMP8OhN/R.INSTALL1a614a316b81/leaflet.extras/man/omnivore.Rd:197: file link ‘addTopoJSON’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMP8OhN/R.INSTALL1a614a316b81/leaflet.extras/man/omnivore.Rd:106: file link ‘markerClusterOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMP8OhN/R.INSTALL1a614a316b81/leaflet.extras/man/omnivore.Rd:150: file link ‘highlightOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/leaflet.extras.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpMQa2oP/R.INSTALL1df147281cf8/leaflet.minicharts/man/addMinicharts.Rd:166: file link ‘addPolygons’ in package ‘leaflet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/leaflet.minicharts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIZA6k4/R.INSTALL434164a22b90/leaflet/man/leaflet-imports.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIZA6k4/R.INSTALL434164a22b90/leaflet/man/map-shiny.Rd:16: file link ‘shinyWidgetOutput’ in package ‘htmlwidgets’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/leaflet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpJQQYvh/R.INSTALL717378fcded5/leafpop/man/popup.Rd:54: file link ‘attachDependencies’ in package ‘htmltools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/leafpop.Rcheck/00install.out’ for details.
BEAPFrOG: no visible global function definition for ‘jags.model’
BEAPFrOG: no visible global function definition for ‘coda.samples’
LEAPFrOG_EM: no visible global function definition for ‘write.table’
LEAPFrOG_EM: no visible global function definition for ‘constrOptim’
LEAPFrOG_plot: no visible global function definition for ‘par’
LEAPFrOG_plot: no visible global function definition for ‘barplot’
LEAPFrOG_plot: no visible global function definition for ‘legend’
constrOptim2: no visible global function definition for ‘optim’
Undefined global functions or variables:
  barplot coda.samples constrOptim jags.model legend optim par
  write.table
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "constrOptim", "optim")
  importFrom("utils", "write.table")
to your NAMESPACE file.
AlternateSVD: no visible binding for global variable ‘sd’
IPOD: no visible global function definition for ‘mad’
IPOD: no visible global function definition for ‘pnorm’
Pvalue: no visible global function definition for ‘pf’
ROCplot: no visible global function definition for ‘png’
ROCplot: no visible global function definition for ‘matplot’
ROCplot: no visible global function definition for ‘legend’
ROCplot: no visible global function definition for ‘dev.off’
leapp: no visible global function definition for ‘png’
leapp: no visible global function definition for ‘dev.off’
ridge: no visible global function definition for ‘sd’
ridge: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dev.off legend mad matplot pf png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpyow9wf/R.INSTALL5f856568dbac/lefko3/man/image3.Rd:22: file link ‘image’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpyow9wf/R.INSTALL5f856568dbac/lefko3/man/image3.lefkoElas.Rd:30: file link ‘image’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpyow9wf/R.INSTALL5f856568dbac/lefko3/man/image3.lefkoMat.Rd:28: file link ‘image’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpyow9wf/R.INSTALL5f856568dbac/lefko3/man/image3.lefkoSens.Rd:30: file link ‘image’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpyow9wf/R.INSTALL5f856568dbac/lefko3/man/image3.list.Rd:25: file link ‘image’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpyow9wf/R.INSTALL5f856568dbac/lefko3/man/image3.matrix.Rd:20: file link ‘image’ in package ‘SparseM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lefko3.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpyCaEBk/R.INSTALL407a2bf0f29c/leiden/man/leiden.Rd:25: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/leiden.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUmlhpL/R.INSTALL4d9f2564315e/LeMaRns/man/calc_Q.Rd:138: file link ‘dlnorm’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LeMaRns.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpE8rONm/R.INSTALL1e486d199d09/lenses/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lenses.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIVNm5Z/R.INSTALL20f366203cab/lfstat/man/cdf_ev.Rd:26: file link ‘quagev’ in package ‘lmom’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIVNm5Z/R.INSTALL20f366203cab/lfstat/man/cdf_ev.Rd:26: file link ‘pelgev’ in package ‘lmom’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lfstat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxrphP0/R.INSTALL2142660bf8d4/LICORS/man/wKDE.Rd:41: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LICORS.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2'
Depends: includes the non-default packages:
  'sn', 'moments', 'BB', 'Bolstad2', 'optimx', 'Rmpfr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Non-standard files/directories found at top level:
  ‘LIHNPSD-manual.pdf’ ‘PSD-Paper.pdf’ ‘Rplots.pdf’
Packages in Depends field not imported from:
  ‘BB’ ‘Bolstad2’ ‘Rmpfr’ ‘moments’ ‘optimx’ ‘sn’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'LIHNPSD-package.Rd':
  \examples lines wider than 100 characters:
       dist <- list( sigma= 0.004625, alpha= 0.292645, gamma= 0.482744, beta= -0.154049, location= 0.002968 )

Rd file 'LIHNPSD_standardfit_fn.Rd':
  \usage lines wider than 90 characters:
     LIHNPSD_standardfit_fn(psd, data_stats, hist, plotqq = 1, weights = list(), merge_tails = c(0, 0), debug = 0)

Rd file 'prepare.Rd':
  \examples lines wider than 100 characters:
       dist <- list( sigma= 0.004625, alpha= 0.292645, gamma= 0.482744, beta= -0.154049, location= 0.002968 )

Rd file 'rawmean.Rd':
  \examples lines wider than 100 characters:
       dist <- list( sigma= 0.004625, alpha= 0.292645, gamma= 0.482744, beta= -0.154049, location= 0.002968 )

These lines will be truncated in the PDF manual.
plotBox: no visible global function definition for ‘sd’
plotBox: no visible global function definition for ‘rect’
plotBox: no visible global function definition for ‘qnorm’
plotBox: no visible global function definition for ‘segments’
plotInit: no visible global function definition for ‘runif’
plotInit: no visible global function definition for ‘mtext’
plotInit: no visible global function definition for ‘segments’
plotStack: no visible global function definition for ‘points’
Undefined global functions or variables:
  mtext points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Plotranges.double: no visible global function definition for ‘strwidth’
Plotranges.double: no visible global function definition for
  ‘strheight’
Plotranges.double: no visible global function definition for ‘plot.new’
Plotranges.double: no visible global function definition for ‘par’
Plotranges.double: no visible global function definition for
  ‘plot.window’
Plotranges.double: no visible global function definition for ‘mtext’
Plotranges.double: no visible global function definition for ‘abline’
Plotranges.double: no visible global function definition for ‘points’
Plotranges.double: no visible global function definition for ‘segments’
Plotranges.double: no visible global function definition for ‘text’
Plotranges.double: no visible global function definition for ‘axis’
Plotranges.double: no visible global function definition for ‘box’
Plotranges.double: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis box mtext par plot.new plot.window points segments
  strheight strwidth text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "mtext", "par",
             "plot.new", "plot.window", "points", "segments",
             "strheight", "strwidth", "text", "title")
to your NAMESPACE file.
class.calib: no visible global function definition for ‘lm’
class.calib: no visible global function definition for ‘coef’
class.calib: no visible global function definition for ‘qt’
hoad.calib: no visible global function definition for ‘lm’
hoad.calib: no visible global function definition for ‘anova’
hoad.calib: no visible global function definition for ‘qt’
hoad.calib: no visible global function definition for ‘rnorm’
huntlam.calib: no visible global function definition for ‘lm’
huntlam.calib: no visible global function definition for ‘anova’
huntlam.calib: no visible global function definition for ‘rnorm’
huntlam.calib: no visible global function definition for ‘qnorm’
inver.calib: no visible global function definition for ‘lm’
inver.calib: no visible global function definition for ‘coef’
inver.calib: no visible global function definition for ‘anova’
inver.calib: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  anova coef lm qnorm qt rnorm
Consider adding
  importFrom("stats", "anova", "coef", "lm", "qnorm", "qt", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp47IkOs/R.INSTALL59f419d79a6d/lingmatch/man/lma_weight.Rd:94: file link ‘log’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lingmatch.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1g7yrB/R.INSTALL1d85f39c775/lingtypology/man/imports.Rd:8: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lingtypology.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPZX2rp/R.INSTALL1e06ccc21ee/linguisticsdown/man/writeIPA.Rd:14: file link ‘insertText’ in package ‘rstudioapi’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/linguisticsdown.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
gcomb: no visible global function definition for ‘complete.cases’
linkim: no visible global function definition for ‘runif’
missing.dist: no visible global function definition for
  ‘complete.cases’
pgdata1: no visible global function definition for ‘barplot’
pgdata1: no visible global function definition for ‘layout’
pgdata1: no visible global function definition for ‘par’
pgdata1: no visible global function definition for ‘rainbow’
singim: no visible global function definition for ‘complete.cases’
singim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot complete.cases layout par rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "barplot", "layout", "par")
  importFrom("stats", "complete.cases", "runif")
to your NAMESPACE file.
gen.lms: no visible global function definition for ‘na.omit’
plot.idf: no visible global function definition for ‘mtext’
plot.idf: no visible global function definition for ‘points’
plot.idf: no visible global function definition for ‘segments’
plot.idf: no visible global function definition for ‘ftable’
plot.idf: no visible global function definition for ‘image’
plot.idf: no visible global function definition for ‘gray’
plot.idf: no visible global function definition for ‘abline’
plot.s.linlir: no visible global function definition for ‘mtext’
plot.s.linlir: no visible global function definition for ‘polygon’
plot.s.linlir: no visible global function definition for ‘points’
plot.s.linlir: no visible global function definition for ‘curve’
s.linlir: no visible global function definition for ‘na.omit’
s.linlir: no visible global function definition for ‘dbinom’
s.linlir: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq points
  polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "points",
             "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
Rd file 'idf.Rd':
  \usage lines wider than 90 characters:
     plot(x, y=NULL, ..., var = NULL, typ="hist", k.x = 1, k.y = 1, inf.margin=10, p.cex=1, col.lev=15, plot.grid=FALSE, x.adj = 0.5, x.padj ... [TRUNCATED]
  \examples lines wider than 100 characters:
     plot(pm.idf, typ="draft", k.x=10, k.y=20, p.cex=0.35, x.adj=0.5, x.padj=4, y.las=0, y.adj=0.5, y.padj=-4, x.lab="temperature", y.lab="p ... [TRUNCATED]

Rd file 's.linlir.Rd':
  \usage lines wider than 90 characters:
     plot(x, y=NULL, ..., typ, para.typ="polygon", b.grid=500, nb.func=1000, seed.func=NULL, pl.lrm=TRUE, pl.band=FALSE, lrm.col="blue", pl. ... [TRUNCATED]
  \examples lines wider than 100 characters:
     plot(test, typ="lrm", lrm.col="red", pl.band=TRUE, pl.dat=TRUE, pl.dat.typ="draft",k.x=10, k.y=10, y.las=1, y.adj=6)

These lines will be truncated in the PDF manual.
Non-standard file/directory found at top level:
  ‘pkg.Rproj’
'library' or 'require' call to ‘lpSolve’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lpSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
solveLP: no visible global function definition for ‘lp’
Undefined global functions or variables:
  lp
Found the following files/directories:
  ‘steinh.mps’
Found the following significant warnings:
  Rd warning: /tmp/RtmpshHZbj/R.INSTALL6c6aadd201/lintr/man/linters.Rd:217: file link ‘seq_len’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpshHZbj/R.INSTALL6c6aadd201/lintr/man/linters.Rd:218: file link ‘seq_along’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpshHZbj/R.INSTALL6c6aadd201/lintr/man/read_settings.Rd:24: file link ‘read.dcf’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lintr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpAntmVp/R.INSTALL1b99294071d6/lipidomeR/man/heatmap_lipidome_from_limma.Rd:91: file link ‘scale_shape_manual’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lipidomeR.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘package.R’
last: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
getMatrix : <anonymous>: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘scatterplot3d’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'lle.Rd':
  \examples lines wider than 100 characters:
             plot( results$id, main="intrinsic dimension", type="l", xlab=expression(x[i]), ylab="id", lwd=2 )

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpqHfYCG/R.INSTALL69ed226c0d98/LLSR/man/AQSysCurve.Rd:47: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqHfYCG/R.INSTALL69ed226c0d98/LLSR/man/AQSysCurve.Rd:92: file link ‘graphical parameters’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LLSR.Rcheck/00install.out’ for details.
lm.beta: no visible global function definition for ‘coef’
lm.beta: no visible global function definition for ‘model.matrix’
lm.beta: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  coef model.frame model.matrix
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmMnZSt/R.INSTALL79d4142aa2bc/lme4/man/bootMer.Rd:71: file link ‘clusterExport’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmMnZSt/R.INSTALL79d4142aa2bc/lme4/man/glmer.nb.Rd:9: file link ‘theta.ml’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmMnZSt/R.INSTALL79d4142aa2bc/lme4/man/glmer.nb.Rd:34: file link ‘theta.ml’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmMnZSt/R.INSTALL79d4142aa2bc/lme4/man/glmer.nb.Rd:65: file link ‘theta.ml’ in package ‘MASS’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lme4.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  ‘compl’ to ‘complete’
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  ‘compl’ to ‘complete’
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
Rd file 'lmec-package.Rd':
  \examples lines wider than 100 characters:
     X<- cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

Rd file 'lmec.Rd':
  \usage lines wider than 90 characters:
     lmec(yL, cens, X, Z, cluster, maxstep = 200, varstruct = "unstructured", init, method = "ML", epsstop = 0.001, abspmv = 0.001, mcmc0 =  ... [TRUNCATED]
  \examples lines wider than 100 characters:
     X = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSYE9ci/R.INSTALL5c5f739a033f/lmeInfo/man/CI_g.Rd:15: file link ‘qt’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lmeInfo.Rcheck/00install.out’ for details.
mq.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for ‘plot.missing’
Undefined global functions or variables:
  plot.missing
Package vignette with placeholder title ‘Vignette Title’:
  ‘lmem.qtler.Rmd’
Found the following files/directories:
  ‘cross.data.file.csv’ ‘qtl_analysis_reports’
Found the following significant warnings:
  Rd warning: /tmp/RtmpeLnUDQ/R.INSTALL32b6435cc344/lmerTest/man/lmer.Rd:52: file link ‘glmerControl’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeLnUDQ/R.INSTALL32b6435cc344/lmerTest/man/lmerModLmerTest-class.Rd:10: file link ‘merMod’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeLnUDQ/R.INSTALL32b6435cc344/lmerTest/man/lmerModLmerTest-class.Rd:34: file link ‘merMod’ in package ‘lme4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lmerTest.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
approx.Z : <anonymous>: no visible global function definition for
  ‘approx’
smspline: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  approx model.frame
Consider adding
  importFrom("stats", "approx", "model.frame")
to your NAMESPACE file.
HTest: no visible global function definition for ‘is.owin’
HTest: no visible global function definition for ‘inside.owin’
HTest: no visible global function definition for ‘area.owin’
HTest: no visible global function definition for ‘union.owin’
HTest: no visible global function definition for ‘intersect.owin’
HTest: no visible global function definition for ‘erosion.owin’
HTest: no visible global function definition for ‘dilation.owin’
area_esh: no visible global function definition for ‘area.owin’
detectability_cps: no visible global function definition for ‘disc’
detectability_cps: no visible global function definition for
  ‘intersect.owin’
detectability_cps: no visible global function definition for ‘edges’
detectability_cps: no visible global function definition for
  ‘lengths.psp’
detectability_cps: no visible global function definition for
  ‘union.owin’
detectability_cps: no visible global function definition for ‘erosion’
detectability_cps: no visible global function definition for ‘dilation’
gg_wind: no visible global function definition for ‘disc’
gg_wind: no visible global function definition for ‘union.owin’
shades: no visible global function definition for ‘owin’
shades: no visible global function definition for ‘union.owin’
shades: no visible global function definition for ‘disc’
visibility_thinning_cps: no visible global function definition for
  ‘disc’
visibility_thinning_cps: no visible global function definition for
  ‘intersect.owin’
visibility_thinning_cps: no visible global function definition for
  ‘inside.owin’
visibility_thinning_cps: no visible global function definition for
  ‘union.owin’
visibility_thinning_cps: no visible global function definition for
  ‘erosion’
visibility_thinning_cps: no visible global function definition for
  ‘dilation’
Undefined global functions or variables:
  area.owin dilation dilation.owin disc edges erosion erosion.owin
  inside.owin intersect.owin is.owin lengths.psp owin union.owin
Found the following significant warnings:
  Rd warning: /tmp/Rtmp95efEk/R.INSTALL6ad715baa7cb/LMMELSM/man/lmmelsm.Rd:16: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LMMELSM.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5dFFal/R.INSTALL529c68d8f855/lmtest/man/coeftest.Rd:99: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lmtest.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpHZ38RE/R.INSTALL5fb242a3e448/lmvar/man/fitted.lmvar.Rd:29: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHZ38RE/R.INSTALL5fb242a3e448/lmvar/man/fwbw.lm.Rd:87: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHZ38RE/R.INSTALL5fb242a3e448/lmvar/man/fwbw.lmvar_no_fit.Rd:92: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHZ38RE/R.INSTALL5fb242a3e448/lmvar/man/plot.lmvar.Rd:22: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lmvar.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘tTestTable.rda’
AnalyticalOptim: no visible global function definition for ‘optim’
LLConstructor : LL: no visible global function definition for ‘dpois’
MixtureDensity: no visible global function definition for ‘glm’
MixtureDensity : f_hat: no visible global function definition for
  ‘predict’
NullDensity : f0: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois glm optim predict
Consider adding
  importFrom("stats", "dpois", "glm", "optim", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: C:/Users/KevinD/AppData/Local/Temp/Rtmpay2n4e/Rbuilde004e245770/lodr/man/coef.lod_lm.Rd:35: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/KevinD/AppData/Local/Temp/Rtmpay2n4e/Rbuilde004e245770/lodr/man/lod_lm.Rd:23: file link ‘as.numeric’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/KevinD/AppData/Local/Temp/Rtmpay2n4e/Rbuilde004e245770/lodr/man/lod_lm.Rd:70: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/KevinD/AppData/Local/Temp/Rtmpay2n4e/Rbuilde004e245770/lodr/man/residuals.lod_lm.Rd:39: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lodr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8ztY07/R.INSTALL7cc5dc481a3/LogConcDEAD/man/plot.LogConcDEAD.Rd:5: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8ztY07/R.INSTALL7cc5dc481a3/LogConcDEAD/man/plot.LogConcDEAD.Rd:38: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8ztY07/R.INSTALL7cc5dc481a3/LogConcDEAD/man/plot.LogConcDEAD.Rd:62: file link ‘heat_hcl’ in package ‘colorspace’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8ztY07/R.INSTALL7cc5dc481a3/LogConcDEAD/man/plot.LogConcDEAD.Rd:78: file link ‘heat_hcl’ in package ‘colorspace’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LogConcDEAD.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpy6Cneg/R.INSTALL64f26056335/loggit/man/handlers.Rd:44: file link ‘getOption’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/loggit.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
EstimateProbability: no visible global function definition for
  ‘predict’
LOGICOIL: no visible binding for global variable ‘pssm’
LOGICOIL: no visible binding for global variable ‘LOGICOILfit’
LOGICOIL: no visible binding for global variable ‘Model_Parameters’
plot_LOGICOIL: no visible global function definition for ‘png’
plot_LOGICOIL: no visible global function definition for ‘par’
plot_LOGICOIL: no visible global function definition for ‘lines’
plot_LOGICOIL: no visible global function definition for ‘axis’
plot_LOGICOIL: no visible global function definition for ‘mtext’
plot_LOGICOIL: no visible global function definition for ‘legend’
plot_LOGICOIL: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par png
  predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par")
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following files/directories:
  ‘GCN4wt’
Malformed Description field: should contain one or more complete sentences.
LogitNet.weight: no visible global function definition for ‘lowess’
LogitNet.weight: no visible global function definition for ‘median’
Undefined global functions or variables:
  lowess median
Consider adding
  importFrom("stats", "lowess", "median")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
rloglognorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LogrankA: no visible global function definition for ‘is.Surv’
LogrankA: no visible global function definition for ‘na.omit’
LogrankA: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  is.Surv na.omit pchisq
Consider adding
  importFrom("stats", "na.omit", "pchisq")
to your NAMESPACE file.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpDSNpu1/R.INSTALL12976e9c8cc/longitudinalData/man/makeLatexFile.Rd:44: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDSNpu1/R.INSTALL12976e9c8cc/longitudinalData/man/parWindows.Rd:25: file link ‘split.screen’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDSNpu1/R.INSTALL12976e9c8cc/longitudinalData/man/plot3dPdf.Rd:58: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDSNpu1/R.INSTALL12976e9c8cc/longitudinalData/man/plotTrajMeans3d.Rd:45: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpDSNpu1/R.INSTALL12976e9c8cc/longitudinalData/man/saveTrianglesAsASY.Rd:28: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/longitudinalData.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘main.tex’ ‘scene.asy’
Found the following significant warnings:
  Rd warning: /tmp/RtmpQRC6l2/R.INSTALL25b4306c21aa/longitudinal/man/dyn.cor.Rd:31: file link ‘cor.shrink’ in package ‘corpcor’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpQRC6l2/R.INSTALL25b4306c21aa/longitudinal/man/dyn.cor.Rd:36: file link ‘var.shrink’ in package ‘corpcor’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/longitudinal.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
fplot: no visible global function definition for ‘rnorm’
fplot: no visible global function definition for ‘segments’
fplot: no visible global function definition for ‘points’
fplot: no visible global function definition for ‘text’
fplot.foodweb: no visible global function definition for ‘segments’
fplot.foodweb: no visible global function definition for ‘points’
fplot.foodweb: no visible global function definition for ‘text’
gplot: no visible global function definition for ‘runif’
groupplot: no visible global function definition for ‘rnorm’
groupplot: no visible global function definition for ‘segments’
groupplot: no visible global function definition for ‘points’
groupplot: no visible global function definition for ‘text’
groupplot.foodweb: no visible global function definition for ‘rnorm’
groupplot.foodweb: no visible global function definition for ‘segments’
groupplot.foodweb: no visible global function definition for ‘points’
groupplot.foodweb: no visible global function definition for ‘text’
Undefined global functions or variables:
  points rnorm runif segments text
Consider adding
  importFrom("graphics", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Rd file 'fplot.Rd':
  \usage lines wider than 90 characters:
     fplot(gemat,type="both",metric="jaccard",addlabels=FALSE,scaled=TRUE,weighted=TRUE,pch=20,bg=1,pcex=3,pcol=4,lty=1,lcol=8,tfont=12,tcol ... [TRUNCATED]

Rd file 'fplot.foodweb.Rd':
  \usage lines wider than 90 characters:
     fplot.foodweb(gemat,ranks,addlabels=FALSE,scaled=TRUE,weighted=TRUE,pch=20,bg=1,pcex=3,pcol=4,lty=1,lcol=8,tfont=12,tcol=1)

Rd file 'groupplot.Rd':
  \usage lines wider than 90 characters:
     groupplot(gemat, groups, type = "both", metric = "jaccard", addlabels = FALSE, scaled = TRUE, pch = 20, bg = 1, pcex = 3, pcol = 4, lty ... [TRUNCATED]

Rd file 'groupplot.foodweb.Rd':
  \usage lines wider than 90 characters:
     groupplot.foodweb(gemat, ranks, groups, addlabels = FALSE, scaled = TRUE, pch = 20, bg = 1, pcex = 3, pcol = 4, lty = 1, lcol = 8, tfon ... [TRUNCATED]
  \examples lines wider than 100 characters:
     groupplot.foodweb(gemat=mat,ranks=rlist,groups=glist,pch=pch,lcol=lcol) #other parameters are set in default

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1jbmw6/R.INSTALL6e227ae6d002/lotri/man/lotri.Rd:17: file link ‘sys.call’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lotri.Rcheck/00install.out’ for details.
Checking should be performed on sources prepared by ‘R CMD build’.
Malformed Description field: should contain one or more complete sentences.
lpint : <anonymous>: no visible global function definition for
  ‘integrate’
lpint: no visible global function definition for ‘integrate’
lpint : lpint : <anonymous>: no visible global function definition for
  ‘integrate’
lplikint : lplikint.fun : <anonymous>: no visible global function
  definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
'library' or 'require' call to ‘Rsymphony’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
mipSolve.Rsymphony: no visible global function definition for
  ‘Rsymphony_solve_LP’
Undefined global functions or variables:
  Rsymphony_solve_LP
learnPattern.default: no visible global function definition for ‘runif’
plot.learnPattern: no visible global function definition for ‘matplot’
plotMDS: no visible global function definition for ‘par’
plotMDS: no visible global function definition for ‘rainbow’
plotMDS: no visible global function definition for ‘pairs’
visualizePattern: no visible global function definition for ‘par’
visualizePattern: no visible global function definition for ‘points’
visualizePattern: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend matplot pairs par points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
LP.comoment: no visible global function definition for ‘cor’
LP.comoment: no visible global function definition for ‘cov’
LP.moment: no visible global function definition for ‘cor’
LPTrans: no visible global function definition for ‘ecdf’
VAR: no visible global function definition for ‘embed’
VAR: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cor cov ecdf embed lm
Consider adding
  importFrom("stats", "cor", "cov", "ecdf", "embed", "lm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpe7IIQ9/R.INSTALL175940604ed7/LSAfun/man/breakdown.Rd:33: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpe7IIQ9/R.INSTALL175940604ed7/LSAfun/man/plot_doclist.Rd:36: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpe7IIQ9/R.INSTALL175940604ed7/LSAfun/man/plot_doclist.Rd:57: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpe7IIQ9/R.INSTALL175940604ed7/LSAfun/man/plot_neighbors.Rd:41: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpe7IIQ9/R.INSTALL175940604ed7/LSAfun/man/plot_wordlist.Rd:34: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpe7IIQ9/R.INSTALL175940604ed7/LSAfun/man/plot_wordlist.Rd:52: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LSAfun.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5O75Ka/R.INSTALL2b305436733b/LSC/man/LSC-utils.Rd:110: file link ‘plot.mixed_LICORS’ in package ‘LICORS’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LSC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: C:/Users/Marcelo/AppData/Local/Temp/Rtmp42WNqX/Rbuild347440411127/LSDsensitivity/man/ergod.test.lsd.rd:34: file link ‘PP.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Marcelo/AppData/Local/Temp/Rtmp42WNqX/Rbuild347440411127/LSDsensitivity/man/ergod.test.lsd.rd:48: file link ‘PP.test’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LSDsensitivity.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Lsdv.formula: no visible global function definition for ‘model.frame’
Lsdv.formula: no visible global function definition for ‘model.matrix’
Lsdv.formula: no visible global function definition for
  ‘model.response’
lsdv: no visible global function definition for ‘pf’
summary.Lsdv: no visible global function definition for ‘coef’
summary.Lsdv: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pf pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pf", "pt")
to your NAMESPACE file.
legend.lshorth: no visible global function definition for ‘legend’
legend.lshorth: no visible global function definition for ‘strwidth’
legend.lshorth: no visible global function definition for ‘text’
plot.lshorth: no visible global function definition for ‘plot.new’
plot.lshorth: no visible global function definition for ‘plot.window’
plot.lshorth: no visible global function definition for ‘axis’
plot.lshorth: no visible global function definition for ‘title’
plot.lshorth: no visible global function definition for ‘box’
plot.lshorth: no visible global function definition for ‘lines’
plot.lshorth: no visible global function definition for ‘legend’
plot.lshorth: no visible global function definition for ‘strwidth’
plot.lshorth: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box legend lines plot.new plot.window strwidth text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot.new",
             "plot.window", "strwidth", "text", "title")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbdoOmt/Rbuild2bcd47d3a48d9/LSTS/man/block.smooth.periodogram.Rd:52: file link ‘trunc’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdoOmt/Rbuild2bcd47d3a48d9/LSTS/man/periodogram.Rd:54: file link ‘Mod’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdoOmt/Rbuild2bcd47d3a48d9/LSTS/man/spectral.density.Rd:39: file link ‘Mod’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/LSTS.Rcheck/00install.out’ for details.
OC : Lnapprox: no visible global function definition for ‘pnorm’
OC : Lnapprox: no visible global function definition for ‘qnorm’
OC : Lt: no visible global function definition for ‘pt’
OC : Lt: no visible global function definition for ‘qnorm’
OC : OC_emwa2: no visible global function definition for ‘pnorm’
OC : OC_emwa2: no visible global function definition for ‘qnorm’
OC: no visible global function definition for ‘pnorm’
OC: no visible global function definition for ‘qnorm’
cmBE : LAtHy: no visible global function definition for ‘phyper’
cmBE: no visible global function definition for ‘uniroot’
planAOQL : Gderivacex: no visible global function definition for
  ‘pnorm’
planAOQL : Mnk: no visible global function definition for ‘uniroot’
planAOQL : k0AOQL : delta: no visible global function definition for
  ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘qnorm’
planAOQL : fMSmodq2: no visible global function definition for
  ‘optimize’
planAOQL : kAOQL: no visible global function definition for ‘uniroot’
planLTPD : nAPPROXL : k0L : g: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L : h: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘pnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL: no visible global function definition for
  ‘uniroot’
planLTPD : kEWMA: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  optimize phyper pnorm pt qnorm uniroot
Consider adding
  importFrom("stats", "optimize", "phyper", "pnorm", "pt", "qnorm",
             "uniroot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘robustbase’
  Please remove these calls from your code.
ltsbase: no visible global function definition for ‘lm’
ltsbase: no visible global function definition for ‘lines’
ltsbase: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines lm
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "lm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUX53SF/R.INSTALL7c443c6b9d35/lumberjack/man/simple.Rd:28: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUX53SF/R.INSTALL7c443c6b9d35/lumberjack/man/simple.Rd:29: file link ‘write.csv’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lumberjack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2DCsvq/R.INSTALL7cb87f765cd1/lunar/man/lunar.distance.Rd:9: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2DCsvq/R.INSTALL7cb87f765cd1/lunar/man/lunar.distance.mean.Rd:10: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2DCsvq/R.INSTALL7cb87f765cd1/lunar/man/lunar.illumination.Rd:9: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2DCsvq/R.INSTALL7cb87f765cd1/lunar/man/lunar.illumination.mean.Rd:10: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2DCsvq/R.INSTALL7cb87f765cd1/lunar/man/lunar.metric.mean.Rd:10: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2DCsvq/R.INSTALL7cb87f765cd1/lunar/man/lunar.phase.Rd:9: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2DCsvq/R.INSTALL7cb87f765cd1/lunar/man/lunar.phase.Rd:48: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2DCsvq/R.INSTALL7cb87f765cd1/lunar/man/lunar.phase.Rd:49: file link ‘POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2DCsvq/R.INSTALL7cb87f765cd1/lunar/man/terrestrial.season.Rd:9: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lunar.Rcheck/00install.out’ for details.
terrestrial.season: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/RtmpMouJ2T/R.INSTALL4b077399cf3/lutz/man/tz_offset.Rd:12: file link ‘OlsonNames’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lutz.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘test’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9Fg2tX/R.INSTALL257117379e01/lvmisc/man/lt.Rd:20: file link ‘last_trace’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9Fg2tX/R.INSTALL257117379e01/lvmisc/man/lunique.Rd:31: file link ‘is.na’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lvmisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7a5Vn4/R.INSTALL66e675a8dbc5/lvnet/man/lav2lvnet.Rd:25: file link ‘lavaanify’ in package ‘lavaan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lvnet.Rcheck/00install.out’ for details.
generate.clonal.data : pcr.rpareto.func: no visible global function
  definition for ‘runif’
generate.clonal.data : get.readcount.given.cellcount: no visible global
  function definition for ‘rlnorm’
generate.clonal.data: no visible global function definition for
  ‘rmultinom’
generate.clonal.data: no visible global function definition for ‘rpois’
infer.clonality: no visible global function definition for ‘cov’
infer.clonality: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output cov rlnorm rmultinom rpois runif
Consider adding
  importFrom("stats", "cov", "rlnorm", "rmultinom", "rpois", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpaFa4CU/R.INSTALL25f4257885d8/m2r/man/reexports.Rd:14: file link ‘edit_r_environ’ in package ‘usethis’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/m2r.Rcheck/00install.out’ for details.
project.M3.1.to.M3.2: no visible global function definition for
  ‘coordinates<-’
project.M3.1.to.M3.2: no visible global function definition for
  ‘proj4string<-’
project.M3.1.to.M3.2: no visible global function definition for ‘CRS’
project.M3.1.to.M3.2: no visible global function definition for
  ‘spTransform’
project.M3.1.to.M3.2: no visible global function definition for
  ‘coordinates’
Undefined global functions or variables:
  CRS coordinates coordinates<- proj4string<- spTransform
Malformed Description field: should contain one or more complete sentences.
maboost.default: no visible global function definition for
  ‘flush.console’
maboost.default: no visible binding for global variable ‘na.pass’
maboost.default : predict.type: no visible global function definition
  for ‘predict’
maboost.formula: no visible global function definition for
  ‘model.extract’
maboost.machine.bin: no visible global function definition for ‘runif’
maboost.machine.bin: no visible binding for global variable ‘na.pass’
maboost.machine.multi: no visible global function definition for
  ‘runif’
maboost.machine.multi: no visible binding for global variable ‘na.pass’
projsplx_k: no visible global function definition for ‘tail’
varplot.maboost: no visible global function definition for ‘dotchart’
Undefined global functions or variables:
  dotchart flush.console model.extract na.pass predict runif tail
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "model.extract", "na.pass", "predict", "runif")
  importFrom("utils", "flush.console", "tail")
to your NAMESPACE file.
logistic_z: no visible global function definition for ‘glm’
logistic_z: no visible binding for global variable ‘binomial’
logistic_z: no visible global function definition for ‘predict’
plsrf_x: no visible global function definition for ‘qnorm’
plsrf_x: no visible global function definition for ‘predict’
plsrf_x_pv: no visible global function definition for ‘qnorm’
plsrf_x_pv: no visible global function definition for ‘predict’
plsrf_xz: no visible global function definition for ‘qnorm’
plsrf_xz: no visible global function definition for ‘predict’
plsrf_xz_pv: no visible global function definition for ‘qnorm’
plsrf_xz_pv: no visible global function definition for ‘predict’
rf_z: no visible global function definition for ‘qnorm’
rf_z: no visible global function definition for ‘predict’
simuldata_list: no visible global function definition for ‘rnorm’
simuldatacluster_list: no visible global function definition for
  ‘rnorm’
svm_x: no visible global function definition for ‘predict’
Undefined global functions or variables:
  binomial glm predict qnorm rnorm
Consider adding
  importFrom("stats", "binomial", "glm", "predict", "qnorm", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘R2wd’
'library' or 'require' calls in package code:
  ‘R2wd’ ‘ggplot2’ ‘metafor’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘maddison_project_database.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpY9W56k/R.INSTALL309e46b21119/madness/man/extract-methods.Rd:21: file link ‘as.integer’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/madness.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpNBQ8rR/R.INSTALL789b3933ce46/MADPop/man/hUM.post.Rd:20: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MADPop.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpjuU7Pc/R.INSTALL2778f3ea516/madrat/man/madapply.Rd:38: file link ‘parallel’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjuU7Pc/R.INSTALL2778f3ea516/madrat/man/madlapply.Rd:29: file link ‘parallel’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/madrat.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘R2wd’
'library' or 'require' calls in package code:
  ‘R2wd’ ‘ggplot2’ ‘metafor’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLdbMGq/R.INSTALL794f2be40429/magclass/man/head.magpie.Rd:35: file link ‘tail’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLdbMGq/R.INSTALL794f2be40429/magclass/man/set_magpie_units.Rd:25: file link ‘set_units’ in package ‘units’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/magclass.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-package-majesticr--rmd.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpg4r932/R.INSTALL7b5b7b807d18/MakefileR/man/Concatenation.Rd:22: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpg4r932/R.INSTALL7b5b7b807d18/MakefileR/man/make_comment.Rd:20: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpg4r932/R.INSTALL7b5b7b807d18/MakefileR/man/make_def.Rd:27: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpg4r932/R.INSTALL7b5b7b807d18/MakefileR/man/make_group.Rd:26: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpg4r932/R.INSTALL7b5b7b807d18/MakefileR/man/make_rule.Rd:32: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpg4r932/R.INSTALL7b5b7b807d18/MakefileR/man/make_text.Rd:21: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpg4r932/R.INSTALL7b5b7b807d18/MakefileR/man/makefile.Rd:24: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MakefileR.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘rJava’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MalletLDA: no visible global function definition for ‘.jnew’
mallet.doc.topics: no visible global function definition for
  ‘.jevalArray’
mallet.import: no visible global function definition for ‘J’
mallet.import: no visible global function definition for ‘.jnew’
mallet.import: no visible global function definition for ‘.jcast’
mallet.subset.topic.words: no visible global function definition for
  ‘.jevalArray’
mallet.topic.hclust: no visible global function definition for ‘hclust’
mallet.topic.hclust: no visible global function definition for ‘dist’
mallet.topic.words: no visible global function definition for
  ‘.jevalArray’
mallet.word.freqs: no visible global function definition for
  ‘.jevalArray’
Undefined global functions or variables:
  .jcast .jevalArray .jnew J dist hclust
Consider adding
  importFrom("stats", "dist", "hclust")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpOjsBSq/R.INSTALLacf654d087d/Mangrove/man/MangroveExamples.Rd:13: file link ‘Mangrove’ in package ‘Mangrove’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpOjsBSq/R.INSTALLacf654d087d/Mangrove/man/plotSampledPrev.Rd:41: file link ‘plot.MangroveSample’ in package ‘Mangrove’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Mangrove.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpNed0WF/R.INSTALL226e7f439478/manhattanly/man/manhattanr.Rd:84: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNed0WF/R.INSTALL226e7f439478/manhattanly/man/qqr.Rd:62: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNed0WF/R.INSTALL226e7f439478/manhattanly/man/volcanor.Rd:64: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/manhattanly.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpsTPzh6/R.INSTALL348836f3c9b2/mapboxer/man/reexports.Rd:15: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpsTPzh6/R.INSTALL348836f3c9b2/mapboxer/man/reexports.Rd:15: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mapboxer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpNxHTNZ/R.INSTALL7a6cc6aa24a/mapcan/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mapcan.Rcheck/00install.out’ for details.
cf1.sample: no visible global function definition for ‘rexp’
cf1.sample: no visible global function definition for ‘rmultinom’
dherlang : <anonymous> : <anonymous>: no visible global function
  definition for ‘dgamma’
erhmm.param.kmeans: no visible global function definition for ‘kmeans’
erhmm.param.kmeans: no visible global function definition for ‘var’
erhmm.param.kmeans: no visible global function definition for ‘runif’
gmmpp.param.kmeans: no visible global function definition for ‘kmeans’
gmmpp.param.kmeans: no visible global function definition for ‘runif’
herlang.param.kmeans: no visible global function definition for
  ‘kmeans’
herlang.param.kmeans: no visible global function definition for ‘var’
map.param.kmeans: no visible global function definition for ‘kmeans’
map.param.kmeans: no visible global function definition for ‘runif’
ph.param.random: no visible global function definition for ‘runif’
ph.sample: no visible global function definition for ‘rmultinom’
ph.sample: no visible global function definition for ‘rexp’
pherlang : <anonymous> : <anonymous>: no visible global function
  definition for ‘pgamma’
rherlang: no visible global function definition for ‘rmultinom’
rherlang : <anonymous>: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  dgamma kmeans pgamma rexp rgamma rmultinom runif var
Consider adding
  importFrom("stats", "dgamma", "kmeans", "pgamma", "rexp", "rgamma",
             "rmultinom", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘mgcv’ which was already attached by Depends.
  Please remove these calls from your code.
ageprofile: no visible global function definition for ‘model.frame’
ageprofile: no visible binding for global variable ‘poisson’
ageprofile: no visible global function definition for ‘predict.gam’
ageprofile: no visible global function definition for ‘as.formula’
ageprofile: no visible global function definition for ‘summary.gam’
ageprofile: no visible global function definition for ‘contrasts<-’
ageprofile: no visible global function definition for ‘anova.gam’
plotap: no visible global function definition for ‘dev.new’
plotap: no visible global function definition for ‘lines’
plotap: no visible global function definition for ‘points’
plotap: no visible global function definition for ‘legend’
splitter: no visible global function definition for ‘reshape’
tabm: no visible global function definition for ‘coef’
tabm: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPVzvBO/R.INSTALL20796f1a809f/mapplots/man/draw.shape.Rd:34: file link ‘read.shapefile’ in package ‘shapefiles’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPVzvBO/R.INSTALL20796f1a809f/mapplots/man/write.grid.Rd:31: file link ‘write.shapefile’ in package ‘shapefiles’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mapplots.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp33iOym/R.INSTALL2d6b3d6e2a4b/mapSpain/man/addProviderEspTiles.Rd:30: file link ‘clearGroup’ in package ‘leaflet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mapSpain.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6Sfyqd/R.INSTALL2451450719f/mapStats/man/mapStats-internal.Rd:31: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6Sfyqd/R.INSTALL2451450719f/mapStats/man/mapStats-internal.Rd:52: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6Sfyqd/R.INSTALL2451450719f/mapStats/man/mapStats.Rd:63: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6Sfyqd/R.INSTALL2451450719f/mapStats/man/mapStats.Rd:82: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6Sfyqd/R.INSTALL2451450719f/mapStats/man/mapStats.Rd:152: file link ‘RColorBrewer’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mapStats.Rcheck/00install.out’ for details.
calcStats: no visible global function definition for ‘as.formula’
calcStats: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  as.formula na.omit
Consider adding
  importFrom("stats", "as.formula", "na.omit")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4Qllal/R.INSTALL4fc52ee8548d/maptiles/man/get_tiles.Rd:38: file link ‘tempdir’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/maptiles.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2k37QU/R.INSTALL79da530b95ee/maptools/man/CCmaps.Rd:17: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2k37QU/R.INSTALL79da530b95ee/maptools/man/CCmaps.Rd:36: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/maptools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4ELl1K/R.INSTALL2e0130f8aa97/mapview/man/mapView.Rd:519: file link ‘popupTable’ in package ‘leafpop’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mapview.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpctDds9/R.INSTALL3704701d06b4/marcher/man/locate_shift.Rd:10: file link ‘POSIXt’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/marcher.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmppJv155/R.INSTALL18d83564f77b/margins/man/cplot.Rd:323: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmppJv155/R.INSTALL18d83564f77b/margins/man/cplot.Rd:347: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmppJv155/R.INSTALL18d83564f77b/margins/man/cplot.Rd:349: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmppJv155/R.INSTALL18d83564f77b/margins/man/dydx.Rd:88: file link ‘contr.poly’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmppJv155/R.INSTALL18d83564f77b/margins/man/dydx.Rd:88: file link ‘contr.treatment’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/margins.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmprvgb6m/R.INSTALL846786cb090/marg/man/cond.rsm.Rd:135: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmprvgb6m/R.INSTALL846786cb090/marg/man/marg.object.Rd:88: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/marg.Rcheck/00install.out’ for details.
negbin.rel.clust: no visible global function definition for ‘kmeans’
negbin.rel.clust: no visible global function definition for ‘matplot’
negbin.rel.pca: no visible global function definition for ‘princomp’
negbin.rel.pca: no visible global function definition for ‘biplot’
pois.rel.clust: no visible global function definition for ‘kmeans’
pois.rel.clust: no visible global function definition for ‘matplot’
pois.rel.pca: no visible global function definition for ‘princomp’
pois.rel.pca: no visible global function definition for ‘biplot’
sim.negbin: no visible global function definition for ‘rnbinom’
sim.pois: no visible global function definition for ‘rpois’
wt.rel.negbin: no visible global function definition for ‘var’
wt.rel.negbin: no visible global function definition for ‘optimize’
wt.rel.negbin: no visible global function definition for ‘integrate’
wt.rel.pois: no visible global function definition for ‘optimize’
wt.rel.pois: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  biplot integrate kmeans matplot optimize princomp rnbinom rpois var
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "biplot", "integrate", "kmeans", "optimize",
             "princomp", "rnbinom", "rpois", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
mAr.pca: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbrTJMr/R.INSTALL25423c891bf7/mason/man/mason.Rd:10: file link ‘dplyr’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbrTJMr/R.INSTALL25423c891bf7/mason/man/mason.Rd:11: file link ‘magrittr’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbrTJMr/R.INSTALL25423c891bf7/mason/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbrTJMr/R.INSTALL25423c891bf7/mason/man/polish.Rd:22: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbrTJMr/R.INSTALL25423c891bf7/mason/man/polish.Rd:43: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbrTJMr/R.INSTALL25423c891bf7/mason/man/polish.Rd:47: file link ‘grepl’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mason.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmprVj17T/R.INSTALL683c447332a1/Matching/man/GenMatch.Rd:314: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Matching.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxmPY41/R.INSTALL212810223c98/MatchIt/man/distance.Rd:26: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MatchIt.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp74Q49V/R.INSTALL1fb518220e21/MatchThem/man/complete.Rd:33: file link ‘complete’ in package ‘mice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp74Q49V/R.INSTALL1fb518220e21/MatchThem/man/complete.Rd:62: file link ‘complete’ in package ‘mice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp74Q49V/R.INSTALL1fb518220e21/MatchThem/man/matchthem.Rd:42: file link ‘complete’ in package ‘mice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp74Q49V/R.INSTALL1fb518220e21/MatchThem/man/weightthem.Rd:27: file link ‘complete’ in package ‘mice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MatchThem.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following possibly unsafe calls:
File ‘matlab/R/zzz.R’:
  unlockBinding("savedTime", .MatlabNamespaceEnv)

colorbar : colorbar.EO: no visible global function definition for ‘par’
colorbar : colorbar.EO: no visible global function definition for
  ‘axis’
colorbar : colorbar.EO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.EO: no visible global function definition for ‘box’
colorbar : colorbar.NO: no visible global function definition for
  ‘axis’
colorbar : colorbar.NO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.NO: no visible global function definition for ‘box’
imagesc : pretty.axp: no visible global function definition for ‘par’
imagesc: no visible global function definition for ‘axis’
imagesc: no visible global function definition for ‘box’
jet.colors: no visible global function definition for ‘rgb’
multiline.plot.colors : get.gca.colororder: no visible global function
  definition for ‘rgb’
std: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axTicks axis box par rgb sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axTicks", "axis", "box", "par")
  importFrom("stats", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9F8eJ4/R.INSTALL3a79709f46bd/matlib/man/arrows3d.Rd:35: file link ‘segments3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9F8eJ4/R.INSTALL3a79709f46bd/matlib/man/arrows3d.Rd:44: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9F8eJ4/R.INSTALL3a79709f46bd/matlib/man/cone3d.Rd:20: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9F8eJ4/R.INSTALL3a79709f46bd/matlib/man/plotEqn3d.Rd:50: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9F8eJ4/R.INSTALL3a79709f46bd/matlib/man/showEig.Rd:55: file link ‘dataEllipse’ in package ‘car’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9F8eJ4/R.INSTALL3a79709f46bd/matlib/man/vectors3d.Rd:39: file link ‘text3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9F8eJ4/R.INSTALL3a79709f46bd/matlib/man/vectors3d.Rd:86: file link ‘texts3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9F8eJ4/R.INSTALL3a79709f46bd/matlib/man/vectors3d.Rd:86: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/matlib.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gputools’
'library' or 'require' call to ‘bigmemory’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
MAT: no visible global function definition for ‘dev.new’
MAT: no visible global function definition for ‘points’
MAT: no visible global function definition for ‘abline’
MAT: no visible global function definition for ‘text’
MAT: no visible global function definition for ‘legend’
MAT: no visible global function definition for ‘lines’
MAT: no visible global function definition for ‘par’
MAT: no visible global function definition for ‘barplot’
MAT: no visible global function definition for ‘cor’
print.MAT: no visible global function definition for ‘sd’
print.MAT: no visible global function definition for ‘cor’
simM3PL: no visible global function definition for ‘rnorm’
simM3PL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par points rnorm runif sd
  text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLAfOeG/R.INSTALL4ded1c2d1b44/matrixNormal/man/matrixNormal_Distribution.Rd:42: file link ‘GenzBretz’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLAfOeG/R.INSTALL4ded1c2d1b44/matrixNormal/man/matrixNormal_Distribution.Rd:43: file link ‘Miwa’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLAfOeG/R.INSTALL4ded1c2d1b44/matrixNormal/man/matrixNormal_Distribution.Rd:43: file link ‘TVPACK’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLAfOeG/R.INSTALL4ded1c2d1b44/matrixNormal/man/matrixNormal_Distribution.Rd:52: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLAfOeG/R.INSTALL4ded1c2d1b44/matrixNormal/man/matrixNormal_Distribution.Rd:64: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/matrixNormal.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpvYJ3RT/R.INSTALL10ee3c594ca0/Matrix/man/abIndex-class.Rd:80: file link ‘Ops’ in package ‘methods’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvYJ3RT/R.INSTALL10ee3c594ca0/Matrix/man/image-methods.Rd:53: file link ‘panel.levelplot.raster’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvYJ3RT/R.INSTALL10ee3c594ca0/Matrix/man/image-methods.Rd:81: file link ‘get.gpar’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvYJ3RT/R.INSTALL10ee3c594ca0/Matrix/man/matrix-products.Rd:406: file link ‘tcrossprod’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvYJ3RT/R.INSTALL10ee3c594ca0/Matrix/man/rankMatrix.Rd:87: file link ‘qr’ in package ‘Matrix’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvYJ3RT/R.INSTALL10ee3c594ca0/Matrix/man/wrld_1deg.Rd:33: file link ‘Sobj_SpatialGrid’ in package ‘maptools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Matrix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpzoF51H/R.INSTALL192f382ed70b/matrixStats/man/rowCollapse.Rd:55: file link ‘[’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzoF51H/R.INSTALL192f382ed70b/matrixStats/man/rowCumsums.Rd:83: file link ‘cumprod’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzoF51H/R.INSTALL192f382ed70b/matrixStats/man/rowCumsums.Rd:84: file link ‘cummin’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzoF51H/R.INSTALL192f382ed70b/matrixStats/man/rowCumsums.Rd:84: file link ‘cummax’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzoF51H/R.INSTALL192f382ed70b/matrixStats/man/rowProds.Rd:54: file link ‘is.nan’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzoF51H/R.INSTALL192f382ed70b/matrixStats/man/rowRanges.Rd:52: file link ‘pmin.int’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzoF51H/R.INSTALL192f382ed70b/matrixStats/man/varDiff.Rd:80: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzoF51H/R.INSTALL192f382ed70b/matrixStats/man/varDiff.Rd:103: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzoF51H/R.INSTALL192f382ed70b/matrixStats/man/weightedVar.Rd:73: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/matrixStats.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6UUCB9/R.INSTALL32d5631f25d7/Matrix.utils/man/dMcast.Rd:115: file link ‘cast’ in package ‘reshape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Matrix.utils.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSlfSTS/R.INSTALL26ad4e80c579/matsbyname/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSlfSTS/R.INSTALL26ad4e80c579/matsbyname/man/quasi-quote-assign.Rd:10: file link ‘:=’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/matsbyname.Rcheck/00install.out’ for details.
Rd file 'mat.dissim.Rd':
  \usage lines wider than 90 characters:
     mat.dissim(inFossil, inModern, llMod = c(), modTaxa = c(), llFoss = c(), fosTaxa = c(), numAnalogs = 1, counts = T, sitenames = 1:lengt ... [TRUNCATED]

Rd file 'mat.fossavg.Rd':
  \usage lines wider than 90 characters:
     mat.fossavg(dObj, modEnvCol, fossEnvCol = 0, fossCols = 0, cutoff = 0, distance = -1, wmethod = "none", numanalogs = length(dObj$positi ... [TRUNCATED]

Rd file 'mat.jumprecon.Rd':
  \usage lines wider than 90 characters:
     mat.jumprecon(dObj, modEnvCol, fossEnvCol, cutoff = 0, alpha = NULL, distance = -1, numanalogs = length(dObj$position[, 1]))

Rd file 'mat.mc.Rd':
  \usage lines wider than 90 characters:
     mat.mc(inModern, modTaxa = c(NULL, NULL), probs = c(0.05, 0.025, 0.01, 0.001), freqint = seq(0, 2, 0.02), sampleSize = length(inModern[ ... [TRUNCATED]

Rd file 'mat.roc.Rd':
  \usage lines wider than 90 characters:
     mat.roc(inModern, modTaxa = c(), colClasses = NULL, numAnalogs = 2, rocEvalSeq = seq(0, 2, 0.05), counts = F, aucmethod = "trap")

Rd file 'mat.roc.allpair.Rd':
  \usage lines wider than 90 characters:
     mat.roc.allpair(inModern, modTaxa = c(), colClasses = NULL, numAnalogs = 2, rocEvalSeq = seq(0, 2, 0.05), counts = F, aucmethod = "trap ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘utilities.R’
Malformed Title field: should not end in a period.
GSTplot : <anonymous>: no visible global function definition for
  ‘t.test’
GSTplot: no visible global function definition for ‘rt’
GSTplot: no visible global function definition for ‘layout’
GSTplot: no visible global function definition for ‘par’
GSTplot: no visible global function definition for ‘text’
GSTplot: no visible global function definition for ‘lines’
GSTplot: no visible global function definition for ‘polygon’
GSTplot: no visible global function definition for ‘abline’
GSTplot: no visible global function definition for ‘ecdf’
GSTplot: no visible global function definition for ‘knots’
GSTplot : <anonymous>: no visible global function definition for ‘aov’
GSTplot: no visible global function definition for ‘qf’
MAVTn : <anonymous>: no visible global function definition for ‘aov’
MAVTn: no visible global function definition for ‘p.adjust’
MAVTn: no visible global function definition for ‘par’
MAVTn: no visible global function definition for ‘abline’
MAVTn: no visible global function definition for ‘legend’
MAVTn: no visible global function definition for ‘locator’
Tols : olsf: no visible global function definition for ‘t.test’
Tols: no visible global function definition for ‘cor’
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
Package in Depends field not imported from: ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catt.test: no visible global function definition for ‘pnorm’
fnorm2: no visible global function definition for ‘sadmvn’
fnorm3: no visible global function definition for ‘sadmvn’
Undefined global functions or variables:
  pnorm sadmvn
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpU0jBcn/R.INSTALL3b1b7d3fc5af/MaxMC/man/mmc.Rd:219: file link ‘GA’ in package ‘GA’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MaxMC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6zPUNy/R.INSTALL4a831fa0d3e8/maxstat/man/maxstat.test.Rd:74: file link ‘pperm’ in package ‘exactRankTests’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/maxstat.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Malformed Description field: should contain one or more complete sentences.
MI.2: no visible global function definition for ‘xtabs’
RNASeq.Data: no visible binding for global variable ‘quantile’
loc.node: no visible global function definition for ‘head’
loc.node: no visible global function definition for ‘tail’
plotHybrid.Tree: no visible global function definition for ‘par’
plotHybrid.Tree: no visible global function definition for ‘text’
plotHybrid.Tree: no visible global function definition for ‘image’
plotHybrid.Tree: no visible global function definition for ‘grey’
plotHybrid.Tree: no visible global function definition for
  ‘heat.colors’
plotHybrid.Tree: no visible global function definition for ‘head’
plotHybrid.Tree: no visible global function definition for ‘segments’
plotbr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  grey head heat.colors image par quantile segments tail text xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/Sigma.2.SigmaStar.Rd:13: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/Sigma.2.SigmaStar.Rd:45: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/ss.aipe.rmsea.sensitivity.Rd:16: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/ss.aipe.rmsea.sensitivity.Rd:75: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/ss.aipe.sem.path.Rd:14: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/ss.aipe.sem.path.Rd:45: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/ss.aipe.sem.path.sensitiv.Rd:15: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/ss.aipe.sem.path.sensitiv.Rd:60: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/theta.2.Sigma.theta.Rd:12: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzj7vA/R.INSTALL3a8de74636a/MBESS/man/theta.2.Sigma.theta.Rd:43: file link ‘specify.model’ in package ‘sem’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MBESS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpn4DSP4/R.INSTALL53c91f6e1fd7/mbest/man/effects.Rd:66: file link ‘fixef’ in package ‘nlme’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpn4DSP4/R.INSTALL53c91f6e1fd7/mbest/man/effects.Rd:66: file link ‘ranef’ in package ‘nlme’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mbest.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
cfull: no visible global function definition for ‘combn’
cl: no visible global function definition for ‘combn’
cn: no visible global function definition for ‘combn’
crep: no visible global function definition for ‘combn’
crich: no visible global function definition for ‘combn’
ct: no visible global function definition for ‘combn’
mjaccard: no visible global function definition for ‘combn’
ml: no visible global function definition for ‘combn’
mn: no visible global function definition for ‘combn’
mrep: no visible global function definition for ‘combn’
mrich: no visible global function definition for ‘combn’
msorensen: no visible global function definition for ‘combn’
mt: no visible global function definition for ‘combn’
wnodf: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpfuWla1/R.INSTALL4a43e9e6582/MBNMAdose/man/cumrank.Rd:18: file link ‘readWKT’ in package ‘rgeos’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/hp17602/AppData/Local/Temp/RtmpqoifUH/Rbuild292c5521114b/MBNMAdose/man/inconsistency.loops.Rd:48: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpfuWla1/R.INSTALL4a43e9e6582/MBNMAdose/man/mbnma.network.Rd:121: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MBNMAdose.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: C:/Users/hp17602/AppData/Local/Temp/RtmpmKFBZa/Rbuild459845806a11/MBNMAtime/man/inconsistency.loops.Rd:29: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpVk2Tbz/R.INSTALL5227df70ac7/MBNMAtime/man/mb.network.Rd:91: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/hp17602/AppData/Local/Temp/RtmpmKFBZa/Rbuild459845806a11/MBNMAtime/man/mb.nodesplit.comparisons.Rd:29: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MBNMAtime.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpVbtfaE/Rbuild59c13af44481/mboost/man/baselearners.Rd:159: file link ‘stationary.cov’ in package ‘fields’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpVbtfaE/Rbuild59c13af44481/mboost/man/cvrisk.Rd:35: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mboost.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpE8ffdw/R.INSTALLffb579858ca/mboxr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mboxr.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Rd file 'VegTypeChanges.Rd':
  \examples lines wider than 100 characters:
     ## vegChanges = VegTypeChanges(ncdf.th <- system.file("netcdf", "WW2100_HadGEM2-ES85_year_sample.nc", PACKAGE = "MC2toPath")path, base. ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘fireFracs.csv’ ‘fireProbabilityMultipliers.txt’
  ‘vegChangeProbabilityMultipliers.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpQuiOal/R.INSTALL7c9c2feb21d2/mcbette/man/default_params_doc.Rd:115: file link ‘create_mcmc_nested_sampling’ in package ‘beautier’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mcbette.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpECcZgI/R.INSTALL5731520f13/mccf1/man/summary.mccf1.Rd:12: file link ‘signif’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mccf1.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘lpSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
laugreen: no visible global function definition for ‘combn’
laugreen: no visible global function definition for ‘lp’
maxpear: no visible global function definition for ‘hclust’
maxpear: no visible global function definition for ‘as.dist’
maxpear : <anonymous>: no visible global function definition for
  ‘cutree’
medv: no visible global function definition for ‘cutree’
medv: no visible global function definition for ‘hclust’
medv: no visible global function definition for ‘as.dist’
minbinder: no visible global function definition for ‘hclust’
minbinder: no visible global function definition for ‘as.dist’
minbinder : <anonymous>: no visible global function definition for
  ‘cutree’
relabel : min.perm.labels: no visible global function definition for
  ‘lp.transport’
Undefined global functions or variables:
  as.dist combn cutree hclust lp lp.transport
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
  importFrom("utils", "combn")
to your NAMESPACE file.
getbetap.A: no visible global function definition for ‘pbeta’
getbetap.A: no visible global function definition for ‘cor.test’
Undefined global functions or variables:
  cor.test pbeta
Consider adding
  importFrom("stats", "cor.test", "pbeta")
to your NAMESPACE file.
Package in Depends field not imported from: ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mcgibbsit: no visible global function definition for ‘is.mcmc.list’
mcgibbsit: no visible global function definition for ‘start’
mcgibbsit: no visible global function definition for ‘end’
mcgibbsit: no visible global function definition for ‘thin’
mcgibbsit: no visible global function definition for ‘nvar’
mcgibbsit: no visible global function definition for ‘mcmc’
mcgibbsit: no visible global function definition for ‘mcmc.list’
mcgibbsit: no visible global function definition for ‘varnames’
mcgibbsit: no visible global function definition for ‘qnorm’
mcgibbsit: no visible global function definition for ‘niter’
mcgibbsit: no visible global function definition for ‘quantile’
mcgibbsit : to.table: no visible global function definition for
  ‘window’
mcgibbsit: no visible global function definition for ‘var’
read.mcmc: no visible global function definition for ‘mcmc.list’
read.mcmc: no visible global function definition for ‘mcmc’
Undefined global functions or variables:
  end is.mcmc.list mcmc mcmc.list niter nvar qnorm quantile start thin
  var varnames window
Consider adding
  importFrom("stats", "end", "qnorm", "quantile", "start", "var",
             "window")
to your NAMESPACE file.
Found the following files/directories:
  ‘dnzcY3e.1’ ‘dnzcY3e.2’ ‘dnzcY3e.3’ ‘mcmc.1.csv’ ‘mcmc.10.csv’
  ‘mcmc.11.csv’ ‘mcmc.12.csv’ ‘mcmc.13.csv’ ‘mcmc.14.csv’ ‘mcmc.15.csv’
  ‘mcmc.16.csv’ ‘mcmc.17.csv’ ‘mcmc.18.csv’ ‘mcmc.19.csv’ ‘mcmc.2.csv’
  ‘mcmc.20.csv’ ‘mcmc.3.csv’ ‘mcmc.4.csv’ ‘mcmc.5.csv’ ‘mcmc.6.csv’
  ‘mcmc.7.csv’ ‘mcmc.8.csv’ ‘mcmc.9.csv’
call_localoptim: no visible global function definition for ‘optim’
call_localoptim: no visible global function definition for ‘nlminb’
call_localoptim: no visible global function definition for
  ‘txtProgressBar’
call_localoptim: no visible global function definition for
  ‘setTxtProgressBar’
call_localoptim : <anonymous>: no visible global function definition
  for ‘optim’
call_localoptim : <anonymous>: no visible global function definition
  for ‘nlminb’
multiStartoptim: no visible global function definition for ‘median’
Undefined global functions or variables:
  median nlminb optim setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "nlminb", "optim")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  ‘rgb’
mcheatmaps : halfcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : fullcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘hclust’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘as.dist’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘sd’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘cophenetic’
mcheatmaps : printDiag: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘strwidth’
mcheatmaps: no visible global function definition for ‘pdf’
mcheatmaps: no visible global function definition for ‘plot.new’
mcheatmaps: no visible global function definition for ‘as.dendrogram’
mcheatmaps: no visible global function definition for ‘reorder’
mcheatmaps: no visible global function definition for ‘par’
mcheatmaps: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘heat.colors’
mcheatmaps: no visible global function definition for ‘terrain.colors’
mcheatmaps: no visible global function definition for ‘as.dist’
mcheatmaps: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘CarStats.pdf’ ‘CarStats_labels.pdf’
Malformed Description field: should contain one or more complete sentences.
lik_locfit: no visible global function definition for ‘predict’
mcll_coeff: no visible global function definition for ‘optim’
mcll_est: no visible global function definition for ‘cov’
mcll_est: no visible global function definition for ‘optim’
mcll_se: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim predict
Consider adding
  importFrom("stats", "cov", "optim", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpFhguNe/R.INSTALL59fe4f4885cd/MCMCglmm/man/rtnorm.Rd:20: file link ‘rtnorm’ in package ‘msm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MCMCglmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGFNILF/R.INSTALL28f068739a0f/mcmcOutput/man/mcmcOutput.Rd:20: file link ‘summary.mcmcOutput’ in package ‘mcmcOutput’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGFNILF/R.INSTALL28f068739a0f/mcmcOutput/man/mcmcOutput.Rd:20: file link ‘plot.mcmcOutput’ in package ‘mcmcOutput’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGFNILF/R.INSTALL28f068739a0f/mcmcOutput/man/mcmcOutput.Rd:20: file link ‘window.mcmcOutput’ in package ‘mcmcOutput’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mcmcOutput.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpdAxOZy/R.INSTALL6efc5141fbb8/MCMCpack/man/SSVSquantreg.Rd:166: file link ‘summary.qrssvs’ in package ‘MCMCpack’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MCMCpack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0CwL0U/R.INSTALL7527487375e/MCMCtreeR/man/estimateSkewNormal.Rd:78: file link ‘qst’ in package ‘sn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0CwL0U/R.INSTALL7527487375e/MCMCtreeR/man/estimateSkewT.Rd:79: file link ‘qst’ in package ‘sn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MCMCtreeR.Rcheck/00install.out’ for details.
do.linear.conjoint: no visible global function definition for
  ‘as.formula’
do.linear.conjoint: no visible global function definition for ‘lm’
do.linear.conjoint: no visible global function definition for
  ‘coefficients’
is.close.to.orthogonal: no visible global function definition for ‘cor’
mc.add.to.design: no visible global function definition for ‘combn’
mc.good.designs: no visible global function definition for ‘combn’
Undefined global functions or variables:
  as.formula coefficients combn cor lm
Consider adding
  importFrom("stats", "as.formula", "coefficients", "cor", "lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpczAffA/R.INSTALL7aab3b232c/mcprofile/man/confint.mcprofile.Rd:31: file link ‘confint.glm’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpczAffA/R.INSTALL7aab3b232c/mcprofile/man/confint.mcprofile.Rd:31: file link ‘confint.glht’ in package ‘multcomp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpczAffA/R.INSTALL7aab3b232c/mcprofile/man/summary.mcprofile.Rd:28: file link ‘summary.glht’ in package ‘multcomp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mcprofile.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘coda’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Checking should be performed on sources prepared by ‘R CMD build’.
Found the following significant warnings:
  Rd warning: /tmp/RtmpND5ffL/R.INSTALL9963298a40f/MDBED/man/CDF_3dPlot.Rd:47: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MDBED.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUUdqEY/R.INSTALL301516e601e9/MDFS/man/plot.MDFS.Rd:14: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MDFS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: C:/Users/sunpn563/AppData/Local/Temp/RtmpcdJ2Pi/Rbuildf2813cb746a/mdmb/man/frm.Rd:97: file link ‘lm.wfit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMtlT1P/R.INSTALL22e7dc363a8/mdmb/man/offset_values_extract.Rd:49: file link ‘model.offset’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/sunpn563/AppData/Local/Temp/RtmpcdJ2Pi/Rbuildf2813cb746a/mdmb/man/yjt_dist.Rd:172: file link ‘dt’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mdmb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6UYXqE/R.INSTALLce34cf77115/mecor/man/mecor.Rd:38: file link ‘lm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mecor.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘AUTHORS’
Authors information should be in file inst/AUTHORS
conf.interval: no visible global function definition for ‘pbinom’
conf.statement: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  pbinom
Consider adding
  importFrom("stats", "pbinom")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8QSEvM/R.INSTALL245971decca0/MEDseq/man/MEDseq_control.Rd:120: file link ‘wcKMedoids’ in package ‘WeightedCluster’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8QSEvM/R.INSTALL245971decca0/MEDseq/man/plot.MEDseq.Rd:134: file link ‘list_seriation_methods’ in package ‘seriation’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MEDseq.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpEDHK2E/R.INSTALL566667748e2d/mefa4/man/Mefa.Rd:77: file link ‘xtab’ in package ‘mefa4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEDHK2E/R.INSTALL566667748e2d/mefa4/man/Mefa.Rd:77: file link ‘taxa’ in package ‘mefa4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEDHK2E/R.INSTALL566667748e2d/mefa4/man/Melt.Rd:29: file link ‘melt’ in package ‘mefa’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mefa4.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
.df: no visible global function definition for ‘logLik’
coef_simple: no visible global function definition for ‘coef’
fitall: no visible binding for global variable ‘as.formula’
fitbest: no visible binding for global variable ‘as.formula’
lmboot: no visible global function definition for ‘lm’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘resid’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘rstudent’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘influence.measures’
stdcoef: no visible global function definition for ‘coef’
stdcoef: no visible global function definition for ‘update’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘logLik’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘AIC’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
summary.resid_ensemble: no visible binding for global variable
  ‘rstudent’
summary.resid_ensemble: no visible global function definition for ‘sd’
summary.variable_ensemble: no visible global function definition for
  ‘sd’
Undefined global functions or variables:
  AIC as.formula coef fitted influence.measures lm logLik resid
  rstudent sd update
Consider adding
  importFrom("stats", "AIC", "as.formula", "coef", "fitted",
             "influence.measures", "lm", "logLik", "resid", "rstudent",
             "sd", "update")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘adegenet’ ‘geosphere’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
codomToPropShared: no visible global function definition for
  ‘df2genind’
codomToPropShared: no visible global function definition for
  ‘propShared’
mgLandscape: no visible global function definition for ‘SpatialPoints’
mgQuick: no visible global function definition for ‘distm’
mgQuick: no visible binding for global variable ‘distMeeus’
Undefined global functions or variables:
  SpatialPoints df2genind distMeeus distm propShared
Package vignette with placeholder title ‘Vignette Title’:
  ‘README.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpf4kOGY/R.INSTALL11dd19617e0c/messaging/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/messaging.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘GenABEL’
Malformed Description field: should contain one or more complete sentences.
dometa: no visible global function definition for ‘qchisq’
dometa: no visible global function definition for ‘median’
dometa: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘qnorm’
forestplot: no visible global function definition for ‘points’
forestplot: no visible global function definition for ‘text’
metagwa.files: no visible global function definition for ‘read.csv’
metagwa.files: no visible global function definition for ‘write.csv’
metagwa.tables: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  median pchisq points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpJPKuRp/R.INSTALL12815e9c20d0/metaBMA/man/plot.meta_pred.Rd:21: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJPKuRp/R.INSTALL12815e9c20d0/metaBMA/man/plot.meta_sensitivity.Rd:33: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJPKuRp/R.INSTALL12815e9c20d0/metaBMA/man/plot.prior.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJPKuRp/R.INSTALL12815e9c20d0/metaBMA/man/plot_default.Rd:17: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJPKuRp/R.INSTALL12815e9c20d0/metaBMA/man/plot_forest.Rd:38: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJPKuRp/R.INSTALL12815e9c20d0/metaBMA/man/plot_posterior.Rd:29: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/metaBMA.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Found the following significant warnings:
  Rd warning: /tmp/RtmpG2lJBY/R.INSTALL303d42b8b9ab/MetaDBparse/man/build.LIPIDMAPS.Rd:31: file link ‘html_nodes’ in package ‘rvest’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpG2lJBY/R.INSTALL303d42b8b9ab/MetaDBparse/man/build.REACTOME.Rd:23: file link ‘html_nodes’ in package ‘rvest’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpG2lJBY/R.INSTALL303d42b8b9ab/MetaDBparse/man/build.REACTOME.Rd:24: file link ‘read_html’ in package ‘xml2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpG2lJBY/R.INSTALL303d42b8b9ab/MetaDBparse/man/build.WIKIPATHWAYS.Rd:27: file link ‘html_nodes’ in package ‘rvest’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpG2lJBY/R.INSTALL303d42b8b9ab/MetaDBparse/man/build.WIKIPATHWAYS.Rd:28: file link ‘read_html’ in package ‘xml2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpG2lJBY/R.INSTALL303d42b8b9ab/MetaDBparse/man/doBT.Rd:41: file link ‘pblapply’ in package ‘pbapply’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MetaDBparse.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
EScombination: no visible global function definition for ‘model.matrix’
EScombination: no visible global function definition for ‘p.adjust’
EScombination: no visible global function definition for ‘pt’
EScombination.paired: no visible global function definition for
  ‘p.adjust’
EScombination.paired: no visible global function definition for ‘pt’
calcfit2Diffrep: no visible global function definition for
  ‘model.matrix’
directEScombi: no visible global function definition for ‘pnorm’
directEScombi: no visible global function definition for ‘p.adjust’
directpvalcombi : fstatmeta: no visible global function definition for
  ‘qnorm’
directpvalcombi: no visible global function definition for ‘pnorm’
directpvalcombi: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for
  ‘model.matrix’
pvalcombination: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for ‘pt’
pvalcombination.paired: no visible global function definition for
  ‘p.adjust’
pvalcombination.paired: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix p.adjust pnorm pt qnorm
Consider adding
  importFrom("stats", "model.matrix", "p.adjust", "pnorm", "pt", "qnorm")
to your NAMESPACE file.
MAPE: no visible global function definition for ‘is’
MAPE: no visible global function definition for ‘new’
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package vignette with placeholder title ‘Vignette Title’:
  ‘how_to_use_crosshairs.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpJl5UwD/R.INSTALL1aa13527274c/metasens/man/copas.Rd:428: file link ‘funnel’ in package ‘meta’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJl5UwD/R.INSTALL1aa13527274c/metasens/man/funnel.limitmeta.Rd:50: file link ‘funnel’ in package ‘meta’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJl5UwD/R.INSTALL1aa13527274c/metasens/man/funnel.limitmeta.Rd:109: file link ‘funnel’ in package ‘meta’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJl5UwD/R.INSTALL1aa13527274c/metasens/man/funnel.limitmeta.Rd:132: file link ‘funnel’ in package ‘meta’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJl5UwD/R.INSTALL1aa13527274c/metasens/man/funnel.limitmeta.Rd:149: file link ‘funnel’ in package ‘meta’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/metasens.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
fit.bivar: no visible binding for global variable ‘binomial’
summary.fit.bivar: no visible global function definition for ‘qt’
summary.fit.bivar: no visible global function definition for ‘pt’
Undefined global functions or variables:
  binomial pt qt
Consider adding
  importFrom("stats", "binomial", "pt", "qt")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpu78MSS/R.INSTALL32f95f84648c/metawho/man/deft_do.Rd:29: file link ‘rma’ in package ‘metafor’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpu78MSS/R.INSTALL32f95f84648c/metawho/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpu78MSS/R.INSTALL32f95f84648c/metawho/man/tidyeval.Rd:17: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpu78MSS/R.INSTALL32f95f84648c/metawho/man/tidyeval.Rd:18: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpu78MSS/R.INSTALL32f95f84648c/metawho/man/tidyeval.Rd:20: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpu78MSS/R.INSTALL32f95f84648c/metawho/man/tidyeval.Rd:21: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpu78MSS/R.INSTALL32f95f84648c/metawho/man/tidyeval.Rd:25: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/metawho.Rcheck/00install.out’ for details.
crosssection: no visible global function definition for
  ‘colorRampPalette’
crosssection: no visible global function definition for
  ‘filled.contour’
crosssection: no visible global function definition for ‘axis’
crosssection: no visible global function definition for ‘par’
crosssection: no visible global function definition for ‘contour’
temperatures: no visible binding for global variable ‘time’
Undefined global functions or variables:
  axis colorRampPalette contour filled.contour par time
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "contour", "filled.contour", "par")
  importFrom("stats", "time")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
getdata: no visible global function definition for ‘read.csv’
plotdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.csv
Consider adding
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
RUVRand: no visible global function definition for ‘barplot’
RUVRand: no visible global function definition for ‘prcomp’
RuvRandIter: no visible global function definition for ‘kmeans’
RuvRandIter: no visible global function definition for ‘barplot’
RuvRandIter: no visible global function definition for ‘prcomp’
opt: no visible global function definition for ‘optim’
printdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  barplot head kmeans optim prcomp
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "kmeans", "optim", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Found the following significant warnings:
  Rd warning: /tmp/RtmpGXxhNV/R.INSTALL3d0c62a6cd7d/metR/man/scale_divergent.Rd:151: file link ‘scale_colour_gradient2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGXxhNV/R.INSTALL3d0c62a6cd7d/metR/man/scale_longitude.Rd:107: file link ‘scale_x_continuous’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGXxhNV/R.INSTALL3d0c62a6cd7d/metR/man/scale_longitude.Rd:108: file link ‘scale_y_continuous’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/metR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmplvSUGC/R.INSTALL1d856c141d57/metsyn/man/make_metdes.Rd:54: file link ‘metsyn’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplvSUGC/R.INSTALL1d856c141d57/metsyn/man/make_metdes.Rd:56: file link ‘metsta’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplvSUGC/R.INSTALL1d856c141d57/metsyn/man/make_metsta.Rd:55: file link ‘metsyn’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplvSUGC/R.INSTALL1d856c141d57/metsyn/man/make_metsta.Rd:57: file link ‘metdes’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplvSUGC/R.INSTALL1d856c141d57/metsyn/man/make_metsyn.Rd:26: file link ‘download_monthly_synop’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplvSUGC/R.INSTALL1d856c141d57/metsyn/man/make_metsyn.Rd:34: file link ‘metdes’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplvSUGC/R.INSTALL1d856c141d57/metsyn/man/make_metsyn.Rd:60: file link ‘download_monthly_synop’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplvSUGC/R.INSTALL1d856c141d57/metsyn/man/make_metsyn.Rd:61: file link ‘metdes’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplvSUGC/R.INSTALL1d856c141d57/metsyn/man/make_metsyn.Rd:63: file link ‘metsta’ in package ‘metsyn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/metsyn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnTW0Av/R.INSTALL141d291a73a6/mev/man/rmev.Rd:31: file link ‘rmvevd’ in package ‘evd’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnTW0Av/R.INSTALL141d291a73a6/mev/man/rmev.Rd:74: file link ‘rbvevd’ in package ‘evd’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnTW0Av/R.INSTALL141d291a73a6/mev/man/rmev.Rd:119: file link ‘rmvevd’ in package ‘evd’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnTW0Av/R.INSTALL141d291a73a6/mev/man/rmev.Rd:119: file link ‘rbvevd’ in package ‘evd’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mev.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
show,mewTyp: no visible global function definition for ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmphhBNOA/R.INSTALL281c1a50aec8/mgcViz/man/l_fitRaster.Rd:11: file link ‘geom_raster’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmphhBNOA/R.INSTALL281c1a50aec8/mgcViz/man/l_gridCheck2D.Rd:21: file link ‘stat_summary_hex’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmphhBNOA/R.INSTALL281c1a50aec8/mgcViz/man/l_gridQCheck2D.Rd:22: file link ‘stat_summary_hex’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmphhBNOA/R.INSTALL281c1a50aec8/mgcViz/man/l_vline.Rd:17: file link ‘geom_vline’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmphhBNOA/R.INSTALL281c1a50aec8/mgcViz/man/print.checkGam.Rd:12: file link ‘grid.arrange’ in package ‘gridExtra’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmphhBNOA/R.INSTALL281c1a50aec8/mgcViz/man/print.plotGam.Rd:23: file link ‘grid.arrange’ in package ‘gridExtra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mgcViz.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9pFCTI/R.INSTALL163020bf66c5/MGDrivE/man/Network.Rd:71: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9pFCTI/R.INSTALL163020bf66c5/MGDrivE/man/Network.Rd:72: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9pFCTI/R.INSTALL163020bf66c5/MGDrivE/man/get_conF_Network.Rd:10: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9pFCTI/R.INSTALL163020bf66c5/MGDrivE/man/get_conM_Network.Rd:10: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9pFCTI/R.INSTALL163020bf66c5/MGDrivE/man/oneDay_Migration_Stochastic_Network.Rd:16: file link ‘rmultinom’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9pFCTI/R.INSTALL163020bf66c5/MGDrivE/man/oneDay_Migration_Stochastic_Network.Rd:17: file link ‘rbinom’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9pFCTI/R.INSTALL163020bf66c5/MGDrivE/man/oneDay_Migration_Stochastic_Network.Rd:21: file link ‘rbinom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MGDrivE.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘mglm_vignette.rmd’
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘corpcor’ ‘evd’ ‘fields’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘RJSONIO’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for ‘packageVersion’
.onAttach: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible global function definition for ‘fromJSON’
call.MGRAST: no visible binding for global variable ‘.MGRAST’
call.MGRAST: no visible global function definition for ‘download.file’
call.MGRAST: no visible global function definition for ‘isValidJSON’
call.MGRAST: no visible global function definition for ‘fromJSON’
doc.MGRAST: no visible binding for global variable ‘.MGRAST’
doc.MGRAST: no visible global function definition for ‘str’
load.MGRAST: no visible binding for global variable ‘.MGRAST’
parse.MGRAST: no visible binding for global variable ‘.MGRAST’
this.package: no visible binding for global variable ‘.MGRAST’
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLQZzlk/R.INSTALL616249a2f42e/mgsub/man/mgsub.Rd:19: file link ‘regexpr’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLQZzlk/R.INSTALL616249a2f42e/mgsub/man/mgsub.Rd:20: file link ‘sub’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mgsub.Rcheck/00install.out’ for details.
calc_z_var: no visible binding for global variable ‘median’
diffScore: no visible global function definition for ‘new’
diffScore: no visible global function definition for ‘model.matrix’
logNORMcdf: no visible global function definition for ‘pnorm’
mGSZ.adj.mean.std: no visible binding for global variable ‘sd’
pick.data.cols: no visible binding for global variable ‘var’
plotProfile: no visible binding for global variable ‘quantile’
plotProfile: no visible global function definition for ‘lines’
plotProfile: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines median model.matrix new pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Unknown package ‘McSpatial’ in Rd xrefs
File
  LICENSE
is not mentioned in the DESCRIPTION file.
BCI: no visible global function definition for ‘quantile’
Metro_Hastings: no visible global function definition for ‘optim’
Metro_Hastings: no visible global function definition for ‘runif’
Metro_Hastings: no visible global function definition for ‘var’
plotMH: no visible global function definition for ‘hist’
plotMH: no visible global function definition for ‘frame’
plotMH: no visible global function definition for ‘text’
Undefined global functions or variables:
  frame hist optim quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘structSSI’
Found the following significant warnings:
  Rd warning: /tmp/RtmpzHha5h/R.INSTALL4ed63df1d559/MHTmult/man/gbonf.p.adjust.Rd:10: file link ‘as.numeric’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzHha5h/R.INSTALL4ed63df1d559/MHTmult/man/gsidak.p.adjust.Rd:10: file link ‘as.numeric’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MHTmult.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpplI8M0/R.INSTALL28cd52fd222c/micEconCES/man/cesEst.Rd:317: file link ‘linear.hypothesis’ in package ‘car’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpplI8M0/R.INSTALL28cd52fd222c/micEconCES/man/dwt.cesEst.Rd:23: file link ‘durbinWatsonTest.lm’ in package ‘car’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/micEconCES.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpKZU0EE/R.INSTALL4fe45ef32e37/michelRodange/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/michelRodange.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpqq8ZmR/R.INSTALL276225698ee/microbenchmark/man/find_prefix.Rd:13: file link ‘min’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/microbenchmark.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Found the following significant warnings:
  Rd warning: /tmp/RtmpYd4aKJ/R.INSTALL243e2d419449/micromap/man/mmplot.Rd:81: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYd4aKJ/R.INSTALL243e2d419449/micromap/man/mmplot.Rd:143: file link ‘scale_x_continuous’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/micromap.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Ex01-WFLung-2000-2004-State-Dot-County-Box.pdf’
  ‘Ex02-WmLung50-70-Arrow-Bar.pdf’ ‘Ex03-Time-Series-with-Conf.pdf’
  ‘Ex04-Scatter-Dots.pdf’ ‘Ex05-Stkd-Bar-var-height.pdf’
  ‘Ex06-Stkd-Bar-fixedheight-nodot.pdf’ ‘Ex07-Educ-Centered-Bar.pdf’
  ‘Ex08-DotSignificants.pdf’ ‘Ex09-Kansas Population and
  Inc-8.5x14-sn.pdf’ ‘Ex10-Kansas Population and Inc-11x17.pdf’
  ‘Ex11-New York Pop 2010 and Change-sn colSize.pdf’ ‘Ex12-MD Pop 1970
  and 2010 plus change-map.pdf’ ‘Ex13-China 2013 Population.pdf’
  ‘Ex14-Seoul 2012 Population.pdf’ ‘Ex15-Utah Population.pdf’
  ‘Ex16_state.x77_no_DC.pdf’ ‘Ex17_state.x77_DCasNA_D.pdf’ ‘Ex18_Africa
  Micromap-11x17.pdf’
migration.cv.in : <anonymous>: no visible global function definition
  for ‘sd’
migration.cv.out : <anonymous>: no visible global function definition
  for ‘sd’
migration.field.diagram: no visible global function definition for
  ‘lines’
migration.field.diagram: no visible global function definition for
  ‘text’
migration.field.diagram: no visible global function definition for
  ‘polygon’
migration.field.diagram: no visible global function definition for ‘lm’
migration.field.diagram: no visible global function definition for
  ‘predict’
migration.field.diagram: no visible global function definition for
  ‘points’
migration.field.diagram: no visible global function definition for
  ‘resid’
migration.field.diagram: no visible global function definition for
  ‘coef’
migration.field.diagram: no visible global function definition for
  ‘mtext’
migration.field.diagram: no visible global function definition for
  ‘density’
migration.field.diagram: no visible global function definition for
  ‘rug’
migration.gini.col : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.in : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.out : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.row : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.total: no visible global function definition for ‘dist’
Undefined global functions or variables:
  coef density dist lines lm mtext points polygon predict resid rug sd
  text
Consider adding
  importFrom("graphics", "lines", "mtext", "points", "polygon", "rug",
             "text")
  importFrom("stats", "coef", "density", "dist", "lm", "predict",
             "resid", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmppcTaJb/R.INSTALL2d267160722c/migui/man/migui.Rd:32: file link ‘mi-package’ in package ‘mi’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/migui.Rcheck/00install.out’ for details.
.default_model: no visible global function definition for ‘is’
.guess_type: no visible global function definition for ‘is.ts’
.parse_trans: no visible binding for global variable ‘qnorm’
do_get_data_from_disk: no visible global function definition for
  ‘read.csv’
do_get_data_from_mi: no visible global function definition for ‘data’
do_get_data_from_r : <anonymous>: no visible global function definition
  for ‘is’
do_parametric_eval : <anonymous>: no visible global function definition
  for ‘dev.off’
do_parametric_eval : <anonymous>: no visible global function definition
  for ‘title’
do_var_options : varHandler2: no visible global function definition for
  ‘is’
do_var_options : varHandler3: no visible global function definition for
  ‘getClass’
do_var_options : varHandler3: no visible global function definition for
  ‘is’
do_var_options : changeHandler: no visible global function definition
  for ‘is’
do_var_options : <anonymous>: no visible global function definition for
  ‘title’
do_var_options: no visible global function definition for ‘getClass’
do_var_options: no visible global function definition for ‘is’
helpHandler: no visible global function definition for ‘browseURL’
is.method_in_mi: no visible global function definition for
  ‘selectMethod’
is.method_in_mi: no visible global function definition for ‘signature’
Undefined global functions or variables:
  browseURL data dev.off getClass is is.ts qnorm read.csv selectMethod
  signature title
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "title")
  importFrom("methods", "getClass", "is", "selectMethod", "signature")
  importFrom("stats", "is.ts", "qnorm")
  importFrom("utils", "browseURL", "data", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2wQgOS/R.INSTALL4f555b79630b/miic/man/getIgraph.Rd:30: file link ‘igraph.plotting’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2wQgOS/R.INSTALL4f555b79630b/miic/man/getIgraph.Rd:31: file link ‘layout’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2wQgOS/R.INSTALL4f555b79630b/miic/man/plot.miic.Rd:18: file link ‘igraph.plotting’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2wQgOS/R.INSTALL4f555b79630b/miic/man/plot.miic.Rd:31: file link ‘igraph.plotting’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/miic.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5vAtZ9/R.INSTALL5cad574d4ccd/MIIVsem/man/miivs.Rd:11: file link ‘lavaanify’ in package ‘lavaan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MIIVsem.Rcheck/00install.out’ for details.
nat_hist: no visible global function definition for ‘data’
nat_hist: no visible binding for global variable ‘current.other’
t_mal: no visible global function definition for ‘uniroot’
t_prog: no visible global function definition for ‘rlnorm’
tdeath_lung: no visible global function definition for ‘data’
tdeath_lung: no visible binding for global variable ‘ci.lung’
tdeath_lung: no visible binding for global variable ‘current.other’
tdeath_lung: no visible binding for global variable ‘former.other’
tdeath_lung: no visible binding for global variable ‘never.other’
tdeath_other: no visible global function definition for ‘data’
tdeath_other: no visible binding for global variable ‘ci.lung’
tdeath_other: no visible binding for global variable ‘current.other’
tdeath_other: no visible binding for global variable ‘former.other’
tdeath_other: no visible binding for global variable ‘never.other’
Undefined global functions or variables:
  ci.lung current.other data former.other never.other rlnorm uniroot
Consider adding
  importFrom("stats", "rlnorm", "uniroot")
  importFrom("utils", "data")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
MImix.default: no visible binding for global variable ‘coef’
MImix.default: no visible binding for global variable ‘vcov’
MImix.one: no visible global function definition for ‘qnorm’
MImix.one: no visible global function definition for ‘uniroot’
mixcdf.target: no visible global function definition for ‘pnorm’
print.MImixresult: no visible global function definition for ‘coef’
print.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘coef’
summary.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  coef pnorm qnorm qt uniroot vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "qt", "uniroot", "vcov")
to your NAMESPACE file.
Rd file 'MImix.Rd':
  \usage lines wider than 90 characters:
     MImix(results,variances,weights = 1/length(results), percentiles = c(0.025, 0.5, 0.975), ...) 

These lines will be truncated in the PDF manual.
miney : plot.initial.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘text’
miney: no visible global function definition for ‘locator’
miney: no visible global function definition for ‘rect’
miney: no visible global function definition for ‘title’
Undefined global functions or variables:
  locator rect text title
Consider adding
  importFrom("graphics", "locator", "rect", "text", "title")
to your NAMESPACE file.
rminimax: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpz0eteS/R.INSTALL3df915609699/miniUI/man/miniContentPanel.Rd:13: file link ‘fillCol’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/miniUI.Rcheck/00install.out’ for details.
read_design: no visible global function definition for ‘model.frame’
read_design: no visible global function definition for ‘read.table’
read_design: no visible global function definition for ‘model.matrix’
read_response: no visible global function definition for ‘read.table’
update_beta: no visible global function definition for ‘update’
update_beta: no visible global function definition for ‘glm’
update_beta: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  glm model.frame model.matrix poisson read.table update
Consider adding
  importFrom("stats", "glm", "model.frame", "model.matrix", "poisson",
             "update")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘glycolysis.xml’ ‘glycolysis_desc.tsv’ ‘glycolysis_met.tsv’
  ‘glycolysis_react.tsv’
minxent.multiple: no visible global function definition for ‘cov.wt’
minxent.single: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  cov.wt optimize
Consider adding
  importFrom("stats", "cov.wt", "optimize")
to your NAMESPACE file.
Rd file 'minxent.multiple.Rd':
  \examples lines wider than 100 characters:
     minxent.multiple(q=q,G=G,eta=eta,c(0,0)) #estimates of lagrangian multipliers and MinxEnt distribution

Rd file 'minxent.single.Rd':
  \examples lines wider than 100 characters:
     minxent.single(q=q,G=G,eta=eta,c(0)) # estimate of lagrangian multipliers and Kullback minimimum cross entropy distribution

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpW5L5ph/R.INSTALL59954ca3076/mipfp/man/CompareMaxDev.Rd:42: file link ‘error.margins.mipfp’ in package ‘mipfp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpW5L5ph/R.INSTALL59954ca3076/mipfp/man/Estimate.Rd:142: file link ‘gof.estimates.mipfp’ in package ‘mipfp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpW5L5ph/R.INSTALL59954ca3076/mipfp/man/Estimate.Rd:145: file link ‘print.mipfp’ in package ‘mipfp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpW5L5ph/R.INSTALL59954ca3076/mipfp/man/ObtainModelEstimates.Rd:50: file link ‘Rsolnp’ in package ‘Rsolnp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpW5L5ph/R.INSTALL59954ca3076/mipfp/man/ObtainModelEstimates.Rd:110: file link ‘Rsolnp’ in package ‘Rsolnp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpW5L5ph/R.INSTALL59954ca3076/mipfp/man/confint.mipfp.Rd:61: file link ‘confint.default’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mipfp.Rcheck/00install.out’ for details.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.

Found the following calls to attach():
File ‘MIPHENO/R/cdf.pval.R’:
  attach(sample.cdf)
See section ‘Good practice’ in ‘?attach’.
.FCLoess: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘median’
.Import.Luminex: no visible global function definition for ‘read.csv’
.Intra.Me: no visible global function definition for ‘sd’
.Intra.Me: no visible global function definition for ‘quantile’
.Intra.Me: no visible global function definition for ‘qchisq’
.Intra.Median: no visible global function definition for ‘median’
.boxplot.rtprofile: no visible global function definition for ‘boxplot’
.denplot: no visible global function definition for ‘density’
.denplot: no visible global function definition for ‘abline’
.normalize.Luminex: no visible global function definition for ‘sd’
.normalize.qrtpcr: no visible global function definition for ‘density’
.validate.default: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  abline boxplot density loess median qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘GGplots.pdf’ ‘Heatmap.pdf’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp59i5SS/R.INSTALL19f89d71bd3/mi/man/bounded.Rd:12: file link ‘rtruncnorm’ in package ‘truncnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp59i5SS/R.INSTALL19f89d71bd3/mi/man/rdata.frame.Rd:42: file link ‘rmsn’ in package ‘sn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpfXCtYY/R.INSTALL291c7c1968ff/MIRES/man/mires.Rd:36: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MIRES.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
fisher.combination: no visible global function definition for ‘pchisq’
gs.test: no visible global function definition for ‘ks.test’
gs.test: no visible global function definition for ‘wilcox.test’
gs.test: no visible global function definition for ‘fisher.test’
inverse.normal.combination: no visible global function definition for
  ‘qnorm’
inverse.normal.combination: no visible global function definition for
  ‘pnorm’
limma.one.sided: no visible global function definition for ‘pt’
Undefined global functions or variables:
  fisher.test ks.test pchisq pnorm pt qnorm wilcox.test
Consider adding
  importFrom("stats", "fisher.test", "ks.test", "pchisq", "pnorm", "pt",
             "qnorm", "wilcox.test")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1oJsPA/R.INSTALL64237eecf5e0/misc3d/man/contour3d.Rd:61: file link ‘drawScene.rgl’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1oJsPA/R.INSTALL64237eecf5e0/misc3d/man/drawScene.Rd:28: file link ‘panel.3dwire’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1oJsPA/R.INSTALL64237eecf5e0/misc3d/man/parametric3d.Rd:52: file link ‘drawScene.rgl’ in package ‘misc3d’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/misc3d.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpiFaMs4/R.INSTALL375f4e19846a/miscF/man/curve.polynomial.rjmcmc.Rd:68: file link ‘sm.spline’ in package ‘pspline’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpiFaMs4/R.INSTALL375f4e19846a/miscF/man/rMultinom.Rd:25: file link ‘rmultinom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/miscF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnzZu6j/R.INSTALL2ea85e065c68/miscset/man/ggplotGrid.Rd:46: file link ‘grid.arrange’ in package ‘gridExtra’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnzZu6j/R.INSTALL2ea85e065c68/miscset/man/info.Rd:23: file link ‘session_info’ in package ‘devtools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnzZu6j/R.INSTALL2ea85e065c68/miscset/man/strextr.Rd:34: file link ‘str_extract_all’ in package ‘stringr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/miscset.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYzmV7N/R.INSTALL291a44d952a5/miscTools/man/compPlot.Rd:18: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYzmV7N/R.INSTALL291a44d952a5/miscTools/man/ddnorm.Rd:30: file link ‘dnorm’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/miscTools.Rcheck/00install.out’ for details.
missForest: no visible global function definition for ‘predict’
missForest: no visible global function definition for ‘idiv’
missForest: no visible global function definition for ‘var’
nrmse: no visible global function definition for ‘var’
Undefined global functions or variables:
  idiv predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3f4XzK/R.INSTALL44607f4cf40a/missSBM/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/missSBM.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘CompQuadForm’ which was already attached by Depends.
  Please remove these calls from your code.
linear.test: no visible global function definition for ‘lm’
linear.test: no visible global function definition for ‘pchisq’
linear.weight.test: no visible global function definition for ‘lm’
linear.weight.test: no visible global function definition for ‘dbeta’
linear.weight.test: no visible global function definition for ‘pchisq’
logit.test: no visible global function definition for ‘glm’
logit.test: no visible global function definition for ‘binomial’
logit.test: no visible binding for global variable ‘logit’
logit.test: no visible global function definition for ‘pchisq’
logit.weight.test: no visible global function definition for ‘glm’
logit.weight.test: no visible global function definition for ‘binomial’
logit.weight.test: no visible binding for global variable ‘logit’
logit.weight.test: no visible global function definition for ‘dbeta’
logit.weight.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  binomial dbeta glm lm logit pchisq
Consider adding
  importFrom("stats", "binomial", "dbeta", "glm", "lm", "pchisq")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpqUbTwO/R.INSTALL52b07ea50191/mistr/man/fdist.Rd:21: file link ‘FDist’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqUbTwO/R.INSTALL52b07ea50191/mistr/man/fdist.Rd:29: file link ‘FDist’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqUbTwO/R.INSTALL52b07ea50191/mistr/man/multinomdist.Rd:21: file link ‘Multinomial’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqUbTwO/R.INSTALL52b07ea50191/mistr/man/multinomdist.Rd:29: file link ‘Multinomial’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqUbTwO/R.INSTALL52b07ea50191/mistr/man/q.default.Rd:45: file link ‘q’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqUbTwO/R.INSTALL52b07ea50191/mistr/man/q_approxfun.Rd:27: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqUbTwO/R.INSTALL52b07ea50191/mistr/man/summary_comp_fit.Rd:15: file link ‘mle2-class’ in package ‘bbmle’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqUbTwO/R.INSTALL52b07ea50191/mistr/man/summary_comp_fit.Rd:21: file link ‘mle2-class’ in package ‘bbmle’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mistr.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [29s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mitre)
  > 
  > testthat::test_check("mitre")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-standard-attck.R:30:3): mitre att&ck techniques data frame ────
  any(apply(df, 2, function(x) all(is.na(x)))) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 98 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  Rd warning: /tmp/Rtmpe8Hq1c/R.INSTALL38ee2404ee73/miWQS/man/make.quantile.matrix.Rd:33: file link ‘.bincode’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/miWQS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYSlGkz/R.INSTALL2b5d615f8af/mixComp/man/Mix.Rd:16: file link ‘distributions’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYSlGkz/R.INSTALL2b5d615f8af/mixComp/man/Mix.Rd:22: file link ‘distributions’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYSlGkz/R.INSTALL2b5d615f8af/mixComp/man/RtoDat.Rd:13: file link ‘distributions’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYSlGkz/R.INSTALL2b5d615f8af/mixComp/man/datMix.Rd:19: file link ‘distributions’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYSlGkz/R.INSTALL2b5d615f8af/mixComp/man/datMix.Rd:23: file link ‘distributions’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mixComp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1HRY95/R.INSTALL63f51478ead4/MixedPsy/man/xplode.Rd:53: file link ‘lme4’ in package ‘lme4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MixedPsy.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Packages in Depends field not imported from:
  ‘MASS’ ‘RODBC’ ‘tcltk’ ‘tcltk2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmpaZGsVA/R.INSTALL2b9255d27993/mixsqp/man/mixkwdual.Rd:37: file link ‘mosek’ in package ‘Rmosek’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mixsqp.Rcheck/00install.out’ for details.
fit.mixtNB: no visible global function definition for ‘dnbinom’
fit.mixtNB: no visible global function definition for ‘nlminb’
wald.test: no visible global function definition for ‘pnorm’
wald.test: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
computeContourValues: no visible global function definition for
  ‘na.omit’
deselectNonMovementSteps : coOccurProb: no visible global function
  definition for ‘dnorm’
deselectNonMovementSteps: no visible global function definition for
  ‘pnorm’
estVarMKDE: no visible global function definition for ‘na.omit’
estVarMKDE: no visible global function definition for ‘qnorm’
estVarMKDE: no visible global function definition for ‘optimize’
plotMKDE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  dnorm na.omit optimize pnorm qnorm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "dnorm", "na.omit", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘ascii3d.txt’ ‘condor_3dMKDE.dat’ ‘condor_3dMKDE.vtk’
  ‘condor_3dMKDE.xdmf’ ‘condor_dem.dat’ ‘condor_dem.vtk’
  ‘condor_dem.xdmf’ ‘condor_locations.vtk’ ‘condor_path.vtk’
Found the following significant warnings:
  Rd warning: /tmp/RtmpkY8HHt/R.INSTALL54459f3d431/mkin/man/loftest.Rd:21: file link ‘lrtest.default’ in package ‘lmtest’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkY8HHt/R.INSTALL54459f3d431/mkin/man/lrtest.mkinfit.Rd:32: file link ‘lrtest.default’ in package ‘lmtest’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mkin.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
mkle: no visible global function definition for ‘sd’
mkle: no visible global function definition for ‘density’
mkle: no visible global function definition for ‘optimize’
mkle.ci: no visible global function definition for ‘sd’
mkle.ci: no visible binding for global variable ‘var’
mkle.ci: no visible global function definition for ‘quantile’
mkle.ci: no visible global function definition for ‘qnorm’
opt.bw: no visible global function definition for ‘sd’
opt.bw : mse: no visible global function definition for ‘var’
opt.bw: no visible global function definition for ‘optimize’
opt.bw: no visible global function definition for ‘var’
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
mkssd: no visible global function definition for ‘txtProgressBar’
mkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘developing-with-mlapi.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpZgFymj/R.INSTALL48a415c1b70/mlearning/man/confusion.Rd:137: file link ‘cm.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mlearning.Rcheck/00install.out’ for details.
Unexported objects imported by ':::' calls:
  ‘MASS:::lda.default’ ‘MASS:::qda.default’
  ‘e1071:::naiveBayes.default’ ‘e1071:::svm.default’
  ‘randomForest:::randomForest.default’
  See the note in ?`:::` about the use of this operator.
confusionBarplot: no visible global function definition for ‘par’
confusionBarplot: no visible global function definition for ‘barplot’
confusionBarplot: no visible global function definition for ‘lines’
confusionBarplot: no visible global function definition for ‘text’
confusionBarplot: no visible global function definition for ‘legend’
confusionBarplot: no visible global function definition for ‘axis’
confusionImage: no visible global function definition for ‘par’
confusionImage: no visible global function definition for ‘image’
confusionImage: no visible global function definition for ‘text’
confusionImage: no visible global function definition for ‘abline’
confusionImage: no visible global function definition for ‘axis’
confusionImage: no visible global function definition for ‘mtext’
confusionStars: no visible global function definition for ‘par’
confusionStars: no visible global function definition for ‘stars’
confusionStars: no visible global function definition for ‘rect’
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "rect", "stars", "text")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
plotCDF1: no visible global function definition for ‘lines’
plotCDF2: no visible global function definition for ‘gray’
plotCDF2: no visible global function definition for ‘image’
plotCDF2: no visible global function definition for ‘box’
plotCDF2: no visible global function definition for ‘par’
plotCDF2: no visible global function definition for ‘rect’
plotCDF2: no visible global function definition for ‘text’
plotCM: no visible global function definition for ‘image’
plotCM: no visible global function definition for ‘axis’
plotCM: no visible global function definition for ‘box’
plotDens1: no visible global function definition for ‘lines’
plotDens2: no visible global function definition for ‘gray’
plotDens2: no visible global function definition for ‘rect’
plotDens2: no visible global function definition for ‘axis’
plotDens2: no visible global function definition for ‘text’
plotHM: no visible global function definition for ‘terrain.colors’
plotHM: no visible global function definition for ‘image’
plotHM: no visible global function definition for ‘box’
plotHM: no visible global function definition for ‘abline’
plotHM: no visible global function definition for ‘text’
plotHM: no visible global function definition for ‘par’
plotHM: no visible global function definition for ‘rect’
plotRects: no visible global function definition for ‘rainbow’
plotRects: no visible global function definition for ‘abline’
plotRects: no visible global function definition for ‘rect’
Undefined global functions or variables:
  abline axis box gray image lines par rainbow rect terrain.colors text
Consider adding
  importFrom("grDevices", "gray", "rainbow", "terrain.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "lines",
             "par", "rect", "text")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXLVt3m/R.INSTALL72a4602ad1bf/mle.tools/man/coxsnell.bc.Rd:127: file link ‘D’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXLVt3m/R.INSTALL72a4602ad1bf/mle.tools/man/expected.varcov.Rd:125: file link ‘D’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXLVt3m/R.INSTALL72a4602ad1bf/mle.tools/man/observed.varcov.Rd:95: file link ‘D’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mle.tools.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
dftest: no visible global function definition for ‘slot’
mctest: no visible global function definition for ‘rnorm’
mleurDiag: no visible global function definition for ‘acf’
mleurDiag: no visible global function definition for ‘pchisq’
mleurDiag: no visible global function definition for ‘par’
mleurDiag: no visible global function definition for ‘boxplot’
mleurDiag: no visible global function definition for ‘shapiroTest’
mleurDiag: no visible global function definition for ‘title’
mleurDiag: no visible global function definition for ‘abline’
mleurDiag: no visible global function definition for ‘lines’
simar1: no visible global function definition for ‘rnorm’
simar1: no visible global function definition for ‘rt’
simar1: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  abline acf boxplot convolve lines par pchisq rnorm rt shapiroTest
  slot title
Consider adding
  importFrom("graphics", "abline", "boxplot", "lines", "par", "title")
  importFrom("methods", "slot")
  importFrom("stats", "acf", "convolve", "pchisq", "rnorm", "rt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘CHANGELOG.txt’
Packages in Depends field not imported from:
  ‘methods’ ‘seqinr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CheckStability: no visible global function definition for ‘cor’
CheckStability: no visible global function definition for ‘var’
PriorNormPCA: no visible global function definition for ‘barplot’
SortModes: no visible global function definition for ‘rnorm’
mlicaMAIN: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot cor rnorm runif var
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "rnorm", "runif", "var")
to your NAMESPACE file.
Rd file 'SortModes.Rd':
  \examples lines wider than 100 characters:
             # A) Computation of relative data power. Store values in vector of size H=ncp. Could use different criterion here.

Rd file 'mlica.rd':
  \examples lines wider than 100 characters:
                 print("Consider either increasing the threshold for pca eigenvalues to perform ICA on a smaller subspace or increasing maxi ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpR22Rjw/R.INSTALL557630106971/mlogitBMA/man/summary.bic.mlogit.Rd:26: file link ‘summary.bic.glm’ in package ‘BMA’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpR22Rjw/R.INSTALL557630106971/mlogitBMA/man/summary.bic.mlogit.Rd:28: file link ‘plot.bic.glm’ in package ‘BMA’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpR22Rjw/R.INSTALL557630106971/mlogitBMA/man/summary.bic.mlogit.Rd:30: file link ‘imageplot.bma’ in package ‘BMA’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mlogitBMA.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘BMA’ ‘abind’ ‘maxLik’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy

Found the following assignments to the global environment:
File ‘mlPhaser/R/mlPhaser.R’:
  assign("validHaploGroups", c(get("validHaploGroups", globalenv()), 
    groupStoreList), globalenv())
  assign("validHaploGroups", list(), globalenv())
Rd file 'phaseReport.Rd':
  \examples lines wider than 100 characters:
     phaseReport(my.genotypes,haplotypes, haploFreqs, outFormat="all")       # outFormat="all" is the default

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘mlr3extralearners’
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Found the following significant warnings:
  Rd warning: /tmp/RtmpxYg92K/R.INSTALL7b643726be01/mmcm/man/reexports.Rd:14: file link ‘GenzBretz’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mmcm.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
mmm2: no visible global function definition for ‘model.frame’
mmm2: no visible global function definition for ‘model.matrix’
mmm2: no visible global function definition for ‘model.response’
mmm2: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
get.score: no visible global function definition for ‘sd’
get.score: no visible global function definition for ‘coef’
get.score: no visible global function definition for ‘as’
get.score.main: no visible global function definition for ‘sd’
get.score.main: no visible global function definition for ‘coef’
get.subgroup: no visible global function definition for ‘sd’
sample.tte: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as coef runif sd
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "runif", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package which this enhances but not available for checking: ‘aMNLFA’
Package suggested but not available for checking: ‘Flury’
Found the following significant warnings:
  Rd warning: /tmp/RtmpqWNR1I/R.INSTALL29c608007d3/mnt/man/SR.Rd:19: file link ‘mvnorm.test’ in package ‘energy’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqWNR1I/R.INSTALL29c608007d3/mnt/man/SR.Rd:29: file link ‘mvnorm.test’ in package ‘energy’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mnt.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘MoBPSmaps’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3XoaQ5/R.INSTALL36a61c4ff35c/model4you/man/objfun.pmtree.Rd:21: file link ‘predict.party’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3XoaQ5/R.INSTALL36a61c4ff35c/model4you/man/pmforest.Rd:145: file link ‘gettree’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3XoaQ5/R.INSTALL36a61c4ff35c/model4you/man/print.pmtree.Rd:36: file link ‘print.party’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3XoaQ5/R.INSTALL36a61c4ff35c/model4you/man/varimp.pmforest.Rd:42: file link ‘varimp.cforest’ in package ‘partykit’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/model4you.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘SparseM’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘glmnet’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘BIO_TCandNLCD_NLCD.jpg’ ‘BIO_TCandNLCD_TCB.jpg’
  ‘BIO_TCandNLCD_TCG.jpg’ ‘BIO_TCandNLCD_TCW.jpg’
  ‘BIO_TCandNLCD_corrplot.jpg’ ‘BIO_TCandNLCD_mask_all_predictors.jpg’
  ‘BIO_TCandNLCD_projections.txt’ ‘RF_BIO_TCandNLCD_01.img’
  ‘RF_BIO_TCandNLCD_01.img.aux.xml’
  ‘RF_BIO_TCandNLCD_01_mapmake_arguments.txt’
  ‘RF_BIO_TCandNLCD_01_projections.txt’ ‘RF_BIO_TCandNLCD_OOB.csv’
  ‘RF_BIO_TCandNLCD_OOB_corrplot.jpg’
  ‘RF_BIO_TCandNLCD_OOB_corrplot.pdf’ ‘RF_BIO_TCandNLCD_OOB_error.jpg’
  ‘RF_BIO_TCandNLCD_OOB_error.pdf’
  ‘RF_BIO_TCandNLCD_OOB_importance.jpg’
  ‘RF_BIO_TCandNLCD_OOB_importance.pdf’
  ‘RF_BIO_TCandNLCD_OOB_scatterplot.jpg’
  ‘RF_BIO_TCandNLCD_OOB_scatterplot.pdf’
  ‘RF_BIO_TCandNLCD_model_building_arguments.txt’
  ‘RF_Bio_TC_model_building_arguments.txt’ ‘example.test.csv’
  ‘example.train.csv’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5FLKiN/R.INSTALL1cb43eebb29a/modelr/man/na.warn.Rd:15: file link ‘na.exclude’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5FLKiN/R.INSTALL1cb43eebb29a/modelr/man/permute.Rd:18: file link ‘select_helpers’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/modelr.Rcheck/00install.out’ for details.
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [31s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modelsummary)
  > 
  > test_check("modelsummary")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  ● On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-gof.R:13:3): custom gof_map omits everything by default ─────────
  Error: When using the `~name` syntax, subsequent values must not have names.
  Backtrace:
      █
   1. └─tibble::tribble(...) test-gof.R:13:2
   2.   └─tibble:::extract_frame_data_from_dots(...)
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 240 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  Rd warning: /tmp/RtmpUM8JiM/R.INSTALL29766a6a5b49/modeltools/man/StatModel-class.Rd:63: file link ‘lm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUM8JiM/R.INSTALL29766a6a5b49/modeltools/man/StatModel-class.Rd:63: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/modeltools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxI70dY/R.INSTALL63621c0a970c/modiscloud/man/get_date_from_POSIXct.Rd:48: file link ‘as.POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxI70dY/R.INSTALL63621c0a970c/modiscloud/man/make_POSIXct_date.Rd:54: file link ‘as.POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/modiscloud.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.clustOrder: no visible global function definition for ‘hclust’
.clustOrder: no visible global function definition for ‘as.dist’
consensusMEDissimilarity: no visible global function definition for
  ‘cor’
mergeCloseModules: no visible global function definition for ‘cor’
mergeCloseModules: no visible global function definition for ‘hclust’
mergeCloseModules: no visible global function definition for ‘as.dist’
moduleEigengenes: no visible global function definition for ‘cor’
moduleEigengenes: no visible global function definition for ‘cov’
moduleNumber: no visible global function definition for ‘cutree’
orderMEs: no visible global function definition for ‘cor’
orderMEs: no visible global function definition for ‘as.dist’
plotHclustColors: no visible global function definition for ‘barplot’
plotHclustColors: no visible global function definition for ‘strwidth’
plotHclustColors: no visible global function definition for ‘rect’
plotHclustColors: no visible global function definition for ‘text’
plotHclustColors: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.dist barplot cor cov cutree hclust lines rect strwidth text
Consider adding
  importFrom("graphics", "barplot", "lines", "rect", "strwidth", "text")
  importFrom("stats", "as.dist", "cor", "cov", "cutree", "hclust")
to your NAMESPACE file.
agostino.test: no visible global function definition for
  ‘complete.cases’
agostino.test: no visible global function definition for ‘pnorm’
anscombe.test: no visible global function definition for
  ‘complete.cases’
anscombe.test: no visible global function definition for ‘pnorm’
bonett.test: no visible global function definition for ‘complete.cases’
bonett.test: no visible global function definition for ‘pnorm’
jarque.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpVIm4Kj/R.INSTALL399b6558dd70/Momocs/man/as_df.Rd:30: file link ‘data_frame’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpVIm4Kj/R.INSTALL399b6558dd70/Momocs/man/layers.Rd:159: file link ‘bw.nrd0’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpVIm4Kj/R.INSTALL399b6558dd70/Momocs/man/reexports.Rd:17: file link ‘%$%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpVIm4Kj/R.INSTALL399b6558dd70/Momocs/man/reexports.Rd:17: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpVIm4Kj/R.INSTALL399b6558dd70/Momocs/man/reexports.Rd:17: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpVIm4Kj/R.INSTALL399b6558dd70/Momocs/man/reexports.Rd:17: file link ‘%T>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Momocs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmplR6TK8/R.INSTALL101d231ab36f/Mondrian/man/mondrian.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplR6TK8/R.INSTALL101d231ab36f/Mondrian/man/mondrian.Rd:49: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Mondrian.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpysx9Ks/R.INSTALL40f33875f721/mongolite/man/mongo.Rd:55: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mongolite.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmptjYNwx/R.INSTALL7602428b38ce/monitoR/man/fileCopyRename.Rd:50: file link ‘OlsonNames’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmptjYNwx/R.INSTALL7602428b38ce/monitoR/man/specCols.Rd:40: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmptjYNwx/R.INSTALL7602428b38ce/monitoR/man/specCols.Rd:40: file link ‘topo.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmptjYNwx/R.INSTALL7602428b38ce/monitoR/man/specCols.Rd:40: file link ‘terrain.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmptjYNwx/R.INSTALL7602428b38ce/monitoR/man/templateMatching.Rd:78: file link ‘OlsonNames’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/monitoR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9p3gqC/R.INSTALL656e54a1bca4/monographaR/man/monographaR-package.Rd:43: file link ‘sp’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/monographaR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpNVkg6V/R.INSTALL412144e52319/MonoPhy/man/AssessMonophyly.Rd:47: file link ‘getMRCA’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MonoPhy.Rcheck/00install.out’ for details.
mopsocd : initialize_pop: no visible global function definition for
  ‘runif’
mopsocd : compute_velocity: no visible global function definition for
  ‘runif’
mopsocd : mutate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
checkTH: no visible global function definition for ‘pchisq’
getOrderPval: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
ametrine : <anonymous>: no visible global function definition for
  ‘approx’
ametrine: no visible global function definition for ‘rgb’
isolum : <anonymous>: no visible global function definition for
  ‘approx’
isolum: no visible global function definition for ‘rgb’
morgenstemning : <anonymous>: no visible global function definition for
  ‘approx’
morgenstemning: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
cor.gen: no visible global function definition for ‘rnorm’
cor.gen: no visible global function definition for ‘resid’
cor.gen: no visible global function definition for ‘lm’
cor.gen: no visible binding for global variable ‘sd’
cor.gen: no visible global function definition for ‘cor’
cor.gen: no visible global function definition for ‘write.table’
stat.gen: no visible global function definition for ‘rexp’
stat.gen: no visible global function definition for ‘rnorm’
stat.gen: no visible binding for global variable ‘sd’
stat.gen: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  cor lm resid rexp rnorm sd write.table
Consider adding
  importFrom("stats", "cor", "lm", "resid", "rexp", "rnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'cor.gen.Rd':
  \usage lines wider than 90 characters:
     cor.gen(num.subj, x.mean, x.sd, y.mean, y.sd, correlation, data.dec = 2, x.name = "Variable X", y.name = "Variable Y")

Rd file 'stat.gen.Rd':
  \usage lines wider than 90 characters:
     stat.gen(num.subj, target.mean, target.sd, data.dec = 2, neg.data = TRUE, x.name = "Variable X")

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘BMI BISS Correlation MorseGen Results.txt’ ‘Control MorseGen
  Results.txt’ ‘Massage MorseGen Results.txt’ ‘Variable X MorseGen
  Results.txt’ ‘Variable X Variable Y Correlation MorseGen Results.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpkwEj1n/R.INSTALL524e3f4a5e51/morse/man/morse-package.Rd:95: file link ‘rjags’ in package ‘rjags’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkwEj1n/R.INSTALL524e3f4a5e51/morse/man/morse-package.Rd:96: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkwEj1n/R.INSTALL524e3f4a5e51/morse/man/plot.reproData.Rd:50: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkwEj1n/R.INSTALL524e3f4a5e51/morse/man/plot.reproFitTT.Rd:80: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkwEj1n/R.INSTALL524e3f4a5e51/morse/man/plotDoseResponse.reproData.Rd:57: file link ‘pois.exact’ in package ‘epitools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkwEj1n/R.INSTALL524e3f4a5e51/morse/man/plotDoseResponse.reproData.Rd:64: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkwEj1n/R.INSTALL524e3f4a5e51/morse/man/plotDoseResponse.reproData.Rd:84: file link ‘pois.exact’ in package ‘epitools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkwEj1n/R.INSTALL524e3f4a5e51/morse/man/plotDoseResponse.survDataCstExp.Rd:56: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/morse.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpTRvjhG/R.INSTALL348267f5798/mosaicCalc/man/connector.Rd:8: file link ‘connector’ in package ‘mosaic’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTRvjhG/R.INSTALL348267f5798/mosaicCalc/man/smoother.Rd:8: file link ‘smoother’ in package ‘mosaic’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTRvjhG/R.INSTALL348267f5798/mosaicCalc/man/spliner.Rd:8: file link ‘spliner’ in package ‘mosaic’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mosaicCalc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpI8x1FJ/R.INSTALL41ff49147cc0/mosmafs/man/slickEcr.Rd:83: file link ‘replaceMuPlusLambda’ in package ‘ecr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mosmafs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpX1BRa5/R.INSTALL19b84639d768/mosum/man/plot.mosum.cpts.Rd:33: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpX1BRa5/R.INSTALL19b84639d768/mosum/man/plot.mosum.stat.Rd:20: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mosum.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpzTcMVW/R.INSTALL425f6c1eb874/motifr/man/plot_mnet.Rd:45: file link ‘layout_as_multilevel’ in package ‘graphlayouts’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/motifr.Rcheck/00install.out’ for details.
getmouseDV: no visible global function definition for ‘tail’
interpltraj: no visible global function definition for ‘approx’
trim1: no visible global function definition for ‘tail’
Undefined global functions or variables:
  approx tail
Consider adding
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpVKA5B5/R.INSTALL54905be0ae47/moveVis/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/moveVis.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Package vignette with placeholder title ‘Vignette Title’:
  ‘mozzie.Rmd’
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘mpa-Ex.R’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘mpa/R/zzz.R’:
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

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

diagram.mpa: no visible global function definition for ‘abline’
diagram.mpa: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline text
Consider adding
  importFrom("graphics", "abline", "text")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXc9D0O/R.INSTALL3450793b96a4/mpath/man/ccsvm_fit.Rd:15: file link ‘matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXc9D0O/R.INSTALL3450793b96a4/mpath/man/ccsvm_fit.Rd:17: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXc9D0O/R.INSTALL3450793b96a4/mpath/man/cv.ccsvm_fit.Rd:14: file link ‘matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXc9D0O/R.INSTALL3450793b96a4/mpath/man/cv.ccsvm_fit.Rd:16: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXc9D0O/R.INSTALL3450793b96a4/mpath/man/predict.zipath.Rd:64: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mpath.Rcheck/00install.out’ for details.
mpcv: no visible binding for global variable ‘median’
mpcv: no visible global function definition for ‘cov’
mpcv: no visible global function definition for ‘dist’
plot.mpcv: no visible binding for global variable ‘median’
plot.mpcv: no visible global function definition for ‘par’
plot.mpcv: no visible global function definition for ‘rect’
plot.mpcv: no visible global function definition for ‘lines’
plot.mpcv: no visible global function definition for ‘points’
plot.mpcv: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cov dist legend lines median par points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "points", "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2RxkE6/R.INSTALL1de855a216d6/MPDiR/man/panel.psyfun.Rd:6: file link ‘panel.lmline’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MPDiR.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
GetExampleData: no visible binding for global variable ‘MPINetData’
Getenvir: no visible binding for global variable ‘MPINetData’
getPSS: no visible global function definition for ‘lines’
performpcls: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  MPINetData binomial lines
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "binomial")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpsQ1tyg/R.INSTALL71651df49d79/mpmcorrelogram/man/mpmcorrelogram.Rd:103: file link ‘mantel.partial’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpsQ1tyg/R.INSTALL71651df49d79/mpmcorrelogram/man/mpmcorrelogram.Rd:164: file link ‘mantel.partial’ in package ‘vegan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mpmcorrelogram.Rcheck/00install.out’ for details.
Dependence on R version ‘3.6.2’ not with patchlevel 0
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KernSmooth’ ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpblMDCi/R.INSTALL1fac6fc2d9d6/mppa/man/place.Rd:4: file link ‘plot,mproc-method’ in package ‘mppa’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpblMDCi/R.INSTALL1fac6fc2d9d6/mppa/man/place.Rd:7: file link ‘plot,mproc-method’ in package ‘mppa’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpblMDCi/R.INSTALL1fac6fc2d9d6/mppa/man/place.Rd:23: file link ‘plot,mproc-method’ in package ‘mppa’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mppa.Rcheck/00install.out’ for details.
place: no visible global function definition for ‘points’
plot,mproc: no visible binding for global variable ‘rainbow’
plot,mproc: no visible global function definition for ‘plot.default’
plot,mproc: no visible global function definition for ‘axis’
plot,mproc: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpEslnEU/R.INSTALL69444166eca2/MPTinR/man/bmpt.fia.Rd:94: file link ‘sfInit’ in package ‘snowfall’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEslnEU/R.INSTALL69444166eca2/MPTinR/man/bmpt.fia.Rd:94: file link ‘sfClusterSplit’ in package ‘snowfall’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MPTinR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnIjwga/R.INSTALL56af35e8f355/mptools/man/mp_animate.Rd:87: file link ‘im.convert’ in package ‘animation’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mptools.Rcheck/00install.out’ for details.
ppersp: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
densityfn: no visible global function definition for ‘dnbinom’
densityfn: no visible global function definition for ‘dpois’
densityfn: no visible global function definition for ‘dgeom’
form.add: no visible global function definition for ‘formula’
mreg: no visible global function definition for ‘model.frame’
mreg: no visible global function definition for ‘model.response’
mreg: no visible global function definition for ‘model.matrix’
mreg: no visible global function definition for ‘model.offset’
mreg: no visible global function definition for ‘nlm’
paper: no visible global function definition for ‘model.matrix’
randfn: no visible global function definition for ‘rnbinom’
randfn: no visible global function definition for ‘rpois’
randfn: no visible global function definition for ‘rgeom’
randfn: no visible global function definition for ‘rbinom’
summary.mreg: no visible global function definition for ‘pnorm’
summary.mreg: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  dgeom dnbinom dpois formula model.frame model.matrix model.offset
  model.response nlm pnorm printCoefmat rbinom rgeom rnbinom rpois
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dpois", "formula",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "nlm", "pnorm", "printCoefmat", "rbinom",
             "rgeom", "rnbinom", "rpois")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpa3Uu8b/R.INSTALL3be0211f9f17/MRFcov/man/MRFcov.Rd:40: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa3Uu8b/R.INSTALL3be0211f9f17/MRFcov/man/MRFcov_spatial.Rd:42: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa3Uu8b/R.INSTALL3be0211f9f17/MRFcov/man/MRFcov_spatial.Rd:62: file link ‘smooth.construct2’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa3Uu8b/R.INSTALL3be0211f9f17/MRFcov/man/MRFcov_spatial.Rd:112: file link ‘smooth.construct2’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa3Uu8b/R.INSTALL3be0211f9f17/MRFcov/man/bootstrap_MRF.Rd:46: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa3Uu8b/R.INSTALL3be0211f9f17/MRFcov/man/cv_MRF_diag.Rd:74: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa3Uu8b/R.INSTALL3be0211f9f17/MRFcov/man/cv_MRF_diag.Rd:135: file link ‘createFolds’ in package ‘caret’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa3Uu8b/R.INSTALL3be0211f9f17/MRFcov/man/predict_MRFnetworks.Rd:70: file link ‘graph.adjacency’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpa3Uu8b/R.INSTALL3be0211f9f17/MRFcov/man/prep_MRF_covariates_spatial.Rd:22: file link ‘smooth.construct2’ in package ‘mgcv’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MRFcov.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘MRH_lung’
Found the following significant warnings:
  Rd warning: /tmp/RtmpYqZ9UV/R.INSTALL279c4464da87/mrregression/man/mrbayes.Rd:139: file link ‘quote’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mrregression.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpg2Z5Q0/R.INSTALL2cef573d0c2a/MrSGUIDE/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MrSGUIDE.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MRsurvival: no visible global function definition for ‘rmvnorm’
MRsurvival: no visible global function definition for ‘optim’
MRsurvival : <anonymous>: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  optim quantile rmvnorm
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZ0cWb1/R.INSTALL734b4dc50d32/msaenet/man/predict.msaenet.Rd:17: file link ‘predict.ncvreg’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZ0cWb1/R.INSTALL734b4dc50d32/msaenet/man/predict.msaenet.Rd:18: file link ‘predict.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/msaenet.Rcheck/00install.out’ for details.
msap: no visible global function definition for ‘packageVersion’
msap: no visible global function definition for ‘read.csv’
msap: no visible global function definition for ‘write.csv’
msap: no visible global function definition for ‘sd’
msap: no visible global function definition for ‘wilcox.test’
msap: no visible global function definition for ‘dist’
msap: no visible global function definition for ‘rainbow’
msap: no visible global function definition for ‘png’
msap: no visible global function definition for ‘legend’
msap: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘cmdscale’
pcoa: no visible global function definition for ‘png’
pcoa: no visible global function definition for ‘par’
pcoa: no visible global function definition for ‘rainbow’
pcoa: no visible global function definition for ‘points’
pcoa: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par png points rainbow
  read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpMNwKeU/R.INSTALL401822c4711b/MSCMT/man/ggplot.mscmt.Rd:34: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMNwKeU/R.INSTALL401822c4711b/MSCMT/man/ggplot.mscmt.Rd:37: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMNwKeU/R.INSTALL401822c4711b/MSCMT/man/improveSynth.Rd:30: file link ‘mscmt’ in package ‘MSCMT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMNwKeU/R.INSTALL401822c4711b/MSCMT/man/improveSynth.Rd:33: file link ‘mscmt’ in package ‘MSCMT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMNwKeU/R.INSTALL401822c4711b/MSCMT/man/plot.mscmt.Rd:66: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MSCMT.Rcheck/00install.out’ for details.
cv.msda: no visible global function definition for ‘predict’
formatoutput: no visible global function definition for ‘new’
msda.prep: no visible global function definition for ‘cov’
plot.msda: no visible global function definition for ‘par’
plot.msda: no visible global function definition for ‘matplot’
plot.msda: no visible global function definition for ‘rainbow’
plot.msda: no visible global function definition for ‘approx’
plot.msda: no visible global function definition for ‘axis’
predict.msda: no visible binding for global variable ‘sd’
predict.msda: no visible global function definition for ‘predict’
zeromat: no visible global function definition for ‘new’
Undefined global functions or variables:
  approx axis cov matplot new par predict rainbow sd
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cov", "predict", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘test.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmppJWZM6/R.INSTALL31cc4ecbe99a/msgr/man/try_pmap.Rd:47: file link ‘pmap’ in package ‘purrr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/msgr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpu2Z7nh/R.INSTALL6a6c1b7c6f04/msigdbr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/msigdbr.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
Found the following significant warnings:
  Rd warning: /tmp/RtmpIwarrw/R.INSTALL41856efbced5/msmtools/man/survplot.Rd:31: file link ‘absorbing.msm’ in package ‘msm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/msmtools.Rcheck/00install.out’ for details.
BS.var: no visible binding for global variable ‘var’
BS.var: no visible global function definition for ‘cov’
Dist.CIs: no visible global function definition for ‘qnorm’
MSM.CIs: no visible global function definition for ‘qnorm’
plot,msSurv-missing: no visible global function definition for ‘update’
summary,msSurv: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov qnorm quantile update var
Consider adding
  importFrom("stats", "cov", "qnorm", "quantile", "update", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Designer.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘mtkMCDesigner.R’ ‘mtkRegressionTestAnalyser.R’ ‘mtkWWEvaluator.R’
Packages in Depends field not imported from:
  ‘DiceKriging’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CrossValidationMuFicokm: no visible global function definition for
  ‘covMatrix’
CrossValidationMuFicokmAll: no visible global function definition for
  ‘covMatrix’
MuFicokm: no visible global function definition for ‘km’
compute.beta.hat: no visible global function definition for ‘lm’
computeAuxVariables: no visible global function definition for
  ‘covMatrix’
kmCok: no visible global function definition for ‘new’
kmCok: no visible global function definition for ‘drop.response’
kmCok: no visible global function definition for ‘model.matrix’
kmCok: no visible global function definition for ‘covStruct.create’
kmCok: no visible global function definition for ‘validObject’
kmCok: no visible global function definition for ‘covParametersBounds’
kmCok: no visible binding for global variable ‘kmEstimate’
kmCok : cv: no visible global function definition for ‘leaveOneOut.km’
predict.kmCok: no visible global function definition for ‘model.matrix’
predict.kmCok: no visible global function definition for ‘covMat1Mat2’
predict.kmCok: no visible global function definition for ‘qnorm’
predict.kmCok: no visible global function definition for ‘qt’
predict.kmCok: no visible global function definition for ‘covMatrix’
summary.MuFicokm: no visible global function definition for
  ‘covparam2vect’
Undefined global functions or variables:
  covMat1Mat2 covMatrix covParametersBounds covStruct.create
  covparam2vect drop.response km kmEstimate leaveOneOut.km lm
  model.matrix new qnorm qt validObject
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'CrossValidationMuFicokmAll.Rd':
  \examples lines wider than 100 characters:
                     apply(matrix(1:DNest$n),1,function(x) CrossValidationMuFicokmAll(mymodel,x)$CVerrall)

Rd file 'MuFicokm.Rd':
  \usage lines wider than 90 characters:
                     noise.var = NULL, estim.method = "MLE", penalty = NULL, optim.method = "BFGS", 

Rd file 'predict.MuFicokm.Rd':
  \examples lines wider than 100 characters:
                                                     rev(predictionsSK_UK$mean-2*sqrt(predictionsSK_UK$sig2))),

These lines will be truncated in the PDF manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘MullerPlot.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpL6UxrA/R.INSTALL34183ca1072/multbxxc/man/mult_bxxc.Rd:12: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/multbxxc.Rcheck/00install.out’ for details.
multeq.diff: no visible global function definition for ‘cov’
multeq.diff: no visible global function definition for ‘pt’
multeq.diff: no visible global function definition for ‘qt’
multeq.rat: no visible global function definition for ‘cov’
multeq.rat: no visible global function definition for ‘pt’
multeq.rat: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cov pt qt
Consider adding
  importFrom("stats", "cov", "pt", "qt")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpdanRBT/R.INSTALL359b280859d2/multfisher/man/plot.multfisher.Rd:20: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/multfisher.Rcheck/00install.out’ for details.
plotOptionValues: no visible global function definition for ‘persp’
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
synthetic_multiband: no visible global function definition for ‘runif’
synthetic_multiband: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
GNU make is a SystemRequirements.
calculate_direction: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmMUk6a/R.INSTALL5fb9406149b/multicolor/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/multicolor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpqmHxFI/R.INSTALL3508aa9879b/multicon/man/multicon-package.Rd:51: file link ‘psych’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/multicon.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpRk7QNE/R.INSTALL74847f8c28c5/multimode/man/locmodes.Rd:26: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRk7QNE/R.INSTALL74847f8c28c5/multimode/man/locmodes.Rd:33: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRk7QNE/R.INSTALL74847f8c28c5/multimode/man/plot.gtmod.Rd:32: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRk7QNE/R.INSTALL74847f8c28c5/multimode/man/plot.gtmod.Rd:34: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRk7QNE/R.INSTALL74847f8c28c5/multimode/man/plot.gtmod.Rd:36: file link ‘image.default’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRk7QNE/R.INSTALL74847f8c28c5/multimode/man/plot.gtmod.Rd:36: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/multimode.Rcheck/00install.out’ for details.
multinb.fit: no visible global function definition for ‘nlminb’
multinbmod: no visible global function definition for ‘is.empty.model’
multinbmod: no visible global function definition for ‘model.matrix’
multinbmod: no visible binding for global variable ‘contrasts’
multinbmod: no visible global function definition for ‘model.response’
multinbmod: no visible global function definition for ‘model.offset’
Undefined global functions or variables:
  contrasts is.empty.model model.matrix model.offset model.response
  nlminb
Consider adding
  importFrom("stats", "contrasts", "is.empty.model", "model.matrix",
             "model.offset", "model.response", "nlminb")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpStnBub/R.INSTALL756c4a5d5ba9/multinets/man/is_multilevel.Rd:43: file link ‘is_bipartite’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/multinets.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rPorta’
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘rgenoud’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for
  ‘packageDescription’
genoudRob: no visible global function definition for ‘genoud’
get.XYdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘model.matrix’
get.xy: no visible global function definition for ‘terms’
get.xynames: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘model.response’
get.ydata: no visible global function definition for ‘model.frame’
mt.dev: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘dt’
mt.mle: no visible global function definition for ‘optim’
multinomRob: no visible global function definition for ‘var’
plot.multinomRob: no visible global function definition for ‘par’
plot.multinomRob: no visible global function definition for ‘title’
rdirich: no visible global function definition for ‘rgamma’
residual.generator: no visible global function definition for ‘median’
rmultinomial: no visible global function definition for ‘runif’
rmultinomial: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZBGM60/R.INSTALL46eb7e3d95b9/multipanelfigure/man/fill_panel.Rd:34: file link ‘gList’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZBGM60/R.INSTALL46eb7e3d95b9/multipanelfigure/man/fill_panel.Rd:35: file link ‘grob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZBGM60/R.INSTALL46eb7e3d95b9/multipanelfigure/man/fill_panel.Rd:53: file link ‘textGrob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZBGM60/R.INSTALL46eb7e3d95b9/multipanelfigure/man/fill_panel.Rd:87: file link ‘grob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZBGM60/R.INSTALL46eb7e3d95b9/multipanelfigure/man/fill_panel.Rd:87: file link ‘gList’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZBGM60/R.INSTALL46eb7e3d95b9/multipanelfigure/man/fill_panel.Rd:88: file link ‘gTree’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZBGM60/R.INSTALL46eb7e3d95b9/multipanelfigure/man/grapes-greater-than-grapes.Rd:7: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZBGM60/R.INSTALL46eb7e3d95b9/multipanelfigure/man/grapes-less-than-greater-than-grapes.Rd:7: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZBGM60/R.INSTALL46eb7e3d95b9/multipanelfigure/man/grob_dimensions.Rd:17: file link ‘grob’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/multipanelfigure.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLtnKvj/R.INSTALL75ca1d2328a4/multiPIM/man/Candidates.Rd:31: file link ‘profL1’ in package ‘penalized’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLtnKvj/R.INSTALL75ca1d2328a4/multiPIM/man/multiPIMboot.Rd:31: file link ‘parallel’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLtnKvj/R.INSTALL75ca1d2328a4/multiPIM/man/multiPIMboot.Rd:33: file link ‘RNGkind’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLtnKvj/R.INSTALL75ca1d2328a4/multiPIM/man/multiPIMboot.Rd:33: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/multiPIM.Rcheck/00install.out’ for details.
multiPIM : expand.factors: no visible global function definition for
  ‘formula’
multiPIM : expand.factors: no visible global function definition for
  ‘model.matrix’
multiPIM : <anonymous>: no visible global function definition for ‘glm’
multiPIM : <anonymous>: no visible binding for global variable
  ‘binomial’
multiPIM : <anonymous>: no visible global function definition for
  ‘qlogis’
multiPIM : <anonymous>: no visible global function definition for
  ‘as.formula’
multiPIM : <anonymous>: no visible global function definition for ‘lm’
multiPIM: no visible global function definition for ‘glm’
multiPIM: no visible global function definition for ‘qlogis’
multiPIM: no visible binding for global variable ‘binomial’
multiPIM: no visible global function definition for ‘plogis’
multiPIM: no visible global function definition for ‘sd’
multiPIM: no visible global function definition for ‘lm’
summary.multiPIM: no visible binding for global variable ‘sd’
summary.multiPIM: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial formula glm lm model.matrix plogis pnorm qlogis
  sd
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm", "lm",
             "model.matrix", "plogis", "pnorm", "qlogis", "sd")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Sensitivity_analysis.Rmd’
CCM_boot : <anonymous>: no visible global function definition for ‘sd’
SSR_check_signal: no visible global function definition for ‘cor’
SSR_check_signal: no visible global function definition for ‘cor.test’
SSR_check_signal: no visible global function definition for ‘lm’
SSR_pred_boot: no visible global function definition for ‘cor’
make_ccm_data: no visible global function definition for ‘rnorm’
make_ccm_data: no visible global function definition for ‘runif’
make_ccm_data: no visible global function definition for ‘rlnorm’
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
PrbMlt.default: no visible binding for global variable ‘na.omit’
PrbMlt.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova na.omit
Consider adding
  importFrom("stats", "anova", "na.omit")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'car', 'pdist', 'pls', 'gplots', 'mvtnorm', 'robustbase', 'gtools',
  'bitops', 'caTools', 'pcaPP', 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘car’ ‘gplots’ ‘pdist’ ‘pls’ ‘rrcov’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘bitops’ ‘caTools’ ‘car’ ‘gplots’ ‘gtools’ ‘mvtnorm’ ‘pcaPP’ ‘pdist’
  ‘pls’ ‘robustbase’ ‘rrcov’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'Plot.pca.score.Rd':
  \examples lines wider than 100 characters:
             ylab = ylab, xlim = lim, ylim = lim, pch = 19, sub = paste("Cumulative Proportion of Variance Explained = ", 

Rd file 'oplsda.Rd':
  \examples lines wider than 100 characters:
             ylab = ylab, xlim = lim, ylim = lim, pch = 19, sub = paste("Cumulative Proportion of Variance Explained = ", 

Rd file 'univariate.Rd':
  \usage lines wider than 90 characters:
     univariate(file, imputation = FALSE, imput, normalize = TRUE, multi.test = TRUE, plot.volcano = FALSE, save.boxplot=TRUE)

Rd file 'volcano.Rd':
  \examples lines wider than 100 characters:
                         sep = ""), sub = "(Variables in Blue are significant (Pvalue<0.05) and showed Fold Changes >1.2 or <0.8)")
                           j, sep = ""), sub = "(Variables in Blue are significant (Pvalue<0.05) and showed Fold Changes >1.2 or <0.8)")

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpM6bqNt/R.INSTALL54af9da17c8/MuMIn/man/AICc.Rd:57: file link ‘aicc’ in package ‘glmulti’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MuMIn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpp9RuH9/R.INSTALL3a1d61690d96/munsellinterpol/man/MunsellNameFromHVC.Rd:31: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpp9RuH9/R.INSTALL3a1d61690d96/munsellinterpol/man/MunsellNameFromHVC.Rd:38: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpp9RuH9/R.INSTALL3a1d61690d96/munsellinterpol/man/MunsellNameFromHVC.Rd:53: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpp9RuH9/R.INSTALL3a1d61690d96/munsellinterpol/man/MunsellNameFromHVC.Rd:69: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/munsellinterpol.Rcheck/00install.out’ for details.
plotFID: no visible global function definition for ‘points’
Undefined global functions or variables:
  points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
Found the following files/directories:
  ‘audio.wav’
prentice.test: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/RtmpntAxW6/R.INSTALL7bd31f1c7cf2/mvabund/man/manyany.Rd:107: file link ‘residuals.manyany’ in package ‘mvabund’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpntAxW6/R.INSTALL7bd31f1c7cf2/mvabund/man/manyglm.Rd:222: file link ‘plot.manyglm’ in package ‘mvabund’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpntAxW6/R.INSTALL7bd31f1c7cf2/mvabund/man/residuals.manyglm.Rd:37: file link ‘plot.manyglm’ in package ‘mvabund’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mvabund.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
mvb.simu: no visible global function definition for ‘runif’
plot.lps: no visible global function definition for ‘matplot’
unifit: no visible global function definition for ‘model.frame’
unifit: no visible global function definition for ‘model.matrix’
unifit: no visible global function definition for ‘model.response’
unilps: no visible global function definition for ‘model.frame’
unilps: no visible global function definition for ‘model.matrix’
unilps: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  matplot model.frame model.matrix model.response runif
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "runif")
to your NAMESPACE file.
Checking should be performed on sources prepared by ‘R CMD build’.
conceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpfDpUa3/R.INSTALL610f21f4dd6b/mvGPS/man/gen_D.Rd:99: file link ‘rmatnorm’ in package ‘matrixNormal’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mvGPS.Rcheck/00install.out’ for details.
mvnpermute: no visible global function definition for ‘lm’
mvnpermute: no visible global function definition for ‘coef’
mvnpermute: no visible global function definition for ‘resid’
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
mvorpb: no visible global function definition for ‘pnorm’
mvorpb: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
rtn: no visible global function definition for ‘runif’
rtn: no visible global function definition for ‘qnorm’
rtn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘RColorBrewer’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mxkssd: no visible global function definition for ‘txtProgressBar’
mxkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
abcpred_nmer: no visible global function definition for ‘write.table’
algpred: no visible global function definition for ‘read.table’
algpred: no visible global function definition for ‘write.table’
allermatch: no visible global function definition for ‘read.table’
allermatch: no visible global function definition for ‘write.table’
bcepred_nmer: no visible global function definition for ‘write.table’
bimas_nmer: no visible global function definition for ‘write.table’
filter.firstlayer: no visible global function definition for
  ‘read.table’
filter.firstlayer: no visible global function definition for
  ‘write.table’
iedb_arb_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_arb_mhcii_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhcii_nmer: no visible global function definition for
  ‘write.table’
netmhcNN_nmer: no visible global function definition for ‘write.table’
netmhcWT_nmer: no visible global function definition for ‘write.table’
propred_nmer: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIuAb4d/R.INSTALL158b1427a933/mycor/man/mycor.Rd:35: file link ‘parallelplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIuAb4d/R.INSTALL158b1427a933/mycor/man/plot.mycor.Rd:13: file link ‘parallelplot’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mycor.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
update_episode: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Rd file 'myepisodes_feed_url.Rd':
  \examples lines wider than 100 characters:
     ## Not run: myepisodes_feed_url("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

Rd file 'shows_from_myepisodes.Rd':
  \examples lines wider than 100 characters:
     ## Not run: shows_from_myepisodes("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpz2rWYG/R.INSTALL47ad29b2b6ec/myTAI/man/DiffGenes.Rd:73: file link ‘exactTestDoubleTail’ in package ‘edgeR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpz2rWYG/R.INSTALL47ad29b2b6ec/myTAI/man/DiffGenes.Rd:74: file link ‘exactTestBySmallP’ in package ‘edgeR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/myTAI.Rcheck/00install.out’ for details.
abs_dif: no visible global function definition for ‘as.formula’
env_dif: no visible global function definition for ‘lm’
env_dif: no visible global function definition for ‘as.formula’
env_dif_logistic: no visible global function definition for
  ‘as.formula’
fam_env: no visible global function definition for ‘as.formula’
log_dif: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula lm
Consider adding
  importFrom("stats", "as.formula", "lm")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpvjPN7r/R.INSTALL50e998193e6/naaccr/man/read_naaccr.Rd:18: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpvjPN7r/R.INSTALL50e998193e6/naaccr/man/read_naaccr.Rd:40: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/naaccr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8OTIsy/R.INSTALL6239573d2a31/NACHO/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8OTIsy/R.INSTALL6239573d2a31/NACHO/man/tidyeval.Rd:17: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8OTIsy/R.INSTALL6239573d2a31/NACHO/man/tidyeval.Rd:18: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8OTIsy/R.INSTALL6239573d2a31/NACHO/man/tidyeval.Rd:20: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8OTIsy/R.INSTALL6239573d2a31/NACHO/man/tidyeval.Rd:21: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8OTIsy/R.INSTALL6239573d2a31/NACHO/man/tidyeval.Rd:25: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/NACHO.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘asreml’
Found the following significant warnings:
  Rd warning: /tmp/RtmpD899oW/R.INSTALL14995fc5fb12/nadiv/man/numPed.Rd:25: file link ‘[’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpD899oW/R.INSTALL14995fc5fb12/nadiv/man/numPed.Rd:63: file link ‘[’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpD899oW/R.INSTALL14995fc5fb12/nadiv/man/proLik.Rd:71: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpD899oW/R.INSTALL14995fc5fb12/nadiv/man/proLik.Rd:73: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nadiv.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘re2r’
Found the following significant warnings:
  Rd warning: /tmp/RtmpKlECpL/R.INSTALL4e8d5d86a24e/namer/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/namer.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘NanoStringNorm_Example_Plots_All.pdf’
  ‘NanoStringNorm_Interactive_Plot’
Found the following significant warnings:
  Rd warning: /tmp/RtmpzWClwq/R.INSTALL46876f8426de/nat.templatebrains/man/nat.templatebrains-package.Rd:47: file link ‘Rprofile’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzWClwq/R.INSTALL46876f8426de/nat.templatebrains/man/nat.templatebrains-package.Rd:100: file link ‘nat’ in package ‘nat’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nat.templatebrains.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIvHYFK/R.INSTALL551d7f9172cf/nawtilus/man/plot.nawt.Rd:58: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nawtilus.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYaLFUd/R.INSTALL5312528e30dc/NBLDA/man/generateCountData.Rd:17: file link ‘rnbinom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/NBLDA.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘sSeq’
NB.estimator: no visible global function definition for ‘optimize’
NB.estimator: no visible global function definition for ‘uniroot’
NB.example.dataset: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  optimize uniroot write.table
Consider adding
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘sample_data.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpoKM4rq/R.INSTALL650f28dd1926/ncappc/man/read_nm_table.Rd:26: file link ‘dplyr’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpoKM4rq/R.INSTALL650f28dd1926/ncappc/man/read_nm_table.Rd:40: file link ‘dplyr’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ncappc.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
ncbit : FUN: no visible global function definition for ‘read.table’
ncbit : FUN: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSydWIT/R.INSTALL3d1960f49c77/ncdf4/man/ncdf4-package.Rd:57: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSydWIT/R.INSTALL3d1960f49c77/ncdf4/man/ncdf4-package.Rd:74: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSydWIT/R.INSTALL3d1960f49c77/ncdf4/man/ncvar_def.Rd:67: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSydWIT/R.INSTALL3d1960f49c77/ncdf4/man/ncvar_def.Rd:108: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSydWIT/R.INSTALL3d1960f49c77/ncdf4/man/ncvar_def.Rd:114: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSydWIT/R.INSTALL3d1960f49c77/ncdf4/man/ncvar_get.Rd:80: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ncdf4.Rcheck/00install.out’ for details.
d0: no visible global function definition for ‘qnorm’
dncgamma: no visible global function definition for ‘dpois’
indncgamma: no visible global function definition for ‘pgamma’
indncgamma: no visible global function definition for ‘dpois’
inxncgamma: no visible global function definition for ‘qnorm’
inxncgamma: no visible global function definition for ‘pgamma’
inxncgamma: no visible global function definition for ‘dpois’
pncgamma: no visible global function definition for ‘pgamma’
pncgamma: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘re2r’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5TrVzP/R.INSTALL55fe5b95bb07/ndtv/man/render.d3movie.Rd:152: file link ‘htmlwidgets’ in package ‘htmlwidgets’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ndtv.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘testNet.dot’ ‘toy_epi_sim.net’
Found the following significant warnings:
  Rd warning: /tmp/RtmpO6oOyO/R.INSTALL728259ec0fbe/neatStats/man/plot_neat.Rd:136: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpO6oOyO/R.INSTALL728259ec0fbe/neatStats/man/ro.Rd:21: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/neatStats.Rcheck/00install.out’ for details.
Found the following assignments to the global environment:
File ‘neatStats/R/rbind_loop.R’:
  assign(merged_str, to_merge, envir = .GlobalEnv)
  assign(merged_str, plyr::rbind.fill(merged, to_merge), envir = .GlobalEnv)
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
population: no visible global function definition for ‘weighted.mean’
population: no visible global function definition for ‘rpois’
population: no visible global function definition for ‘lm’
population: no visible global function definition for ‘coefficients’
population: no visible global function definition for ‘sd’
population: no visible global function definition for ‘par’
population: no visible global function definition for ‘lines’
Undefined global functions or variables:
  coefficients lines lm par rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5I5EQc/R.INSTALL2b9a3b34e463/neldermead/man/costf.transposex.Rd:27: file link ‘neldermead.costf’ in package ‘neldermead’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5I5EQc/R.INSTALL2b9a3b34e463/neldermead/man/neldermead.restart.Rd:25: file link ‘neldermead.updatesimp’ in package ‘neldermead’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/neldermead.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1ZAdU0/R.INSTALL660528be9601/neo4r/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/neo4r.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
netVal: no visible global function definition for ‘cutree’
netVal: no visible global function definition for ‘hclust’
netVal: no visible global function definition for ‘as.dist’
Undefined global functions or variables:
  as.dist cutree hclust
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘buildcmds’
EnvInd: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fastshp’
Found the following significant warnings:
  Rd warning: /tmp/RtmptUbFCw/R.INSTALL4b6374287e5b/NetLogoR/man/quickPlot-methods.Rd:66: file link ‘gpar’ in package ‘quickPlot’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/NetLogoR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpKdu8c1/R.INSTALL317b6a56a717/networkDynamic/man/activate.Rd:105: file link ‘get.edge.attribute’ in package ‘network’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKdu8c1/R.INSTALL317b6a56a717/networkDynamic/man/activity.attribute.Rd:54: file link ‘get.edge.attribute’ in package ‘network’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKdu8c1/R.INSTALL317b6a56a717/networkDynamic/man/add.methods.networkDynamic.Rd:60: file link ‘add.edge’ in package ‘network’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKdu8c1/R.INSTALL317b6a56a717/networkDynamic/man/network.extensions.Rd:83: file link ‘get.edgeIDs’ in package ‘network’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/networkDynamic.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Found the following significant warnings:
  Rd warning: /tmp/RtmpUyDdWH/R.INSTALL5cb41f77b337/NetworkRiskMeasures/man/communicability_matrix.Rd:10: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUyDdWH/R.INSTALL5cb41f77b337/NetworkRiskMeasures/man/contagion.Rd:20: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUyDdWH/R.INSTALL5cb41f77b337/NetworkRiskMeasures/man/criticality.Rd:15: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUyDdWH/R.INSTALL5cb41f77b337/NetworkRiskMeasures/man/impact_susceptibility.Rd:40: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUyDdWH/R.INSTALL5cb41f77b337/NetworkRiskMeasures/man/risk_matrix.Rd:32: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/NetworkRiskMeasures.Rcheck/00install.out’ for details.
simulate.sisnetwork: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
mlptrain : rect: no visible global function definition for ‘polygon’
mlptrain : drawnet: no visible global function definition for ‘title’
mlptrain : drawnet: no visible global function definition for ‘polygon’
mlptrain : drawnet: no visible global function definition for ‘text’
mlptrain : drawnet: no visible global function definition for ‘lines’
mlptrain: no visible global function definition for ‘runif’
mlptrain: no visible global function definition for ‘locator’
mlptrain: no visible global function definition for ‘polygon’
mlptrain: no visible global function definition for ‘text’
rbftrain : rect: no visible global function definition for ‘polygon’
rbftrain : drawnet: no visible global function definition for ‘title’
rbftrain : drawnet: no visible global function definition for ‘polygon’
rbftrain : drawnet: no visible global function definition for ‘text’
rbftrain : drawnet: no visible global function definition for ‘lines’
rbftrain : graph: no visible global function definition for ‘title’
rbftrain : graph: no visible global function definition for ‘polygon’
rbftrain : graph: no visible global function definition for ‘text’
rbftrain : graph: no visible global function definition for ‘lines’
rbftrain : graph: no visible global function definition for ‘points’
rbftrain: no visible global function definition for ‘runif’
rbftrain: no visible global function definition for ‘locator’
rbftrain: no visible global function definition for ‘polygon’
rbftrain: no visible global function definition for ‘text’
rbftrain: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans lines locator points polygon runif text title
Consider adding
  importFrom("graphics", "lines", "locator", "points", "polygon", "text",
             "title")
  importFrom("stats", "kmeans", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxBxwJF/R.INSTALL4d0c4e16a8cf/neurocInstall/man/neuro_install.Rd:42: file link ‘install_github’ in package ‘devtools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxBxwJF/R.INSTALL4d0c4e16a8cf/neurocInstall/man/neuro_install.Rd:47: file link ‘install_github’ in package ‘devtools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/neurocInstall.Rcheck/00install.out’ for details.
balloon: no visible global function definition for ‘convolve’
physnoise: no visible global function definition for ‘sd’
physnoise: no visible global function definition for ‘rnorm’
rrice: no visible global function definition for ‘rnorm’
simTSrestingstate: no visible global function definition for ‘runif’
simTSrestingstate: no visible global function definition for ‘fft’
spatialnoise: no visible global function definition for ‘rnorm’
spatialnoise: no visible global function definition for ‘qgamma’
spatialnoise: no visible global function definition for ‘pnorm’
specifydesign: no visible global function definition for ‘convolve’
systemnoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘sd’
temporalnoise: no visible global function definition for ‘arima.sim’
Undefined global functions or variables:
  arima.sim convolve fft pnorm qgamma rnorm runif sd
Consider adding
  importFrom("stats", "arima.sim", "convolve", "fft", "pnorm", "qgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
nfca : nFCAmain: no visible global function definition for ‘hist’
nfca : nFCAmain: no visible global function definition for
  ‘flush.console’
nfca : nFCAmain: no visible global function definition for ‘qnorm’
nfca : nFCAmain: no visible global function definition for ‘read.csv’
nfca : nFCAmain: no visible global function definition for ‘cor’
nfca : nFCAmain: no visible global function definition for ‘as.dist’
nfca : nFCAmain: no visible global function definition for ‘cophenetic’
nfca : nFCAmain: no visible global function definition for ‘hclust’
nfca : thresholdTEST: no visible global function definition for
  ‘read.csv’
nfca : gScript: no visible global function definition for ‘read.csv’
nfca : gScript0: no visible global function definition for ‘read.csv’
nfca : gMatrix: no visible global function definition for ‘read.csv’
nfca: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘Hgraph.dot’ ‘Igraph.dot’
Package suggested but not available for checking: ‘NFPdata’
Found the following significant warnings:
  Rd warning: /tmp/RtmpfIbB3D/R.INSTALL6c9c8d6b417/NFP/man/calc_sim_score.Rd:11: file link ‘graphNEL’ in package ‘graph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/NFP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUW5FLW/R.INSTALL66d76d0e812f/ngramrr/man/dtmwrappers.Rd:41: file link ‘DocumentTermMatrix’ in package ‘tm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpUW5FLW/R.INSTALL66d76d0e812f/ngramrr/man/dtmwrappers.Rd:41: file link ‘TermDocumentMatrix’ in package ‘tm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ngramrr.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Package vignette with placeholder title ‘Vignette Title’:
  ‘nitrcbot.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpT8t4zd/R.INSTALL4c187284f670/nixmass/man/plot.nixmass.Rd:10: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nixmass.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpugq5xR/R.INSTALL6ecb5ca56b3d/nlcv/man/nldaI.Rd:21: file link ‘ldaI’ in package ‘MLInterfaces’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpugq5xR/R.INSTALL6ecb5ca56b3d/nlcv/man/pamrI.Rd:31: file link ‘MLearn’ in package ‘MLInterfaces’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nlcv.Rcheck/00install.out’ for details.
nlmeODE: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Pwr.lme: no visible global function definition for ‘anova’
Pwr.lme: no visible global function definition for ‘qf’
Pwr.lme: no visible global function definition for ‘pf’
logLik1.lme: no visible global function definition for ‘coef’
logLik1.lme: no visible global function definition for ‘model.matrix’
logLik1.lme: no visible global function definition for ‘predict’
logLik1.lme: no visible global function definition for ‘formula’
runScript: no visible binding for global variable ‘example’
sigmaTolme: no visible global function definition for ‘vcov’
simulateY.lme: no visible global function definition for ‘runif’
simulateY.lme: no visible global function definition for ‘fitted’
simulateY.lme: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpizjL2G/R.INSTALL6efdaa68e79/nlmixr/man/dynmodelControl.Rd:440: file link ‘rxControl’ in package ‘RxODE’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nlmixr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpkEXMaB/R.INSTALL63001be4504a/nlpred/man/xgboost_wrapper.Rd:25: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkEXMaB/R.INSTALL63001be4504a/nlpred/man/xgboost_wrapper.Rd:27: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkEXMaB/R.INSTALL63001be4504a/nlpred/man/xgboost_wrapper.Rd:29: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkEXMaB/R.INSTALL63001be4504a/nlpred/man/xgboost_wrapper.Rd:31: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkEXMaB/R.INSTALL63001be4504a/nlpred/man/xgboost_wrapper.Rd:33: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkEXMaB/R.INSTALL63001be4504a/nlpred/man/xgboost_wrapper.Rd:35: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkEXMaB/R.INSTALL63001be4504a/nlpred/man/xgboost_wrapper.Rd:37: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkEXMaB/R.INSTALL63001be4504a/nlpred/man/xgboost_wrapper.Rd:39: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkEXMaB/R.INSTALL63001be4504a/nlpred/man/xgboost_wrapper.Rd:59: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nlpred.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpFzAzG0/R.INSTALL8ed5c3a8077/nlreg/man/nlreg.Rd:133: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFzAzG0/R.INSTALL8ed5c3a8077/nlreg/man/nlreg.contours.object.Rd:18: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFzAzG0/R.INSTALL8ed5c3a8077/nlreg/man/nlreg.profile.objects.Rd:20: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFzAzG0/R.INSTALL8ed5c3a8077/nlreg/man/plot.nlreg.contours.Rd:7: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFzAzG0/R.INSTALL8ed5c3a8077/nlreg/man/plot.nlreg.diag.Rd:12: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFzAzG0/R.INSTALL8ed5c3a8077/nlreg/man/plot.nlreg.profiles.Rd:104: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFzAzG0/R.INSTALL8ed5c3a8077/nlreg/man/profile.nlreg.Rd:104: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nlreg.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘proto’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘stats:::nlsModel’ ‘stats:::nlsModel.plinear’
  See the note in ?`:::` about the use of this operator.
nls2: no visible global function definition for ‘nls.control’
nls2: no visible global function definition for ‘as.formula’
nls2: no visible global function definition for ‘coef’
nls2: no visible global function definition for ‘runif’
nls2 : <anonymous>: no visible global function definition for
  ‘deviance’
Undefined global functions or variables:
  as.formula coef deviance nls.control runif
Consider adding
  importFrom("stats", "as.formula", "coef", "deviance", "nls.control",
             "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpi2tYtn/R.INSTALL15803690ee54/nlstools/man/confint2.Rd:26: file link ‘confint.nls’ in package ‘MASS’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nlstools.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
nnmf_als: no visible global function definition for ‘rnorm’
nnmf_mm: no visible global function definition for ‘rnorm’
nnmf_prob: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/RNG.Rd:32: file link ‘getRNG’ in package ‘rngtools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/aheatmap.Rd:39: file link ‘display.brewer.all’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/fitted.Rd:62: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/grid.Rd:29: file link ‘current.vpPath’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/heatmaps.Rd:108: file link ‘display.brewer.all’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/nmfApply.Rd:35: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/options.Rd:50: file link ‘getOption’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/registry-algorithm.Rd:37: file link ‘pkgreg_fetch’ in package ‘pkgmaker’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/registry-algorithm.Rd:38: file link ‘pkgreg_remove’ in package ‘pkgmaker’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkT7qCN/R.INSTALL3bcd2fa5ba60/NMF/man/setNMFSeed.Rd:32: file link ‘pkgreg_remove’ in package ‘pkgmaker’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/NMF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpFiYhnL/R.INSTALL65e711badecd/Nmisc/man/is.POSIXct.Rd:16: file link ‘is.POSIXt’ in package ‘lubridate’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFiYhnL/R.INSTALL65e711badecd/Nmisc/man/keep_at.Rd:17: file link ‘select_helpers’ in package ‘tidyselect’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Nmisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpKIiLsR/R.INSTALLbf8719dd112/nmixgof/man/chat.Rd:10: file link ‘unmarkedFit’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKIiLsR/R.INSTALLbf8719dd112/nmixgof/man/nmixgof.Rd:10: file link ‘unmarked’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKIiLsR/R.INSTALLbf8719dd112/nmixgof/man/residcov.Rd:10: file link ‘unmarkedFit’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKIiLsR/R.INSTALLbf8719dd112/nmixgof/man/residqq.Rd:11: file link ‘unmarkedFit’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKIiLsR/R.INSTALLbf8719dd112/nmixgof/man/rqresiduals.Rd:10: file link ‘unmarkedFit’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKIiLsR/R.INSTALLbf8719dd112/nmixgof/man/shoveler.Rd:18: file link ‘unmarked’ in package ‘unmarked’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nmixgof.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘hurricaneexposuredata’
makeRules: no visible global function definition for ‘sd’
makeRules: no visible global function definition for ‘rnorm’
nodeHarvest: no visible global function definition for ‘capture.output’
nodeHarvest: no visible global function definition for ‘lm’
nodeHarvest: no visible global function definition for ‘coef’
plot.nodeHarvest: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  capture.output coef lm rgb rnorm sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "coef", "lm", "rnorm", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpuDbcDi/R.INSTALL79f9306037ea/nofrills/man/as_fn.Rd:13: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuDbcDi/R.INSTALL79f9306037ea/nofrills/man/curry.Rd:42: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuDbcDi/R.INSTALL79f9306037ea/nofrills/man/curry.Rd:19: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuDbcDi/R.INSTALL79f9306037ea/nofrills/man/fn.Rd:30: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuDbcDi/R.INSTALL79f9306037ea/nofrills/man/fn.Rd:11: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuDbcDi/R.INSTALL79f9306037ea/nofrills/man/fn.Rd:45: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpuDbcDi/R.INSTALL79f9306037ea/nofrills/man/fn.Rd:58: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nofrills.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘rms’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘pwt’ ‘rms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
additive: no visible global function definition for ‘lp’
ar.dual.dea: no visible global function definition for ‘lp’
cost.dea: no visible global function definition for ‘lp’
ddf: no visible global function definition for ‘lp’
dea: no visible global function definition for ‘lp’
direc.dea: no visible global function definition for ‘lp’
dual.dea: no visible global function definition for ‘lp’
effdea.b.f: no visible global function definition for ‘convhulln’
effdea.b.f: no visible global function definition for ‘lp’
faremalm2: no visible binding for global variable ‘Lag’
faremalm2: no visible global function definition for ‘na.omit’
int.dea: no visible global function definition for ‘lp’
lp2: no visible global function definition for ‘lp’
revenue.dea: no visible global function definition for ‘lp’
sbm.tone: no visible global function definition for ‘lp’
sbm.vrs: no visible global function definition for ‘lp’
Undefined global functions or variables:
  Lag convhulln lp na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘histogram’ ‘optimx’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dnormgam: no visible global function definition for ‘qgamma’
dnormgam: no visible global function definition for ‘fft’
dnormgam: no visible global function definition for ‘dgamma’
dnormgam: no visible global function definition for ‘approx’
normgam.fit : mkdfftNormalGammaOptim : <anonymous>: no visible global
  function definition for ‘dnorm’
normgam.fit : estimation_param_normexp_RMA : max.density: no visible
  global function definition for ‘density’
normgam.fit: no visible global function definition for ‘sd’
normgam.fit: no visible global function definition for ‘median’
normgam.fit: no visible global function definition for ‘IQR’
normgam.fit: no visible global function definition for ‘optimx’
normgam.fit: no visible global function definition for ‘coef’
normgam.signal: no visible global function definition for ‘approx’
normgam.signal: no visible global function definition for ‘hist’
Undefined global functions or variables:
  IQR approx coef density dgamma dnorm fft hist median optimx qgamma sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "IQR", "approx", "coef", "density", "dgamma",
             "dnorm", "fft", "median", "qgamma", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable ‘var’
mi.inference: no visible global function definition for ‘qt’
mi.inference: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
ajb.norm.test: no visible global function definition for ‘rnorm’
frosini.norm.test: no visible global function definition for ‘var’
frosini.norm.test: no visible global function definition for ‘pnorm’
frosini.norm.test: no visible global function definition for ‘rnorm’
geary.norm.test: no visible global function definition for ‘rnorm’
hegazy1.norm.test: no visible global function definition for ‘var’
hegazy1.norm.test: no visible global function definition for ‘qnorm’
hegazy1.norm.test: no visible global function definition for ‘rnorm’
hegazy2.norm.test: no visible global function definition for ‘var’
hegazy2.norm.test: no visible global function definition for ‘qnorm’
hegazy2.norm.test: no visible global function definition for ‘rnorm’
jb.norm.test: no visible global function definition for ‘rnorm’
kurtosis.norm.test: no visible global function definition for ‘rnorm’
skewness.norm.test: no visible global function definition for ‘rnorm’
spiegelhalter.norm.test: no visible global function definition for
  ‘rnorm’
wb.norm.test: no visible global function definition for ‘qnorm’
wb.norm.test: no visible global function definition for ‘var’
wb.norm.test: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
normality.test1: no visible global function definition for ‘cov.wt’
normality.test1: no visible global function definition for ‘cor’
normality.test1: no visible global function definition for ‘pnorm’
normality.test1: no visible global function definition for ‘pchisq’
normality.test2: no visible global function definition for ‘cov.wt’
normality.test2: no visible global function definition for ‘cor’
normality.test2: no visible global function definition for ‘acf’
normality.test2: no visible global function definition for ‘pnorm’
normality.test2: no visible global function definition for ‘pchisq’
whitenoise.test: no visible global function definition for ‘acf’
whitenoise.test: no visible global function definition for ‘spec.pgram’
whitenoise.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  acf cor cov.wt pchisq pnorm spec.pgram
Consider adding
  importFrom("stats", "acf", "cor", "cov.wt", "pchisq", "pnorm",
             "spec.pgram")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmptt1E3D/R.INSTALL6b521d3f2d3f/nos/man/NOSM_POT_dir.Rd:14: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmptt1E3D/R.INSTALL6b521d3f2d3f/nos/man/NOSM_POT_undir.Rd:14: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmptt1E3D/R.INSTALL6b521d3f2d3f/nos/man/NOSM_bip.Rd:16: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmptt1E3D/R.INSTALL6b521d3f2d3f/nos/man/NOSM_dir.Rd:17: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmptt1E3D/R.INSTALL6b521d3f2d3f/nos/man/NOSM_undir.Rd:14: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmptt1E3D/R.INSTALL6b521d3f2d3f/nos/man/freqMat_2_edge.Rd:48: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmptt1E3D/R.INSTALL6b521d3f2d3f/nos/man/nos-package.Rd:49: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nos.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpyLk8xC/R.INSTALL4c67ca2a5d5/NostalgiR/man/nos.density.Rd:51: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpyLk8xC/R.INSTALL4c67ca2a5d5/NostalgiR/man/nos.density.Rd:51: file link ‘txtdensity’ in package ‘txtplot’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpyLk8xC/R.INSTALL4c67ca2a5d5/NostalgiR/man/nos.ecdf.Rd:42: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpyLk8xC/R.INSTALL4c67ca2a5d5/NostalgiR/man/nos.qqnorm.Rd:44: file link ‘qqline’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpyLk8xC/R.INSTALL4c67ca2a5d5/NostalgiR/man/nos.qqplot.Rd:53: file link ‘qqplot’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpyLk8xC/R.INSTALL4c67ca2a5d5/NostalgiR/man/nos.qqplot.Rd:53: file link ‘qqline’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpyLk8xC/R.INSTALL4c67ca2a5d5/NostalgiR/man/nos.xyplot.Rd:56: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/NostalgiR.Rcheck/00install.out’ for details.
Rd file 'notifyR-package.Rd':
  \examples lines wider than 100 characters:
     send_push(userkey,message="finished.",title="World Simulation",url="http://www.myRresults.com/",url_title="View Results online.",priori ... [TRUNCATED]

Rd file 'send_push.Rd':
  \usage lines wider than 90 characters:
     send_push(user, message, title = "", device = "", url = "", url_title = "", priority = FALSE, timestamp = Sys.time())
  \examples lines wider than 100 characters:
     send_push(userkey,message="finished.",title="World Simulation",url="http://www.myRresults.com/",url_title="View Results online.",priori ... [TRUNCATED]

These lines will be truncated in the PDF manual.
.newReportId : <anonymous>: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘smcure’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NPHMC: no visible global function definition for ‘integrate’
NPHMC: no visible global function definition for ‘qnorm’
NPHMC: no visible global function definition for ‘pnorm’
NPHMC: no visible global function definition for ‘lines’
NPHMC: no visible global function definition for ‘smcure’
NPHMC: no visible global function definition for ‘coxph’
Undefined global functions or variables:
  coxph integrate lines pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘tmp.R’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3hCcau/R.INSTALL521a4a8ed1eb/np/man/np.quantile.Rd:154: file link ‘qlogspline’ in package ‘logspline’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3hCcau/R.INSTALL521a4a8ed1eb/np/man/np.quantile.Rd:155: file link ‘qkde’ in package ‘ks’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/np.Rcheck/00install.out’ for details.
nps.test: no visible global function definition for ‘qnorm’
nps.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  mclapply
Found the following significant warnings:
  Rd warning: /tmp/RtmpTzGrpr/R.INSTALL14ad499ea7bb/nseval/man/compat.Rd:15: file link ‘as.lazy_dots’ in package ‘lazyeval’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nseval.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘mco’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boundedPolyMutation: no visible global function definition for ‘runif’
boundedSBXover: no visible global function definition for ‘runif’
nsga2R : <anonymous>: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3ezD0O/R.INSTALL74fd1182e796/nsga3/man/nsga3fs.Rd:25: file link ‘low’ in package ‘rPref’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nsga3.Rcheck/00install.out’ for details.
.mcmc.bar: no visible global function definition for ‘rnorm’
.mcmc.bar: no visible global function definition for ‘runif’
.mcmc.comb: no visible global function definition for ‘rnorm’
.mcmc.comb: no visible global function definition for ‘runif’
.mcmc.rd: no visible global function definition for ‘rnorm’
.mcmc.rd: no visible global function definition for ‘runif’
.mcmc.trans: no visible global function definition for ‘rnorm’
.mcmc.trans: no visible global function definition for ‘runif’
.simulate.bar: no visible global function definition for ‘rlnorm’
.simulate.bar: no visible global function definition for ‘rbeta’
.simulate.bar: no visible global function definition for ‘rbinom’
.simulate.comb: no visible global function definition for ‘rlnorm’
.simulate.comb: no visible global function definition for ‘rbeta’
.simulate.comb: no visible global function definition for ‘rbinom’
.simulate.rd: no visible global function definition for ‘rlnorm’
.simulate.rd: no visible global function definition for ‘rbinom’
.simulate.trans: no visible global function definition for ‘rlnorm’
.simulate.trans: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbeta rbinom rlnorm rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rlnorm", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpQgwNyI/R.INSTALL18fa550ceaf7/nvctr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/nvctr.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of ‘env’ to ‘envir’
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of ‘env’ to ‘envir’
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
Rd file 'nwsVariable-methods.Rd':
  \usage lines wider than 90 characters:
     nwsVariable(.Object, xName, mode=c('fifo','lifo','multi','single'),env=parent.frame(),force=FALSE,quietly=FALSE)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpL6zVha/R.INSTALL1c427f1ae134/OAIHarvester/man/serialize.Rd:24: file link ‘saveRDS’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OAIHarvester.Rcheck/00install.out’ for details.
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpNeTKfw/R.INSTALL52d43306f63b/objectProperties/man/PropertySet-class.Rd:9: file link ‘setRefClass’ in package ‘methods’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpNeTKfw/R.INSTALL52d43306f63b/objectProperties/man/PropertySet-class.Rd:20: file link ‘setRefClass’ in package ‘methods’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/objectProperties.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘objectSignals’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Color: no visible global function definition for ‘new’
NegativeInteger: no visible global function definition for ‘new’
NonnegativeInteger: no visible global function definition for ‘new’
NonpositiveInteger: no visible global function definition for ‘new’
PositiveInteger: no visible global function definition for ‘new’
setMultipleEnum: no visible global function definition for ‘setClass’
setMultipleEnum: no visible global function definition for ‘prototype’
setNumericWithRange: no visible global function definition for
  ‘setClass’
setNumericWithRange: no visible global function definition for
  ‘prototype’
setPropertySet: no visible binding for global variable ‘extends’
setPropertySet: no visible global function definition for ‘setRefClass’
setSingleEnum: no visible global function definition for ‘setClass’
setSingleEnum: no visible global function definition for ‘prototype’
as.list,PropertySet: no visible global function definition for ‘as’
initialize,SingleEnum: no visible global function definition for
  ‘callNextMethod’
initialize,SingleEnum: no visible global function definition for ‘head’
Undefined global functions or variables:
  as callNextMethod extends head new prototype setClass setRefClass
Consider adding
  importFrom("methods", "as", "callNextMethod", "extends", "new",
             "prototype", "setClass", "setRefClass")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'Enum-class.Rd':
  \examples lines wider than 100 characters:
     PointSizeSingleEnum.gen <- setGlyphEnum("PointSize", levels = c("1", "2", "5", "10"), contains = "GlyphEnum")

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpMOwabF/R.INSTALL402f34599506/objectSignals/man/fieldWithPrototype.Rd:7: file link ‘prototype’ in package ‘methods’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/objectSignals.Rcheck/00install.out’ for details.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Signal.gen: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  ‘ROCR’ ‘e1071’ ‘mda’ ‘pls’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
log_wrapper: no visible global function definition for ‘glm’
log_wrapper: no visible global function definition for ‘binomial’
log_wrapper: no visible global function definition for ‘coef’
log_wrapper: no visible global function definition for ‘anova’
obliqueRF.default: no visible binding for global variable ‘predict’
obliqueRF.default: no visible global function definition for
  ‘prediction’
obliqueRF.default: no visible global function definition for
  ‘performance’
pls_wrapper: no visible global function definition for ‘kernelpls.fit’
pls_wrapper: no visible global function definition for ‘coef’
ridge_slow_wrapper: no visible global function definition for
  ‘gen.ridge’
ridge_slow_wrapper: no visible global function definition for ‘predict’
ridge_svd_wrapper: no visible global function definition for
  ‘gen.ridge’
rnd_wrapper: no visible global function definition for ‘rnorm’
svm_wrapper: no visible global function definition for ‘svm’
svm_wrapper: no visible global function definition for ‘predict’
Undefined global functions or variables:
  anova binomial coef gen.ridge glm kernelpls.fit performance predict
  prediction rnorm svm
Consider adding
  importFrom("stats", "anova", "binomial", "coef", "glm", "predict",
             "rnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
IBMD: no visible global function definition for ‘runif’
IBMD: no visible global function definition for ‘quantile’
RAI: no visible global function definition for ‘runif’
RAI: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile runif
Consider adding
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIJL13s/R.INSTALL559d14824766/Observation/man/manual_data_collection_program.Rd:45: file link ‘diff.POSIXt’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Observation.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpD6kyWA/R.INSTALL723deca9260/observer/man/check_that.Rd:77: file link ‘check_that’ in package ‘ensurer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpD6kyWA/R.INSTALL723deca9260/observer/man/check_that.Rd:77: file link ‘ensure_that’ in package ‘ensurer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpD6kyWA/R.INSTALL723deca9260/observer/man/observations.Rd:37: file link ‘observe_if_’ in package ‘observer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpD6kyWA/R.INSTALL723deca9260/observer/man/reobserve.Rd:34: file link ‘ensure_that’ in package ‘observer’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/observer.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
obsSensCCC: no visible global function definition for ‘coef’
obsSensCCC: no visible global function definition for ‘confint’
obsSensCCN: no visible global function definition for ‘coef’
obsSensCCN: no visible global function definition for ‘confint’
obsSensCNN: no visible global function definition for ‘coef’
obsSensCNN: no visible global function definition for ‘confint’
obsSensCNN: no visible global function definition for ‘sd’
obsSensCNN: no visible global function definition for ‘model.matrix’
obsSensNNN: no visible global function definition for ‘coef’
obsSensNNN: no visible global function definition for ‘confint’
obsSensNNN: no visible global function definition for ‘sd’
obsSensNNN: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  coef confint model.matrix sd
Consider adding
  importFrom("stats", "coef", "confint", "model.matrix", "sd")
to your NAMESPACE file.
Rd file 'obsSensCCC.Rd':
  \usage lines wider than 90 characters:
     obsSensCCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, logOdds = FALSE, method = c("approx", "sim"))
     obsSensCCN(model, which = 2, gamma = round(seq(0, 2 * bstar, length = 6), 4), delta = seq(0, 3, 0.5), logOdds = FALSE, method = c("appr ... [TRUNCATED]
     obsSensCNN(model, which = 2, gamma = round(seq(0, 2 * bstar, length = 6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx,  ... [TRUNCATED]
     obsSensNCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, log = TRUE, method = c("approx", "sim"))
     obsSensNCN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), delta = seq(0, 3, 0.5), log = TRUE, method = c("approx", "sim"))
     6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx, log = TRUE, method = c("approx", "sim"))
     obsSensSCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, logHaz = FALSE, method = c("approx", "sim"))
     obsSensSCN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), delta = seq(0, 3, 0.5), logHaz = FALSE, method = c("approx", "sim ... [TRUNCATED]
     obsSensSNN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx, logHaz = ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpQyRY4L/R.INSTALL137428836dd3/oceanmap/man/empty.plot.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/oceanmap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp451h9C/R.INSTALL775b42249234/oddstream/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/oddstream.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0OWx8Q/R.INSTALL74527a526b25/ODEsensitivity/man/ODEmorris.default.Rd:87: file link ‘sensitivity’ in package ‘sensitivity’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0OWx8Q/R.INSTALL74527a526b25/ODEsensitivity/man/ODEsobol.default.Rd:89: file link ‘sensitivity’ in package ‘sensitivity’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0OWx8Q/R.INSTALL74527a526b25/ODEsensitivity/man/ODEsobol.default.Rd:92: file link ‘sensitivity’ in package ‘sensitivity’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ODEsensitivity.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpKMAfY4/R.INSTALL190c7ecb5324/OHPL/man/OHPL.Rd:34: file link ‘plsr’ in package ‘pls’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKMAfY4/R.INSTALL190c7ecb5324/OHPL/man/cv.OHPL.Rd:37: file link ‘plsr’ in package ‘pls’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OHPL.Rcheck/00install.out’ for details.
Found the following hidden files and directories:
  .Rapp.history
  data/.Rapp.history
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RCurl’ ‘maps’
A package should be listed in only one of these fields.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘OIdata/R/mapvar.R’:
  data(state.fips)
See section ‘Good practice’ in ‘?data’.
avgokmts: no visible global function definition for ‘aggregate’
downloadstn: no visible global function definition for ‘read.csv’
nearstn: no visible binding for global variable ‘okstations’
nearstn: no visible binding for global variable ‘Commissioned’
nearstn: no visible binding for global variable ‘Decommissioned’
okcurobs: no visible global function definition for ‘read.csv’
okmts: no visible binding for global variable ‘okstations’
okmts: no visible binding for global variable ‘TIME’
retrievemts: no visible global function definition for ‘read.csv’
totalprecip: no visible binding for global variable ‘TIME’
totalprecip: no visible global function definition for ‘aggregate’
vincenty: no visible global function definition for ‘runif’
Undefined global functions or variables:
  Commissioned Decommissioned TIME aggregate okstations read.csv runif
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
OLScurve: no visible global function definition for ‘as.formula’
OLScurve: no visible global function definition for ‘na.omit’
OLScurve: no visible global function definition for ‘lm’
OLScurve: no visible global function definition for ‘predict’
OLScurve: no visible global function definition for ‘residuals’
OLScurve: no visible global function definition for ‘model.frame’
OLScurve: no visible global function definition for ‘model.matrix’
plot.OLScurve : plotOLScurve: no visible global function definition for
  ‘reshape’
print.OLScurve: no visible global function definition for ‘na.omit’
print.OLScurve: no visible global function definition for ‘model.frame’
print.OLScurve: no visible global function definition for
  ‘model.matrix’
print.OLScurve: no visible global function definition for ‘cov’
print.OLScurve: no visible global function definition for ‘cor’
print.OLScurve: no visible global function definition for ‘sd’
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for ‘devAskNewPage’
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for ‘reshape’
subjplot.OLScurve : plotOLScurve : mypanel: no visible global function
  definition for ‘gray’
subjplot.OLScurve: no visible global function definition for
  ‘devAskNewPage’
Undefined global functions or variables:
  as.formula cor cov devAskNewPage gray lm model.frame model.matrix
  na.omit predict reshape residuals sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "gray")
  importFrom("stats", "as.formula", "cor", "cov", "lm", "model.frame",
             "model.matrix", "na.omit", "predict", "reshape",
             "residuals", "sd")
to your NAMESPACE file.
fhcor: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Found an obsolete/platform-specific call in the following function:
  ‘comp.freq’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
Undefined global functions or variables:
  optim par x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
Rd file 'oncomodel-package.Rd':
  \examples lines wider than 100 characters:
       #plot.phylog(y.phyl, cnodes =1,  clabel.n=0.6, f=0.75, sub="Oncogenetic tree of given aberrations")

These lines will be truncated in the PDF manual.
generate.data: no visible global function definition for ‘rbinom’
least.common.ancestor: no visible global function definition for
  ‘na.omit’
oncotree.fit : estimate.error.rates: no visible global function
  definition for ‘optim’
plot.boottree: no visible global function definition for ‘par’
plot.boottree: no visible global function definition for
  ‘dev.interactive’
plot.boottree: no visible global function definition for ‘mtext’
plot.oncotree: no visible global function definition for ‘par’
plot.oncotree: no visible global function definition for ‘xinch’
plot.oncotree: no visible global function definition for ‘yinch’
plot.oncotree: no visible global function definition for ‘lines’
plot.oncotree: no visible global function definition for ‘rect’
plot.oncotree: no visible global function definition for ‘strwidth’
plot.oncotree: no visible global function definition for ‘strheight’
plot.oncotree: no visible global function definition for ‘text’
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpFjOUf1/R.INSTALL1b525c6f77dc/onelogin/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/onelogin.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxH03JO/R.INSTALL521e4d7716c1/onemap/man/set_map_fun.Rd:26: file link ‘kosambi’ in package ‘onemap’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxH03JO/R.INSTALL521e4d7716c1/onemap/man/set_map_fun.Rd:26: file link ‘haldane’ in package ‘onemap’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/onemap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpAogRtC/R.INSTALL1b8e7ec78a50/onlinePCA/man/batchpca.Rd:22: file link ‘eigs_sym’ in package ‘RSpectra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/onlinePCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7rJw6j/R.INSTALL794e77c41f68/OOBCurve/man/OOBCurve.Rd:18: file link ‘makeClassifTask’ in package ‘mlr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7rJw6j/R.INSTALL794e77c41f68/OOBCurve/man/OOBCurve.Rd:18: file link ‘makeRegrTask’ in package ‘mlr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7rJw6j/R.INSTALL794e77c41f68/OOBCurve/man/OOBCurvePars.Rd:14: file link ‘makeClassifTask’ in package ‘mlr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp7rJw6j/R.INSTALL794e77c41f68/OOBCurve/man/OOBCurvePars.Rd:14: file link ‘makeRegrTask’ in package ‘mlr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OOBCurve.Rcheck/00install.out’ for details.
ci.prop: no visible global function definition for ‘qf’
ci.prop: no visible global function definition for ‘qnorm’
ePCP: no visible global function definition for ‘qnorm’
sevennum: no visible global function definition for ‘na.omit’
sevennum: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZovASh/R.INSTALL7fb51c82e148/opendatatoronto/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/opendatatoronto.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7bIRZp/R.INSTALL7aa74cc1655a/openEBGM/man/openEBGM.Rd:60: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/openEBGM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4Xv8jj/R.INSTALL1e546e544f58/OpenML/man/OMLDataSetDescription.Rd:46: file link ‘POSIXt’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OpenML.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/mxGenerateData.Rd:46: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/mxJiggle.Rd:21: file link ‘runif’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/mxJiggle.Rd:21: file link ‘rnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/mxJiggle.Rd:21: file link ‘rcauchy’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/mxTryHard.Rd:57: file link ‘runif’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/mxTryHard.Rd:57: file link ‘rnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/mxTryHard.Rd:57: file link ‘rcauchy’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/omxApply.Rd:22: file link ‘sfApply’ in package ‘snowfall’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/omxLapply.Rd:22: file link ‘sfLapply’ in package ‘snowfall’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplHx2yw/R.INSTALL2d10feaa56d/OpenMx/man/omxSapply.Rd:22: file link ‘sfSapply’ in package ‘snowfall’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OpenMx.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘openNLPmodels.en’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpkjz6u4/R.INSTALL549d16c6525b/OpenSpecy/man/data_norm.Rd:45: file link ‘min’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpkjz6u4/R.INSTALL549d16c6525b/OpenSpecy/man/human_ts.Rd:26: file link ‘format.Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpkjz6u4/R.INSTALL549d16c6525b/OpenSpecy/man/read_spec.Rd:66: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpkjz6u4/R.INSTALL549d16c6525b/OpenSpecy/man/read_spec.Rd:101: file link ‘read.spc’ in package ‘hyperSpec’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpkjz6u4/R.INSTALL549d16c6525b/OpenSpecy/man/run_app.Rd:17: file link ‘tempdir’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OpenSpecy.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmphp2NWK/R.INSTALL7c7a50ba5ca/openSTARS/man/openSTARS.Rd:9: file link ‘SSN’ in package ‘SSN’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/openSTARS.Rcheck/00install.out’ for details.
Df2SpLinesDf: no visible global function definition for ‘slot’
PlotTraj: no visible global function definition for ‘par’
PlotTraj: no visible global function definition for ‘grid’
PlotTraj: no visible global function definition for ‘box’
PlotTrajFreq: no visible global function definition for ‘par’
PlotTrajFreq: no visible global function definition for ‘grid’
PlotTrajFreq: no visible global function definition for
  ‘colorRampPalette’
PlotTrajFreq: no visible global function definition for ‘legend’
PlotTrajFreq: no visible binding for global variable ‘title’
PlotTrajFreq: no visible global function definition for ‘dev.off’
ReadFiles: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  box colorRampPalette dev.off grid legend par read.table slot title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "box", "grid", "legend", "par", "title")
  importFrom("methods", "slot")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘nbc4va’
Package suggested but not available for checking: ‘gurobi’
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nlsolve: no visible global function definition for ‘optim’
nlsolve: no visible global function definition for ‘runif’
optAUC: no visible global function definition for ‘var’
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
Rd file 'optAUC-package.Rd':
  \examples lines wider than 100 characters:
     Y1Y2<-mvrnorm(n, c(y1.mean,y2.mean), matrix(c(y1.sd^2,rho*y1.sd*y2.sd, rho*y1.sd*y2.sd, y2.sd^2),2,2))
     # two markers in the model, the AUC from GCV is smaller than just first marker in the model, because the second marker is noise
     # the AUC from ACV (apearent estimate by substituting the estimated beta into the model) is larger than previous model, because overfit ... [TRUNCATED]

Rd file 'optAUC.Rd':
  \examples lines wider than 100 characters:
     Y1Y2<-mvrnorm(n, c(y1.mean,y2.mean), matrix(c(y1.sd^2,rho*y1.sd*y2.sd, rho*y1.sd*y2.sd, y2.sd^2),2,2))
     # two markers in the model, the AUC from GCV is smaller than just first marker in the model, because the second marker is noise
     # the AUC from ACV (apearent estimate by substituting the estimated beta into the model) is larger than previous model, because overfit ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1XdaKs/R.INSTALL5e7249472c31/optCluster/man/optCluster.Rd:22: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1XdaKs/R.INSTALL5e7249472c31/optCluster/man/optCluster.Rd:266: file link ‘som’ in package ‘kohonen’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/optCluster.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Rd warning: /tmp/RtmphOJqHu/R.INSTALL16f4278af5fb/opticut/man/opticut.Rd:305: file link ‘rspf’ in package ‘ResourceSelection’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/opticut.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘gurobi’
Found the following significant warnings:
  Rd warning: /tmp/RtmpWf4IK2/R.INSTALL174a14f7aae2/optimalThreshold/man/cdf.Rd:74: file link ‘pnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWf4IK2/R.INSTALL174a14f7aae2/optimalThreshold/man/cdf.Rd:74: file link ‘plnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWf4IK2/R.INSTALL174a14f7aae2/optimalThreshold/man/cdf.Rd:74: file link ‘pgamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWf4IK2/R.INSTALL174a14f7aae2/optimalThreshold/man/cdf.Rd:74: file link ‘plogis’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWf4IK2/R.INSTALL174a14f7aae2/optimalThreshold/man/gradient.Rd:74: file link ‘dnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWf4IK2/R.INSTALL174a14f7aae2/optimalThreshold/man/gradient.Rd:74: file link ‘dlnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWf4IK2/R.INSTALL174a14f7aae2/optimalThreshold/man/gradient.Rd:74: file link ‘dgamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWf4IK2/R.INSTALL174a14f7aae2/optimalThreshold/man/gradient.Rd:74: file link ‘dlogis’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/optimalThreshold.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpkuBS4L/R.INSTALL6f8322bbbc7b/optimbase/man/optimbase.destroy.Rd:30: file link ‘optimbase.logshutdown’ in package ‘optimbase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/optimbase.Rcheck/00install.out’ for details.
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpi3fAeD/R.INSTALL13233dae356/optimParallel/man/optimParallel.Rd:50: file link ‘setDefaultCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpi3fAeD/R.INSTALL13233dae356/optimParallel/man/optimParallel.Rd:89: file link ‘clusterExport’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpi3fAeD/R.INSTALL13233dae356/optimParallel/man/optimParallel.Rd:182: file link ‘setDefaultCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpi3fAeD/R.INSTALL13233dae356/optimParallel/man/optimParallel.Rd:183: file link ‘stopCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/optimParallel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6MpNEl/R.INSTALL7c8219569c11/optimsimplex/man/optimsimplex.gradientfv.Rd:66: file link ‘optimsimplex.dirmat’ in package ‘optimsimplex’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6MpNEl/R.INSTALL7c8219569c11/optimsimplex/man/optimsimplex.gradientfv.Rd:67: file link ‘optimsimplex.deltafv’ in package ‘optimsimplex’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/optimsimplex.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXIL4P2/R.INSTALL5fb820b77135/optimus/man/find_optimal.Rd:13: file link ‘as.factor’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXIL4P2/R.INSTALL5fb820b77135/optimus/man/get_characteristic.Rd:13: file link ‘as.factor’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXIL4P2/R.INSTALL5fb820b77135/optimus/man/merge_clusters.Rd:13: file link ‘as.factor’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXIL4P2/R.INSTALL5fb820b77135/optimus/man/plot.aicsums.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/optimus.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Rd file 'TestStage.Rd':
  \examples lines wider than 100 characters:
     object1 <- OptimDes(B.init,m.init,alpha,beta,param,x,target="EDA",sf="futility",num.arm=1,num.stage=2)
     mda <- ifelse(l>1,B.init[l-1]+(B.init[l]-B.init[l-1])*(n-sum(m.init[1:(l-1)]))/m.init[l],B.init[l]*(n/m.init[l]))

Rd file 'np.OptimDes.Rd':
  \examples lines wider than 100 characters:
     object14 <- np.OptimDes(B.init,m.init,alpha,beta,param,x,pt=1.1,target="ETSL",sf="futility",num.arm=1,num.stage=2)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpVfr7Ci/R.INSTALL5cfeb1dfe1e/optinterv/man/plot_change.Rd:23: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/optinterv.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘UserGuide.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpeyQr5e/R.INSTALL188a335f28c0/optpart/man/classmatch.Rd:48: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeyQr5e/R.INSTALL188a335f28c0/optpart/man/clique.test.Rd:29: file link ‘mss.test’ in package ‘optpart’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeyQr5e/R.INSTALL188a335f28c0/optpart/man/lambda.Rd:34: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeyQr5e/R.INSTALL188a335f28c0/optpart/man/mergeclust.Rd:28: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/optpart.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
getMinimumArborescence: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for ‘par’
getMinimumSpanningTree: no visible global function definition for
  ‘capture.output’
getShortestPathTree: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output par
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpwoRJU2/R.INSTALL606313648b52/opusminer/man/opus.Rd:13: file link ‘transactions’ in package ‘arules’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpwoRJU2/R.INSTALL606313648b52/opusminer/man/opus.Rd:47: file link ‘transactions’ in package ‘arules’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpwoRJU2/R.INSTALL606313648b52/opusminer/man/opus.Rd:34: file link ‘itemsets’ in package ‘arules’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpwoRJU2/R.INSTALL606313648b52/opusminer/man/read_transactions.Rd:19: file link ‘transactions’ in package ‘arules’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/opusminer.Rcheck/00install.out’ for details.
Agrestiind.CI: no visible global function definition for ‘qnorm’
BPexact.CI: no visible global function definition for ‘uniroot’
BPmidp.CI: no visible global function definition for ‘uniroot’
Cornfieldexact.CI: no visible global function definition for ‘uniroot’
Cornfieldmidp.CI: no visible global function definition for ‘uniroot’
Gart.CI: no visible global function definition for ‘qnorm’
Invsinh.CI: no visible global function definition for ‘qnorm’
Woolf.CI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm uniroot
Consider adding
  importFrom("stats", "qnorm", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to ‘psych’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'dmes.Rd':
  \examples lines wider than 100 characters:
     > #cf. Efron, B. & Tibshirani (1993). An Introduction to the Bootstrap. New York/London: Chapman&Hall.
     > #Ruscio, J. & Mullen, T. (2012). Confidence Intervals for the Probability of Superiority Effect Size Measure and the Area Under a Rec ... [TRUNCATED]

Rd file 'orddom_f.Rd':
  \examples lines wider than 100 characters:
     orddom_f(ex_pre,ex_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within exp 01 to 02") 
     orddom_f(con_pre,con_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within con 01 to 02") 

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘orddom_csv.txt’ ‘orddom_csv_tab.txt’ ‘tmp_r.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘splines’
  Please remove these calls from your code.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nr’ to ‘nrow’
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nc’ to ‘ncol’
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /private/var/folders/pn/mz1zt3vs765b7x5ldr8bckvj8064w7/T/RtmpKjXmks/Rbuild89c341f210bf/ordinalgmifs/man/ordinalgmifs-package.Rd:26: file link ‘VGAM’ in package ‘VGAM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ordinalgmifs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxEQDfO/R.INSTALL4ac822728413/ordinal/man/addtermOld.Rd:71: file link ‘clm2’ in package ‘ordinal’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxEQDfO/R.INSTALL4ac822728413/ordinal/man/anovaOld.Rd:48: file link ‘clm2’ in package ‘ordinal’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxEQDfO/R.INSTALL4ac822728413/ordinal/man/predictOld.Rd:40: file link ‘clm2’ in package ‘ordinal’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxEQDfO/R.INSTALL4ac822728413/ordinal/man/predictOld.Rd:40: file link ‘clmm2’ in package ‘ordinal’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ordinal.Rcheck/00install.out’ for details.
genRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘intro.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1MVOcz/R.INSTALL4995472e8da9/orgutils/man/readOrg.Rd:56: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1MVOcz/R.INSTALL4995472e8da9/orgutils/man/readOrg.Rd:71: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/orgutils.Rcheck/00install.out’ for details.
ORICC1: no visible binding for global variable ‘sd’
ORICC1: no visible global function definition for ‘write.table’
ORICC1: no visible global function definition for ‘postscript’
ORICC1: no visible global function definition for ‘jpeg’
ORICC1: no visible global function definition for ‘points’
ORICC1: no visible global function definition for ‘dev.off’
ORICC1: no visible global function definition for ‘par’
ORICC2: no visible binding for global variable ‘sd’
ORICC2: no visible global function definition for ‘write.table’
ORICC2: no visible global function definition for ‘postscript’
ORICC2: no visible global function definition for ‘jpeg’
ORICC2: no visible global function definition for ‘points’
ORICC2: no visible global function definition for ‘dev.off’
ORICC2: no visible global function definition for ‘par’
Undefined global functions or variables:
  dev.off jpeg par points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
mdr.c: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0vCe6a/R.INSTALL65eca696f9c/oro.dicom/man/dicom2analyze.Rd:53: file link ‘convert.datatype.anlz’ in package ‘oro.nifti’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0vCe6a/R.INSTALL65eca696f9c/oro.dicom/man/dicom2nifti.Rd:71: file link ‘convert.datatype’ in package ‘oro.nifti’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/oro.dicom.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘genefilter’ ‘gtools’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of ‘ties’ to ‘ties.method’
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpyXpeiC/R.INSTALL639f7fc7fc67/orsifronts/man/orsifronts.Rd:7: file link ‘SpatialLinesDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/orsifronts.Rcheck/00install.out’ for details.
plot.SplineBasis: no visible global function definition for ‘matplot’
plot,SplineBasis-matrix: no visible global function definition for
  ‘matplot’
plot,SplineBasis-missing: no visible global function definition for
  ‘matplot’
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
'library' or 'require' call to ‘polynom’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
chebyshev.c.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.s.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
gegenbauer.polynomials: no visible global function definition for
  ‘polynomial’
ghermite.h.polynomials: no visible global function definition for
  ‘polynomial’
glaguerre.polynomials: no visible global function definition for
  ‘polynomial’
hermite.h.polynomials: no visible global function definition for
  ‘polynomial’
hermite.he.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.g.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.p.polynomials: no visible global function definition for
  ‘polynomial’
legendre.polynomials: no visible global function definition for
  ‘polynomial’
monic.polynomials: no visible global function definition for
  ‘polynomial’
orthogonal.polynomials: no visible global function definition for
  ‘polynomial’
orthonormal.polynomials: no visible global function definition for
  ‘polynomial’
polynomial.derivatives: no visible global function definition for
  ‘deriv’
polynomial.integrals: no visible global function definition for
  ‘integral’
polynomial.values: no visible global function definition for ‘predict’
schebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
schebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
slegendre.polynomials: no visible global function definition for
  ‘polynomial’
Undefined global functions or variables:
  deriv integral polynomial predict
Consider adding
  importFrom("stats", "deriv", "predict")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘igraph’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
as_igraph : <anonymous>: no visible global function definition for
  ‘distHaversine’
as_igraph: no visible global function definition for ‘graph.edgelist’
as_igraph: no visible global function definition for ‘E’
as_igraph: no visible global function definition for ‘E<-’
as_sp_lines: no visible global function definition for ‘Lines’
as_sp_points: no visible global function definition for
  ‘SpatialPointsDataFrame’
as_sp_polygons: no visible global function definition for ‘Polygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
make_SLDF: no visible global function definition for ‘SpatialLines’
make_SLDF: no visible global function definition for
  ‘SpatialLinesDataFrame’
osm_crs: no visible global function definition for ‘CRS’
plot.osmar: no visible global function definition for ‘gray’
plot_nodes: no visible global function definition for ‘points’
plot_ways: no visible global function definition for ‘lines’
ways_nodes2Line: no visible global function definition for ‘Line’
ways_nodes2Polygon: no visible global function definition for ‘Polygon’
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "points")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpdcgGUI/R.INSTALL57629262978/osmplotr/man/add_osm_groups.Rd:56: file link ‘shape’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpdcgGUI/R.INSTALL57629262978/osmplotr/man/add_osm_objects.Rd:26: file link ‘shape’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/osmplotr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpkmsm3f/R.INSTALL4dc713198b/OSMscale/man/proj.Rd:26: file link ‘CRS’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OSMscale.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
odm: no visible binding for global variable ‘sd’
odm : <anonymous>: no visible global function definition for ‘sd’
odm : <anonymous>: no visible global function definition for ‘quantile’
odm: no visible global function definition for ‘prcomp’
quant.const: no visible global function definition for ‘quantile’
quant.const.D: no visible global function definition for ‘reshape’
quant.const.D: no visible global function definition for ‘quantile’
quant.linear.D: no visible global function definition for ‘reshape’
quant.nonlin : FrankModel: no visible global function definition for
  ‘qt’
quant.nonlin : FrankModel: no visible global function definition for
  ‘pt’
quant.nonlin: no visible global function definition for ‘predict’
quant.nonlin.D: no visible global function definition for ‘reshape’
quant.nonlin.D: no visible global function definition for ‘predict’
quant.nonpar.D: no visible global function definition for ‘reshape’
rgrubbs.test: no visible global function definition for ‘sd’
plot,OutlierDM-missing: no visible binding for global variable ‘pch’
summary,OutlierDM: no visible global function definition for ‘head’
Undefined global functions or variables:
  head pch prcomp predict pt qt quantile reshape sd
Consider adding
  importFrom("stats", "prcomp", "predict", "pt", "qt", "quantile",
             "reshape", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
Found the following files/directories:
  ‘result.txt’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7oUDNd/R.INSTALLc3f707c485b/outsider/man/ssh_setup.Rd:10: file link ‘ssh_connect’ in package ‘ssh’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/outsider.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpueQ0Nh/R.INSTALL6fa6e2bffbf/owdbr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/owdbr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpATVOCS/R.INSTALL7bb1b488973/owmr/man/add_owm_tiles.Rd:15: file link ‘addTiles’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpATVOCS/R.INSTALL7bb1b488973/owmr/man/add_weather.Rd:32: file link ‘addMarkers’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpATVOCS/R.INSTALL7bb1b488973/owmr/man/reexports.Rd:15: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpATVOCS/R.INSTALL7bb1b488973/owmr/man/reexports.Rd:15: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/owmr.Rcheck/00install.out’ for details.
loadCSVtoP2distance: no visible global function definition for
  ‘read.table’
p2distance : calcularDistancia: no visible binding for global variable
  ‘sd’
p2distance : ordenarVariables: no visible global function definition
  for ‘cor’
p2distance : calculoFactoresPonderacion: no visible global function
  definition for ‘lm’
p2distance: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for ‘survfit’
p3state: no visible global function definition for ‘terms’
p3state: no visible global function definition for ‘as.formula’
p3state: no visible global function definition for ‘coxph’
p3state: no visible binding for global variable ‘na.exclude’
plot.p3state: no visible global function definition for ‘matplot’
plot.p3state: no visible global function definition for ‘devAskNewPage’
plot.p3state: no visible global function definition for ‘persp’
plot.p3state: no visible global function definition for ‘colours’
plot.p3state: no visible global function definition for
  ‘filled.contour’
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
pacbpred : thetaFunc: no visible global function definition for ‘lsfit’
pacbpred : thetaFunc: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘var’
pacbpred: no visible global function definition for ‘runif’
pacbpred: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpJp4YqD/R.INSTALLa0b3e4da2cd/packager/man/add_github_url_to_desc.Rd:36: file link ‘git_signature_default’ in package ‘gert’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJp4YqD/R.INSTALLa0b3e4da2cd/packager/man/git_add_commit.Rd:22: file link ‘git_commit_all’ in package ‘gert’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJp4YqD/R.INSTALLa0b3e4da2cd/packager/man/git_tag.Rd:18: file link ‘git_tag_list’ in package ‘gert’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/packager.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Non-standard files/directories found at top level:
  ‘DESCRIPTION_EX’ ‘divers’ ‘main.R’ ‘testsDev’
Found the following significant warnings:
  Rd warning: /tmp/RtmpvKYVns/R.INSTALL1e64fd27593/packrat/man/lockfile-metadata.Rd:18: file link ‘package_version’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/packrat.Rcheck/00install.out’ for details.
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  ‘EXP’ to ‘EXPR’
[,ClassW: warning in return(x@u1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@u2): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@w1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in x@u1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@u2 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@w1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
paf: no visible global function definition for ‘as.formula’
paf: no visible global function definition for ‘model.response’
paf: no visible global function definition for ‘model.frame’
paf: no visible global function definition for ‘model.matrix’
plot.paf: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
CalGIF: no visible binding for global variable ‘PAGIData’
CalGIF2: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible global function definition for ‘p.adjust’
PAGI.Main: no visible global function definition for ‘pt’
getclass.labels: no visible binding for global variable ‘ExampleData’
getdataset: no visible binding for global variable ‘ExampleData’
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###

Rd file 'PAGI.Main.Rd':
  \examples lines wider than 100 characters:
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘p2data’
Found the following significant warnings:
  Rd warning: /tmp/RtmpWd3rOa/R.INSTALLb7853b71a89/pagoda2/man/projectKNNs.Rd:80: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pagoda2.Rcheck/00install.out’ for details.
paired.Loc: no visible global function definition for ‘qt’
paired.Loc: no visible global function definition for ‘median’
paired.Loc: no visible global function definition for ‘qsignrank’
paired.Loc: no visible global function definition for ‘qnorm’
paired.Scale: no visible global function definition for ‘var’
paired.Scale: no visible global function definition for ‘cor’
paired.Scale: no visible global function definition for ‘qt’
paired.Scale: no visible global function definition for ‘median’
paired.Scale: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
Rd file 'paired.Loc.Rd':
  \usage lines wider than 90 characters:
     paired.Loc(x, y, method = "parametric", exact = FALSE, conf.level = 0.95, alternative = "two.sided")
  \examples lines wider than 100 characters:
     astra <- c(2.4, 4.8, 4, 4.9, 3.9, 4.1, 3.8, 3.5, 4.6, 2.9, 4.9, 3.7, 4.8, 3.7, 3.8, 4.1, 4.2, 4.3, 3.9, 3.8)
     flame <- c(2.4, 4.8, 4, 4.7, 3.9, 4.2, 3.8, 3.3, 4.6, 3, 5, 3.6, 4.9, 3.8, 3.9, 4.6, 4.2, 4.4, 4, 3.4)

Rd file 'paired.Scale.Rd':
  \examples lines wider than 100 characters:
     astra <- c(2.4, 4.8, 4, 4.9, 3.9, 4.1, 3.8, 3.5, 4.6, 2.9, 4.9, 3.7, 4.8, 3.7, 3.8, 4.1, 4.2, 4.3, 3.9, 3.8)
     flame <- c(2.4, 4.8, 4, 4.7, 3.9, 4.2, 3.8, 3.3, 4.6, 3, 5, 3.6, 4.9, 3.8, 3.9, 4.6, 4.2, 4.4, 4, 3.4)

Rd file 'pairedCI-package.Rd':
  \examples lines wider than 100 characters:
     astra <- c(2.4, 4.8, 4, 4.9, 3.9, 4.1, 3.8, 3.5, 4.6, 2.9, 4.9, 3.7, 4.8, 3.7, 3.8, 4.1, 4.2, 4.3, 3.9, 3.8)
     flame <- c(2.4, 4.8, 4, 4.7, 3.9, 4.2, 3.8, 3.3, 4.6, 3, 5, 3.6, 4.9, 3.8, 3.9, 4.6, 4.2, 4.4, 4, 3.4)

These lines will be truncated in the PDF manual.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'pairheatmap.Rd':
  \examples lines wider than 100 characters:
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),

These lines will be truncated in the PDF manual.
pairsD3: no visible global function definition for ‘gray.colors’
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0jAidz/R.INSTALLc0e5f9bd9f5/palaeoSig/man/centipede_plot.Rd:26: file link ‘caterpillar’ in package ‘analogue’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0jAidz/R.INSTALLc0e5f9bd9f5/palaeoSig/man/obs.cor.Rd:28: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0jAidz/R.INSTALLc0e5f9bd9f5/palaeoSig/man/obs.cor.Rd:116: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0jAidz/R.INSTALLc0e5f9bd9f5/palaeoSig/man/palaeoSig-package.Rd:46: file link ‘rioja-package’ in package ‘rioja’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0jAidz/R.INSTALLc0e5f9bd9f5/palaeoSig/man/randomTF.Rd:35: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0jAidz/R.INSTALLc0e5f9bd9f5/palaeoSig/man/randomTF.Rd:107: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/palaeoSig.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘CorShrink’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpta4VR2/R.INSTALL6d836ae08423/palasso/man/methods.Rd:52: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/palasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpBVaBVU/R.INSTALLeeadff8557/paleofire/man/pfSimpleGrid.Rd:101: file link ‘Raster-class’ in package ‘raster’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpBVaBVU/R.INSTALLeeadff8557/paleofire/man/plot.pfGridding.Rd:45: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpBVaBVU/R.INSTALLeeadff8557/paleofire/man/plot.pfSiteSel.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/paleofire.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCUxavQ/R.INSTALL2e03578ffe55/paleoMAS/man/analog.mult.Rd:45: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCUxavQ/R.INSTALL2e03578ffe55/paleoMAS/man/analog.mult.Rd:47: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCUxavQ/R.INSTALL2e03578ffe55/paleoMAS/man/analog.mult.Rd:50: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/paleoMAS.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘lattice’ ‘vegan’
  Please remove these calls from your code.
Rd file 'syas.Rd':
  \examples lines wider than 100 characters:
     bcrossv.sa(modernq[,1],perq2,a.d,delta=25,method="canberra",quant=0.05,trials=c(5, 0.05),detrend=FALSE)

Rd file 'vcrossv.all.Rd':
  \examples lines wider than 100 characters:
     #build a dummy factor assuming that the first 10 species belong to group1 and the send ten belong to group 2

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Dispersion.pdf’
Found the following significant warnings:
  Rd warning: /tmp/RtmpFPsKOx/R.INSTALLecb68ec8a90/pammtools/man/dplyr_verbs.Rd:213: file link ‘summarize_all’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFPsKOx/R.INSTALLecb68ec8a90/pammtools/man/geom_hazard.Rd:130: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFPsKOx/R.INSTALLecb68ec8a90/pammtools/man/geom_hazard.Rd:131: file link ‘geom_step’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFPsKOx/R.INSTALLecb68ec8a90/pammtools/man/pamm.Rd:30: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFPsKOx/R.INSTALLecb68ec8a90/pammtools/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFPsKOx/R.INSTALLecb68ec8a90/pammtools/man/tidy_smooth.Rd:20: file link ‘qqline’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pammtools.Rcheck/00install.out’ for details.
GOpredict: no visible global function definition for ‘fisher.test’
KEGGpredict: no visible global function definition for ‘fisher.test’
ProteinCluster: no visible global function definition for ‘ecdf’
ProteinCluster: no visible global function definition for ‘as.hclust’
ProteinCluster: no visible global function definition for
  ‘as.dendrogram’
ProteinCluster : addE: no visible global function definition for
  ‘is.leaf’
SignificantSubcluster: no visible global function definition for
  ‘order.dendrogram’
SignificantSubcluster: no visible global function definition for
  ‘fisher.test’
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
Consider adding
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Paneldata.formula: no visible global function definition for
  ‘model.frame’
Paneldata.formula: no visible global function definition for
  ‘model.matrix’
Paneldata.formula: no visible global function definition for
  ‘model.response’
summary.Paneldata: no visible global function definition for ‘coef’
summary.Paneldata: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmppXfwI1/R.INSTALL7aa15ae1ef73/papeR/man/confint.Rd:29: file link ‘mcmcsamp’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmppXfwI1/R.INSTALL7aa15ae1ef73/papeR/man/confint.Rd:35: file link ‘mcmcsamp’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmppXfwI1/R.INSTALL7aa15ae1ef73/papeR/man/prettify.Rd:132: file link ‘mcmcsamp’ in package ‘lme4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/papeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp77c5uv/R.INSTALL74d361d6add/parallelMap/man/parallelRegisterLevels.Rd:24: file link ‘.onLoad’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp77c5uv/R.INSTALL74d361d6add/parallelMap/man/parallelStart.Rd:157: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp77c5uv/R.INSTALL74d361d6add/parallelMap/man/parallelStart.Rd:159: file link ‘mcmapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp77c5uv/R.INSTALL74d361d6add/parallelMap/man/parallelStart.Rd:180: file link ‘clusterMap’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp77c5uv/R.INSTALL74d361d6add/parallelMap/man/parallelStop.Rd:16: file link ‘stopCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/parallelMap.Rcheck/00install.out’ for details.
parallelSVM.default: no visible binding for global variable ‘na.omit’
parallelSVM.formula: no visible binding for global variable ‘na.omit’
predict.parallelSVM: no visible binding for global variable ‘predict’
Undefined global functions or variables:
  na.omit predict
Consider adding
  importFrom("stats", "na.omit", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5PJO0k/R.INSTALL65c3a8ed67f/ParamHelpers/man/evaluateParamExpressions.Rd:10: file link ‘ParamSet’ in package ‘ParamHelpers’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5PJO0k/R.INSTALL65c3a8ed67f/ParamHelpers/man/evaluateParamExpressions.Rd:21: file link ‘ParamSet’ in package ‘ParamHelpers’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5PJO0k/R.INSTALL65c3a8ed67f/ParamHelpers/man/getParamSet.Rd:14: file link ‘ParamSet’ in package ‘ParamHelpers’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5PJO0k/R.INSTALL65c3a8ed67f/ParamHelpers/man/hasExpression.Rd:10: file link ‘ParamSet’ in package ‘ParamHelpers’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ParamHelpers.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpFN0skQ/R.INSTALL61847ef44ee1/parboost/man/parboost.Rd:56: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFN0skQ/R.INSTALL61847ef44ee1/parboost/man/parboost.Rd:62: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpFN0skQ/R.INSTALL61847ef44ee1/parboost/man/parboost.Rd:63: file link ‘boost_control’ in package ‘mboost’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/parboost.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.formula.make: no visible global function definition for ‘formula’
regress: no visible global function definition for ‘lm’
regress: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-parcoords-.Rmd’
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘NUL’
Package suggested but not available for checking: ‘liquidSVM’
Found the following significant warnings:
  Rd warning: /tmp/RtmpOvvtJh/R.INSTALLf596fdc2bb4/partialCI/man/fit.pci.Rd:140: file link ‘partialAR’ in package ‘partialAR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpOvvtJh/R.INSTALLf596fdc2bb4/partialCI/man/hedge.pci.Rd:153: file link ‘partialAR’ in package ‘partialAR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpOvvtJh/R.INSTALLf596fdc2bb4/partialCI/man/loglik.pci.Rd:99: file link ‘partialAR’ in package ‘partialAR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpOvvtJh/R.INSTALLf596fdc2bb4/partialCI/man/multigetYahooPrices.Rd:39: file link ‘getYahooData’ in package ‘TTR’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpOvvtJh/R.INSTALLf596fdc2bb4/partialCI/man/statehistory.pci.Rd:51: file link ‘partialAR’ in package ‘partialAR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/partialCI.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘nnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for ‘multinom’
fitOR: no visible global function definition for ‘formula’
fitOR: no visible global function definition for ‘coef’
fitOR: no visible global function definition for ‘optim’
reportOR: no visible global function definition for ‘qnorm’
reportOR: no visible global function definition for ‘pchisq’
reportOR: no visible global function definition for ‘coef’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/reexports.Rd:20: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/reexports.Rd:22: file link ‘filter’ in package ‘tidygraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/reexports.Rd:22: file link ‘slice’ in package ‘tidygraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/reexports.Rd:22: file link ‘mutate’ in package ‘tidygraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/reexports.Rd:22: file link ‘mutate_at’ in package ‘tidygraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/reexports.Rd:22: file link ‘mutate_all’ in package ‘tidygraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/simulate.Rd:73: file link ‘as_tbl_graph’ in package ‘tidygraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/simulation_modification.Rd:44: file link ‘mutate_at’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/simulation_modification.Rd:46: file link ‘bind_nodes’ in package ‘tidygraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPYiOb5/R.INSTALLfdaf7f75e7/particles/man/simulation_modification.Rd:46: file link ‘bind_edges’ in package ‘tidygraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/particles.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
partitionMap: no visible global function definition for ‘predict’
partitionMap: no visible global function definition for ‘rnorm’
partitionMap: no visible binding for global variable ‘sd’
partitionMap: no visible global function definition for ‘sd’
partitionMap: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCREwPw/R.INSTALL11a23c361939/partition/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/partition.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpmlik9D/R.INSTALL4846360881e/partykit/man/ctree_control.Rd:44: file link ‘GenzBretz’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmlik9D/R.INSTALL4846360881e/partykit/man/glmtree.Rd:45: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmlik9D/R.INSTALL4846360881e/partykit/man/lmtree.Rd:41: file link ‘lm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmlik9D/R.INSTALL4846360881e/partykit/man/lmtree.Rd:42: file link ‘lm.wfit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmlik9D/R.INSTALL4846360881e/partykit/man/prune.modelparty.Rd:31: file link ‘prune’ in package ‘rpart’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpmlik9D/R.INSTALL4846360881e/partykit/man/prune.modelparty.Rd:58: file link ‘prune’ in package ‘rpart’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/partykit.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
parviol: no visible global function definition for ‘plot.new’
parviol: no visible global function definition for ‘plot.window’
parviol: no visible global function definition for ‘title’
parviol: no visible global function definition for ‘lines’
parviol: no visible global function definition for ‘text’
parviol: no visible global function definition for ‘rgb’
selecto: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘ape’ ‘caper’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for ‘read.tree’
conch: no visible global function definition for ‘reorder’
conch: no visible global function definition for ‘read.nexus’
conch: no visible global function definition for ‘.compressTipLabel’
conch: no visible global function definition for ‘drop.tip’
conch: no visible global function definition for ‘extract.clade’
conch: no visible global function definition for ‘which.edge’
conch: no visible global function definition for ‘write.tree’
pastis_main: no visible global function definition for ‘combn’
read_input: no visible global function definition for ‘read.tree’
read_input: no visible global function definition for ‘reorder’
read_input: no visible global function definition for ‘read.csv’
read_input: no visible global function definition for ‘read.dna’
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘pastis_data_1’ ‘pastis_data_2’ ‘pastis_data_3’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘e1071’
  Please remove these calls from your code.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1g6xdb/R.INSTALL698a37af9150/path.chain/man/temp_path.Rd:22: file link ‘dir.create’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/path.chain.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpjEyTGF/R.INSTALL5bd355f69067/pathfindR/man/enrichment_chart.Rd:45: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjEyTGF/R.INSTALL5bd355f69067/pathfindR/man/visualize_hsa_KEGG.Rd:39: file link ‘gravity_types’ in package ‘magick’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjEyTGF/R.INSTALL5bd355f69067/pathfindR/man/visualize_hsa_KEGG.Rd:42: file link ‘gravity_types’ in package ‘magick’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjEyTGF/R.INSTALL5bd355f69067/pathfindR/man/visualize_term_interactions.Rd:29: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjEyTGF/R.INSTALL5bd355f69067/pathfindR/man/visualize_term_interactions.Rd:33: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pathfindR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpsapNfz/R.INSTALL6d127e94513/pathlibr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pathlibr.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘pathlibr.Rmd’
Checking should be performed on sources prepared by ‘R CMD build’.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSmAEXW/R.INSTALL5c683caad693/patrick/man/with_parameters_test_that.Rd:32: file link ‘!!!’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/patrick.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpHqboAY/R.INSTALL645d51a5686/patternize/man/lanArray.Rd:5: file link ‘Morpho’ in package ‘Morpho’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHqboAY/R.INSTALL645d51a5686/patternize/man/lanArray.Rd:23: file link ‘Morpho’ in package ‘Morpho’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHqboAY/R.INSTALL645d51a5686/patternize/man/patRDA.Rd:7: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHqboAY/R.INSTALL645d51a5686/patternize/man/patRDA.Rd:118: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHqboAY/R.INSTALL645d51a5686/patternize/man/patternize.Rd:86: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/patternize.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
add_noise: no visible global function definition for ‘rnorm’
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for ‘var’
generate_sample: no visible global function definition for ‘rnorm’
generate_sample: no visible global function definition for ‘runif’
sample_function: no visible global function definition for ‘runif’
sample_function : <anonymous>: no visible global function definition
  for ‘var’
sample_function_multi_mod_weight: no visible global function definition
  for ‘runif’
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for ‘var’
sample_function_single_mod: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpY634nu/R.INSTALL75da16ea76ce/pbo/man/dotplot.pbo.Rd:16: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpY634nu/R.INSTALL75da16ea76ce/pbo/man/dotplot.pbo.Rd:19: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpY634nu/R.INSTALL75da16ea76ce/pbo/man/dotplot.pbo.Rd:22: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpY634nu/R.INSTALL75da16ea76ce/pbo/man/dotplot.pbo.Rd:32: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpY634nu/R.INSTALL75da16ea76ce/pbo/man/histogram.pbo.Rd:29: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpY634nu/R.INSTALL75da16ea76ce/pbo/man/histogram.pbo.Rd:29: file link ‘panel.abline’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpY634nu/R.INSTALL75da16ea76ce/pbo/man/histogram.pbo.Rd:36: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpY634nu/R.INSTALL75da16ea76ce/pbo/man/histogram.pbo.Rd:37: file link ‘panel.abline’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pbo.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘foreach’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dotplot.pbo: no visible global function definition for ‘reorder’
pbo: no visible global function definition for ‘%dopar%’
pbo: no visible global function definition for ‘foreach’
pbo: no visible global function definition for ‘lm’
xyplot.pbo: no visible global function definition for ‘ecdf’
xyplot.pbo: no visible global function definition for ‘doubleYScale’
xyplot.pbo: no visible global function definition for ‘reorder’
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
a_get_native: no visible global function definition for ‘par’
a_get_relative: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘dist’
brackets: no visible global function definition for ‘lines’
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmphiLLpF/R.INSTALL656174a433bc/PBSddesolve/man/dde.Rd:66: file link ‘pastgradient’ in package ‘PBSddesolve’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PBSddesolve.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGtiszB/R.INSTALL4cc952332c3f/PBSmapping/man/bcBathymetry.Rd:55: file link ‘nepacLLhigh’ in package ‘PBSmapping’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGtiszB/R.INSTALL4cc952332c3f/PBSmapping/man/plotMap.Rd:83: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PBSmapping.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Running examples in ‘PCA4you-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PCA.Plotter
> ### Title: PCA.Plotter
> ### Aliases: PCA.Plotter
> 
> ### ** Examples
> 
> set.seed(5)
> num.of.variables <- 14
> num.of.observations <- 34
> rn <- rnorm(num.of.variables * num.of.observations)
> data.mat <- matrix(rn, nrow = num.of.observations, ncol = num.of.variables)
> PCA.Plotter(data.mat)
Warning in min(x, na.rm = na.rm) :
  no non-missing arguments to min; returning Inf
Warning in max(x, na.rm = na.rm) :
  no non-missing arguments to max; returning -Inf
Warning in min(x, na.rm = na.rm) :
  no non-missing arguments to min; returning Inf
Warning in max(x, na.rm = na.rm) :
  no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: PCA.Plotter -> plot -> plot.default -> localWindow -> plot.window
Execution halted
draw.pcaBootPlot: no visible global function definition for ‘grid’
draw.pcaBootPlot: no visible global function definition for ‘points’
draw.pcaBootPlot: no visible global function definition for ‘symbols’
draw.pcaBootPlot: no visible global function definition for ‘legend’
pcaBootPlot: no visible global function definition for ‘prcomp’
pcaBootPlot: no visible global function definition for ‘cor’
pcaBootPlot: no visible global function definition for ‘quantile’
pcaBootPlot: no visible global function definition for ‘pdf’
pcaBootPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  cor dev.off grid legend pdf points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp92MTcl/R.INSTALL8954c1be1b8/pcalg/man/randDAG.Rd:85: file link ‘graphNEL’ in package ‘graph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp92MTcl/R.INSTALL8954c1be1b8/pcalg/man/randDAG.Rd:99: file link ‘random.graph.game’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp92MTcl/R.INSTALL8954c1be1b8/pcalg/man/randDAG.Rd:99: file link ‘barabasi.game’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pcalg.Rcheck/00install.out’ for details.
PCDReg.wf: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpWvvxLp/R.INSTALL7a4a3942e869/pcensmix/man/mixgen.Rd:27: file link ‘rnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWvvxLp/R.INSTALL7a4a3942e869/pcensmix/man/mixgen.Rd:27: file link ‘rlnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWvvxLp/R.INSTALL7a4a3942e869/pcensmix/man/mixgen.Rd:28: file link ‘rweibull’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWvvxLp/R.INSTALL7a4a3942e869/pcensmix/man/mixgen.Rd:28: file link ‘rgamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWvvxLp/R.INSTALL7a4a3942e869/pcensmix/man/mixgen.Rd:29: file link ‘rcauchy’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWvvxLp/R.INSTALL7a4a3942e869/pcensmix/man/mixgen.Rd:29: file link ‘rbeta’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pcensmix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpRcgDOn/R.INSTALL1b147505a716/pcFactorStan/man/pcStan.Rd:23: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpRcgDOn/R.INSTALL1b147505a716/pcFactorStan/man/pcStan.Rd:31: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pcFactorStan.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp2Ys5mQ/R.INSTALL6951190b9654/pcoxtime/man/pcoxsurvfit.pcoxtime.Rd:24: file link ‘pcoxbasehaz.pcoxtime’ in package ‘pcoxtime’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Ys5mQ/R.INSTALL6951190b9654/pcoxtime/man/pcoxtime.Rd:68: file link ‘model.matrix.default’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Ys5mQ/R.INSTALL6951190b9654/pcoxtime/man/pkgsExport.Rd:26: file link ‘Score’ in package ‘riskRegression’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Ys5mQ/R.INSTALL6951190b9654/pcoxtime/man/plot.Score.Rd:22: file link ‘Score’ in package ‘riskRegression’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Ys5mQ/R.INSTALL6951190b9654/pcoxtime/man/plot.Score.Rd:10: file link ‘Score’ in package ‘riskRegression’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Ys5mQ/R.INSTALL6951190b9654/pcoxtime/man/plot.Score.Rd:25: file link ‘Score’ in package ‘riskRegression’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp2Ys5mQ/R.INSTALL6951190b9654/pcoxtime/man/plot.pcoxsurvfit.Rd:17: file link ‘pcoxbasehaz.pcoxtime’ in package ‘pcoxtime’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pcoxtime.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpI7cV9f/R.INSTALL69da12ec0db9/PCRedux/man/armor.Rd:45: file link ‘suppressMessages’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpI7cV9f/R.INSTALL69da12ec0db9/PCRedux/man/armor.Rd:46: file link ‘inherits’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpI7cV9f/R.INSTALL69da12ec0db9/PCRedux/man/earlyreg.Rd:50: file link ‘coefficients’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpI7cV9f/R.INSTALL69da12ec0db9/PCRedux/man/winklR.Rd:63: file link ‘acos’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PCRedux.Rcheck/00install.out’ for details.
PdofCSGt.bootstrap5: no visible global function definition for ‘rnorm’
PdofCSGt.bootstrap5: no visible global function definition for ‘rt’
PdofCSt.T1or2: no visible global function definition for ‘combn’
PofCSGt: no visible global function definition for ‘combn’
PofCSLt.bootstrap5: no visible global function definition for ‘rnorm’
PofCSLt.bootstrap5: no visible global function definition for ‘rt’
PofCSt: no visible global function definition for ‘pnorm’
tindep: no visible binding for global variable ‘var’
tindep: no visible global function definition for ‘pt’
Undefined global functions or variables:
  combn pnorm pt rnorm rt var
Consider adding
  importFrom("stats", "pnorm", "pt", "rnorm", "rt", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmphmuf5Z/R.INSTALL14721d0716e2/pcts/man/pcts_reexports.Rd:19: file link ‘as.Date’ in package ‘zoo’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pcts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3UI7BG/R.INSTALL75091d5511a/pdfCluster/man/plot.kepdf.Rd:87: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3UI7BG/R.INSTALL75091d5511a/pdfCluster/man/plot.pdfCluster.Rd:81: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pdfCluster.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘PythonInR’
Found the following significant warnings:
  Rd warning: /tmp/RtmphoH9UH/R.INSTALL19646bfa7cd4/pdftools/man/qpdf.Rd:26: file link ‘pdf_combine’ in package ‘qpdf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmphoH9UH/R.INSTALL19646bfa7cd4/pdftools/man/qpdf.Rd:26: file link ‘pdf_compress’ in package ‘qpdf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmphoH9UH/R.INSTALL19646bfa7cd4/pdftools/man/qpdf.Rd:26: file link ‘pdf_length’ in package ‘qpdf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmphoH9UH/R.INSTALL19646bfa7cd4/pdftools/man/qpdf.Rd:26: file link ‘pdf_split’ in package ‘qpdf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmphoH9UH/R.INSTALL19646bfa7cd4/pdftools/man/qpdf.Rd:26: file link ‘pdf_subset’ in package ‘qpdf’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pdftools.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pdist: no visible global function definition for ‘dist’
pdist: no visible global function definition for ‘new’
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
band.chol.cv: no visible global function definition for ‘cov’
pdsoft.cv: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘peakPick-vignette.Rmd’
PearsonICA: no visible global function definition for ‘rnorm’
PearsonICAdemo: no visible global function definition for ‘rnorm’
PearsonICAdemo: no visible global function definition for ‘dev.new’
PearsonICAdemo: no visible global function definition for ‘par’
PearsonICAdemo: no visible global function definition for ‘axis’
PearsonICAdemo: no visible global function definition for ‘title’
PearsonICAdemo: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis dev.new lines par rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Rd file 'PearsonICA.Rd':
  \usage lines wider than 90 characters:
     PearsonICA(X, n.comp = 0, row.norm = FALSE, maxit = 200, tol = 1e-04, border.base = c(2.6, 4), border.slope = c(0, 1), verbose = FALSE, ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for ‘rbinom’
AssoTestProc: no visible global function definition for ‘princomp’
AssoTestProc: no visible global function definition for ‘loadings’
AssoTestProc: no visible global function definition for ‘lm’
CNVtypeAnay: no visible global function definition for ‘cov’
ClusProc: no visible global function definition for ‘princomp’
ClusProc: no visible global function definition for ‘prcomp’
ClusProc0: no visible global function definition for ‘kmeans’
ClusProc0: no visible global function definition for ‘cov’
Inde: no visible global function definition for ‘lm’
Inde: no visible global function definition for ‘var’
STE: no visible global function definition for ‘pchisq’
STIM: no visible global function definition for ‘cor’
STIM: no visible global function definition for ‘pchisq’
plot.clust: no visible global function definition for ‘princomp’
plot.clust: no visible global function definition for ‘loadings’
plot.clust: no visible global function definition for ‘qplot’
plot.clust: no visible global function definition for ‘geom_histogram’
plot.clust: no visible global function definition for ‘aes_string’
plot.clust: no visible global function definition for ‘barplot’
plot.clust: no visible global function definition for ‘title’
plot.clust: no visible global function definition for ‘mtext’
plot.clust: no visible global function definition for ‘text’
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
blup: no visible global function definition for ‘model.matrix’
blup: no visible global function definition for ‘model.frame’
blup: no visible global function definition for ‘read.table’
calcG: no visible global function definition for ‘as’
gblup: no visible global function definition for ‘model.matrix’
gblup: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘A.txt’ ‘Ainv.txt’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/numint.Rd:81: file link ‘is.numeric’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/numint.Rd:81: file link ‘is.integer’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/numint.Rd:82: file link ‘is.factor’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/plotCor.Rd:15: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/plotHD.Rd:83: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/plotHD.Rd:83: file link ‘panel.mathdensity’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/plotHD.Rd:99: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/plotHD.Rd:99: file link ‘panel.mathdensity’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/plotMS.Rd:69: file link ‘cm.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp6hZcIz/R.INSTALL729a3d0a8a22/pedometrics/man/rowMinCpp.Rd:27: file link ‘rowMins’ in package ‘matrixStats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pedometrics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpg1T3XQ/R.INSTALL1ab175081962/pegas/man/conversion.Rd:71: file link ‘genind-class’ in package ‘adegenet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpg1T3XQ/R.INSTALL1ab175081962/pegas/man/geod.Rd:33: file link ‘as.dist’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpg1T3XQ/R.INSTALL1ab175081962/pegas/man/na.omit.loci.Rd:5: file link ‘na.omit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpg1T3XQ/R.INSTALL1ab175081962/pegas/man/nuc.div.Rd:48: file link ‘GC.content’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pegas.Rcheck/00install.out’ for details.
PEMM_fun : find.lambda: no visible global function definition for
  ‘optimize’
PEMM_fun: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpoAMAZP/R.INSTALL31792e0c604a/peperr/man/complexity.LASSO.Rd:22: file link ‘optL1’ in package ‘penalized’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/peperr.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘PARMA21del1_ident’
performance.curves.plot: no visible global function definition for
  ‘postscript’
performance.curves.plot: no visible global function definition for
  ‘axis’
performance.curves.plot: no visible global function definition for
  ‘lines’
performance.curves.plot: no visible global function definition for
  ‘legend’
performance.curves.plot: no visible global function definition for
  ‘grid’
performance.curves.plot: no visible global function definition for
  ‘dev.off’
precision.recall.curves.plot: no visible global function definition for
  ‘postscript’
precision.recall.curves.plot: no visible global function definition for
  ‘axis’
precision.recall.curves.plot: no visible global function definition for
  ‘lines’
precision.recall.curves.plot: no visible global function definition for
  ‘legend’
precision.recall.curves.plot: no visible global function definition for
  ‘grid’
precision.recall.curves.plot: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  axis dev.off grid legend lines postscript
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "grid", "legend", "lines")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4vmYWp/R.INSTALL558f681623fa/PerformanceAnalytics/man/PerformanceAnalytics-package.Rd:180: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4vmYWp/R.INSTALL558f681623fa/PerformanceAnalytics/man/Return.read.Rd:22: file link ‘as.yearmon’ in package ‘zoo’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4vmYWp/R.INSTALL558f681623fa/PerformanceAnalytics/man/Return.read.Rd:23: file link ‘as.yearqtr’ in package ‘zoo’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4vmYWp/R.INSTALL558f681623fa/PerformanceAnalytics/man/chart.QQPlot.Rd:183: file link ‘qqplot’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4vmYWp/R.INSTALL558f681623fa/PerformanceAnalytics/man/chart.StackedBar.Rd:109: file link ‘barchart’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PerformanceAnalytics.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘DMwR’
Package suggested but not available for checking: ‘dendextendRcpp’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpxd9iNZ/R.INSTALL199d767c7933/periscope/man/downloadablePlotUI.Rd:43: file link ‘hoverOpts’ in package ‘shiny’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpxd9iNZ/R.INSTALL199d767c7933/periscope/man/downloadablePlotUI.Rd:94: file link ‘hoverOpts’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/periscope.Rcheck/00install.out’ for details.
permalgorithm: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘permus_per_dist_4’ ‘permus_per_shape_bin_4_0’
  ‘permus_per_shape_bin_4_1’ ‘permus_per_shape_bin_4_2’
  ‘permus_per_shape_bin_4_3’
Malformed Description field: should contain one or more complete sentences.
ksample.pclt: no visible global function definition for ‘pchisq’
pCI: no visible global function definition for ‘qbeta’
permKS.formula: no visible global function definition for ‘terms’
permTREND.default: no visible global function definition for ‘cor’
permTREND.formula: no visible global function definition for ‘terms’
permTS.formula: no visible global function definition for ‘terms’
trend.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
Rd file 'perm-internal.Rd':
  \usage lines wider than 90 characters:
     ksample.exact.mc(scores, group, nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TRUE)
     trend.exact.mc(scores, group, alternative = "two.sided", nmc = 10^3 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TR ... [TRUNCATED]
     twosample.exact.mc(scores, group, alternative = "two.sided", nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED  ... [TRUNCATED]

Rd file 'perm.Rd':
  \usage lines wider than 90 characters:
     permKS(x, g, exact = NULL, method = NULL, methodRule = methodRuleKS1, control=permControl(), ...)
     permTREND(x, y, alternative = c("two.sided", "less", "greater"), exact = NULL, method = NULL, methodRule = methodRuleTREND1, control=pe ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpi4d86n/R.INSTALL76284ec1c6d8/perry/man/perryPlot.Rd:89: file link ‘geom_pointrange’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpi4d86n/R.INSTALL76284ec1c6d8/perry/man/perryPlot.Rd:90: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpi4d86n/R.INSTALL76284ec1c6d8/perry/man/perryPlot.Rd:156: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/perry.Rcheck/00install.out’ for details.
hasMethod: no visible global function definition for ‘getS3method’
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpJKn7cG/R.INSTALL7fa0721cfba8/PerseusR/man/as.ExpressionSet.matrixData.Rd:19: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJKn7cG/R.INSTALL7fa0721cfba8/PerseusR/man/as.ExpressionSet.matrixData.Rd:13: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJKn7cG/R.INSTALL7fa0721cfba8/PerseusR/man/as.matrixData.ExpressionSet.Rd:16: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpJKn7cG/R.INSTALL7fa0721cfba8/PerseusR/man/as.matrixData.ExpressionSet.Rd:10: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PerseusR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpzJYHma/R.INSTALL123c178dcb42/persiandictionary/man/dictionary-package.Rd:38: file link ‘as.roman’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/persiandictionary.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0SW6M1/R.INSTALL270cd4b89eb/peRspective/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/peRspective.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘animation.gif’
PharmPow_crossover: no visible global function definition for
  ‘read.table’
PharmPow_crossover: no visible global function definition for
  ‘write.csv’
PharmPow_crossover: no visible global function definition for ‘pdf’
PharmPow_crossover: no visible global function definition for ‘dev.off’
PharmPow_parallel: no visible global function definition for
  ‘read.table’
PharmPow_parallel: no visible global function definition for
  ‘write.csv’
PharmPow_parallel: no visible global function definition for ‘pdf’
PharmPow_parallel: no visible global function definition for ‘dev.off’
fig_PharmPow_crossover: no visible global function definition for
  ‘read.csv’
fig_PharmPow_parallel: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpI2pGO6/R.INSTALL1a9a15a6d487/phaseR/man/flowField.Rd:78: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpI2pGO6/R.INSTALL1a9a15a6d487/phaseR/man/flowField.Rd:166: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpI2pGO6/R.INSTALL1a9a15a6d487/phaseR/man/nullclines.Rd:64: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpI2pGO6/R.INSTALL1a9a15a6d487/phaseR/man/nullclines.Rd:153: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpI2pGO6/R.INSTALL1a9a15a6d487/phaseR/man/numericalSolution.Rd:62: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpI2pGO6/R.INSTALL1a9a15a6d487/phaseR/man/phasePortrait.Rd:100: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpI2pGO6/R.INSTALL1a9a15a6d487/phaseR/man/trajectory.Rd:145: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/phaseR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘test.pdf’
fox: no visible binding for global variable ‘sd’
fox: no visible global function definition for ‘cor’
fox: no visible global function definition for ‘interaction.plot’
fox: no visible global function definition for ‘reorder’
kang: no visible global function definition for ‘var’
kang: no visible binding for global variable ‘sd’
kang: no visible global function definition for ‘cor’
kang: no visible global function definition for ‘interaction.plot’
kang: no visible global function definition for ‘reorder’
nahu: no visible global function definition for ‘interaction.plot’
nahu: no visible global function definition for ‘reorder’
thsu: no visible global function definition for ‘median’
thsu: no visible binding for global variable ‘sd’
thsu: no visible global function definition for ‘cor’
thsu: no visible global function definition for ‘interaction.plot’
thsu: no visible global function definition for ‘reorder’
Undefined global functions or variables:
  cor interaction.plot median reorder sd var
Consider adding
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9Bs9De/R.INSTALL38c733509646/pheno/man/pheno.ddm.Rd:38: file link ‘matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pheno.Rcheck/00install.out’ for details.
pheno.ddm: no visible global function definition for ‘new’
pheno.flm.fit: no visible binding for global variable ‘na.exclude’
pheno.flm.fit: no visible global function definition for ‘terms’
pheno.flm.fit: no visible global function definition for ‘residuals’
pheno.flm.fit: no visible global function definition for ‘qt’
pheno.lad.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'pheno.mlm.fit.Rd':
  \examples lines wider than 100 characters:
             R <- pheno.mlm.fit(DWD)                                                         # parameter estimation
             summary(tr)$coef[2]                                                                     # slope of trend
             summary(tr)$coef[4]                                                                     # standard error of trend

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLM5ylR/R.INSTALL1e1a6f0e4cce/PhenotypeSimulator/man/correlatedBgEffects.Rd:59: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PhenotypeSimulator.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmprADdDa/R.INSTALL407299c7bf4/phonR/man/normVowels.Rd:50: file link ‘exp’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprADdDa/R.INSTALL407299c7bf4/phonR/man/normVowels.Rd:66: file link ‘colMeans’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprADdDa/R.INSTALL407299c7bf4/phonR/man/repulsiveForce.Rd:26: file link ‘log’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/phonR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Found the following significant warnings:
  Rd warning: /tmp/RtmpFHpsF7/R.INSTALL48c918933a2b/photobiology/man/merge2object_spct.Rd:45: file link ‘join’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/photobiology.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7qe8kx/R.INSTALL64642369cb43/photobiologyWavebands/man/NDVI.Rd:42: file link ‘NDxI’ in package ‘photobiology’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/photobiologyWavebands.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGND1zT/R.INSTALL623e4bac0aba/phylocanvas/man/as_tree-methods.Rd:23: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGND1zT/R.INSTALL623e4bac0aba/phylocanvas/man/as_tree-methods.Rd:24: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGND1zT/R.INSTALL623e4bac0aba/phylocanvas/man/get.descendants.Rd:10: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGND1zT/R.INSTALL623e4bac0aba/phylocanvas/man/load.tree.Rd:23: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGND1zT/R.INSTALL623e4bac0aba/phylocanvas/man/load.tree.Rd:25: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGND1zT/R.INSTALL623e4bac0aba/phylocanvas/man/load.tree.Rd:15: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGND1zT/R.INSTALL623e4bac0aba/phylocanvas/man/phylocanvas.Rd:13: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGND1zT/R.INSTALL623e4bac0aba/phylocanvas/man/phylocanvas.Rd:14: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/phylocanvas.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmptQS56e/R.INSTALL3d7a432f75f9/phyloclim/man/hypothesis.tests.Rd:28: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/phyloclim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbdP8cA/R.INSTALL14fe23e43490/phylogram/man/ladder.Rd:24: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdP8cA/R.INSTALL14fe23e43490/phylogram/man/ladder.Rd:42: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdP8cA/R.INSTALL14fe23e43490/phylogram/man/prune.Rd:45: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdP8cA/R.INSTALL14fe23e43490/phylogram/man/read.dendrogram.Rd:26: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdP8cA/R.INSTALL14fe23e43490/phylogram/man/read.dendrogram.Rd:54: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdP8cA/R.INSTALL14fe23e43490/phylogram/man/write.dendrogram.Rd:45: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/phylogram.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpkfEJBk/R.INSTALL629369f69432/phylopath/man/plot.DAG.Rd:32: file link ‘create_layout’ in package ‘ggraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkfEJBk/R.INSTALL629369f69432/phylopath/man/plot.fitted_DAG.Rd:38: file link ‘create_layout’ in package ‘ggraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkfEJBk/R.INSTALL629369f69432/phylopath/man/plot_model_set.Rd:32: file link ‘create_layout’ in package ‘ggraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/phylopath.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘INLA’
incident: no visible global function definition for ‘splinefun’
incident: no visible global function definition for ‘integrate’
phytoprod: no visible global function definition for ‘approx’
phytoprod: no visible global function definition for ‘splinefun’
phytoprod: no visible global function definition for ‘integrate’
reflectance: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
Running examples in ‘piecepackr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: piece3d
> ### Title: Draw board game pieces using rgl
> ### Aliases: piece3d
> 
> ### ** Examples
> 
> if ((Sys.getenv("TRAVIS") == "") && require("rgl")) {
+     open3d()
+     cfg <- game_systems("sans3d")$piecepack
+     piece3d("tile_back", suit = 3, rank = 3, cfg = cfg, x = 0, y = 0, z = 0)
+     piece3d("coin_back", suit = 4, rank = 2, cfg = cfg, x = 0.5, y = 0.5, z = 0.25)
+     piece3d("pawn_top", suit = 1, cfg = cfg, x = -0.5, y = 0.5, z = 0.6)
+     piece3d("die_face", suit = 3, cfg = cfg, x = -0.5, y = -0.5, z = 0.375)
+     piece3d("pyramid_top", suit = 2, rank = 3, cfg = cfg, x = 1.5, y = 0.0, z = 0.)
+ }
Loading required package: rgl
Warning in max(inds) : no non-missing arguments to max; returning -Inf
Error in rep_len(vals, max(inds)) : invalid 'length.out' value
Calls: piece3d ... <Anonymous> -> shade3d.mesh3d -> getArgs -> cbind -> repfn
Execution halted
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0Ottxj/R.INSTALL221a4eea29af/pim/man/Extract.pim.summary.Rd:20: file link ‘as.integer’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp0Ottxj/R.INSTALL221a4eea29af/pim/man/estimators.Rd:121: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9T7Bie/R.INSTALL312e4f2996cd/pinbasic/man/pin_confint.Rd:29: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8r4vU7/Rbuild34455ee0dd49/pinbasic/man/pinbasic.Rd:23: file link ‘lubridate’ in package ‘lubridate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pinbasic.Rcheck/00install.out’ for details.
plot.pred.int: no visible global function definition for ‘plot.default’
plot.pred.int: no visible global function definition for ‘axis’
plot.pred.int: no visible global function definition for ‘box’
plot.pred.int : cidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : negcidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : pi.col.fun: no visible global function definition for
  ‘gray’
plot.pred.int: no visible global function definition for ‘segments’
plot.pred.int: no visible global function definition for ‘points’
plot.pred.int: no visible global function definition for ‘abline’
pred.int: no visible binding for global variable ‘sd’
prop.test.mult: no visible global function definition for ‘qnorm’
sim.basic: no visible global function definition for ‘rbinom’
sim.basic: no visible global function definition for ‘rnorm’
t.test.mult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ggsubplot’
Found the following significant warnings:
  Rd warning: /tmp/RtmpS4z8qQ/R.INSTALL7a0073f78b95/pixiedust/man/dust.Rd:195: file link ‘glance’ in package ‘broom’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpS4z8qQ/R.INSTALL7a0073f78b95/pixiedust/man/dust.Rd:234: file link ‘tidy’ in package ‘broom’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpS4z8qQ/R.INSTALL7a0073f78b95/pixiedust/man/sprinkle.Rd:572: file link ‘latexTranslate’ in package ‘Hmisc’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpS4z8qQ/R.INSTALL7a0073f78b95/pixiedust/man/sprinkle.Rd:574: file link ‘latexTranslate’ in package ‘Hmisc’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpS4z8qQ/R.INSTALL7a0073f78b95/pixiedust/man/sprinkle.Rd:576: file link ‘latexTranslate’ in package ‘Hmisc’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpS4z8qQ/R.INSTALL7a0073f78b95/pixiedust/man/sprinkle_sanitize.Rd:87: file link ‘latexTranslate’ in package ‘Hmisc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pixiedust.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpB38rSv/R.INSTALL484a3d1538dc/pkgcond/man/dot-underscore.Rd:23: file link ‘gettextf’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pkgcond.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcond)
  > 
  > test_check("pkgcond")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (assert_that.R:34:5): .test_assert_that ───────────────────────────────
  Error: there is no package called 'assertthat'
  Backtrace:
       █
    1. ├─testthat::expect_true(assert_that(1 == 1))
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─pkgcond::assert_that(1 == 1)
    5.   └─assertthat::see_if
    6.     └─base::getExportedValue(pkg, name)
    7.       └─base::asNamespace(ns)
    8.         └─base::getNamespace(ns)
    9.           └─base::loadNamespace(name)
   10.             └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   11.               └─base:::withOneRestart(expr, restarts[[1L]])
   12.                 └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9UulMd/R.INSTALL34f5ee8da62/pkgmaker/man/messagef.Rd:25: file link ‘getOption’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9UulMd/R.INSTALL34f5ee8da62/pkgmaker/man/packages.Rd:29: file link ‘.libPaths’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9UulMd/R.INSTALL34f5ee8da62/pkgmaker/man/source_files.Rd:12: file link ‘regular expression’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pkgmaker.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmABue6/R.INSTALL398b64c57f46/pkgnet/man/DirectedGraph.Rd:9: file link ‘igraph-package’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmABue6/R.INSTALL398b64c57f46/pkgnet/man/DirectedGraph.Rd:102: file link ‘neighborhood.size’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmABue6/R.INSTALL398b64c57f46/pkgnet/man/DirectedGraph.Rd:106: file link ‘neighborhood.size’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmABue6/R.INSTALL398b64c57f46/pkgnet/man/DirectedGraphMeasures.Rd:29: file link ‘neighborhood.size’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmABue6/R.INSTALL398b64c57f46/pkgnet/man/DirectedGraphMeasures.Rd:33: file link ‘neighborhood.size’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmABue6/R.INSTALL398b64c57f46/pkgnet/man/InheritanceReporter.Rd:21: file link ‘ReferenceClasses’ in package ‘methods’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmABue6/R.INSTALL398b64c57f46/pkgnet/man/InheritanceReporter.Rd:24: file link ‘ReferenceClasses’ in package ‘methods’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pkgnet.Rcheck/00install.out’ for details.
PKmod: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable ‘jpeg’
PKadjust: no visible binding for global variable ‘bmp’
PKadjust: no visible binding for global variable ‘png’
PKadjust: no visible binding for global variable ‘tiff’
PKadjust: no visible binding for global variable ‘dev.new’
PKadjust: no visible global function definition for ‘dev.off’
PKfigure: no visible global function definition for ‘dev.cur’
PKfigure: no visible global function definition for ‘dev.off’
PKoutput: no visible global function definition for ‘heatmap’
PKoutput: no visible global function definition for
  ‘packageDescription’
PKshow: no visible global function definition for ‘browseURL’
addList1: no visible global function definition for ‘formula’
addList1.old: no visible global function definition for ‘formula’
addList2: no visible global function definition for ‘formula’
generate.plot: no visible global function definition for ‘dev.off’
writeHTML: no visible global function definition for
  ‘packageDescription’
writeLst: no visible global function definition for
  ‘packageDescription’
writeLst.tab: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for ‘quantile’
initialize,nonmem: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘Indometh_Bolus_Linear_CoreOutput.txt’
  ‘Indometh_Bolus_Log_CoreOutput.txt’
  ‘Indometh_Infusion_Linear_CoreOutput.txt’
  ‘Indometh_Infusion_Log_CoreOutput.txt’ ‘Output’
  ‘Theoph_Linear_CoreOutput.txt’ ‘Theoph_Log_CoreOutput.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpmE3wN5/R.INSTALL4172464c0ce/plainview/man/plainView.Rd:104: file link ‘SpatialPixelsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/plainview.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Malformed Description field: should contain one or more complete sentences.
bwfw.hmm: no visible global function definition for ‘dnorm’
bwfw1.hmm: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Rd file 'em.hmm.Rd':
  \examples lines wider than 100 characters:
     #all.Rlts=cbind(rbind(chr1.data,chr6.data), LIS=c(chr1.L2rlts$LIS,chr6.L2rlts$LIS), gFDR=plis.rlts$aLIS, fdr001state=plis.rlts$States)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpiBTMnY/R.INSTALL3f11fdba6b4/PLMIX/man/as.top_ordering.Rd:73: file link ‘as.rankings’ in package ‘PlackettLuce’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpiBTMnY/R.INSTALL3f11fdba6b4/PLMIX/man/gsPLMIX_to_mcmc.Rd:34: file link ‘as.mcmc’ in package ‘coda’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PLMIX.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘Formula’ ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmpVZLIYq/R.INSTALL64da22aa8757/plotluck/man/plotluck.Rd:159: file link ‘RColorBrewer’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpVZLIYq/R.INSTALL64da22aa8757/plotluck/man/plotluck.Rd:171: file link ‘plot.data.frame’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/plotluck.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmprfFr2B/R.INSTALL327e10cbf752/plot.matrix/man/assignColors.Rd:44: file link ‘heat.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprfFr2B/R.INSTALL327e10cbf752/plot.matrix/man/plot.matrix.Rd:37: file link ‘heat.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprfFr2B/R.INSTALL327e10cbf752/plot.matrix/man/plot.matrix.Rd:67: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprfFr2B/R.INSTALL327e10cbf752/plot.matrix/man/plot.matrix.Rd:105: file link ‘heat.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/plot.matrix.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
generateEnvelope: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

Rd file 'generateEnvelope.Rd':
  \examples lines wider than 100 characters:
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")
     grid.polygon(envelopeXY[,1], envelopeXY[,2], gp=gpar(fill="pink", col="transparent", lwd=5), default.units="npc")

Rd file 'tangentLine.Rd':
  \examples lines wider than 100 characters:
                     tangent <- tangentLine(centers[1,], centers[2,], r0, r[2], k=k)  # compute coefficients for the tangent line, if NA, th ... [TRUNCATED]
                             grid.abline(-tangent["c"] / tangent["b"], -tangent["a"] / tangent["b"], gp=gpar(col="blue", lwd=ii), units="npc ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4HsiU3/R.INSTALL35763e299bd0/plotscale/man/plotsize.default.Rd:35: file link ‘current.vpTree’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/plotscale.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
llla.bi: no visible global function definition for ‘as.formula’
llla.bi: no visible global function definition for ‘glm’
llla.bi: no visible global function definition for ‘binomial’
llla.bi: no visible binding for global variable ‘logit’
llla.bi: no visible global function definition for ‘vcov’
llla.bi: no visible global function definition for ‘coef’
llla.mc: no visible global function definition for ‘model.matrix’
llla.mc: no visible global function definition for ‘as.formula’
llla.mc: no visible global function definition for ‘coxph’
llla.mc: no visible global function definition for ‘vcov’
llla.mc: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘as.formula’
llla.mle: no visible global function definition for ‘glm’
llla.mle: no visible global function definition for ‘poisson’
llla.mle: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘vcov’
mclgen: no visible global function definition for ‘reshape’
simRasch.1D: no visible global function definition for ‘rnorm’
simRasch.1D: no visible global function definition for ‘runif’
vcov.sandwich.glm: no visible global function definition for
  ‘model.matrix’
vcov.sandwich.glm: no visible global function definition for ‘weights’
vcov.sandwich.glm: no visible global function definition for
  ‘residuals’
vcov.sandwich.glm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
Package suggested but not available for checking: ‘plspm’
Found the following significant warnings:
  Rd warning: /tmp/RtmpMWt5Vg/R.INSTALL3a5463cfe95e/plsmselect/man/gamlasso.Rd:87: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMWt5Vg/R.INSTALL3a5463cfe95e/plsmselect/man/summary.gamlasso.Rd:79: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/plsmselect.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpljGj2k/R.INSTALL398e5d5c7a6e/plsRglm/man/plots.confints.bootpls.Rd:42: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpljGj2k/R.INSTALL398e5d5c7a6e/plsRglm/man/plots.confints.bootpls.Rd:44: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpljGj2k/R.INSTALL398e5d5c7a6e/plsRglm/man/plots.confints.bootpls.Rd:63: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/plsRglm.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction.Rmd’
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Rd file 'predict.plus.Rd':
  \examples lines wider than 100 characters:
     extracted.values <- predict(object, lam = sort(object$lam.path[1:10],decreasing=TRUE), newx=object$x)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpRfZwMM/R.INSTALL28956e479c9a/plyr/man/rbind.fill.matrix.Rd:48: file link ‘rbind’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/plyr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpEs6tti/R.INSTALL2a854c30cf7e/pm4py/man/reexports.Rd:15: file link ‘py_to_r’ in package ‘reticulate’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpEs6tti/R.INSTALL2a854c30cf7e/pm4py/man/reexports.Rd:15: file link ‘r_to_py’ in package ‘reticulate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pm4py.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
.MCM: no visible global function definition for ‘runif’
.MCM: no visible global function definition for ‘rmultinom’
.MCM: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘optimize’
.MCM : f: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘alarm’
.igpark: no visible global function definition for ‘kmeans’
.loglik: no visible global function definition for ‘mahalanobis’
.plot.gpcm: no visible global function definition for ‘lines’
.plot.gpcm: no visible global function definition for ‘legend’
.rwgpar: no visible global function definition for ‘rexp’
.weights: no visible global function definition for ‘mahalanobis’
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize rexp rmultinom runif
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpT5yL4G/R.INSTALL2b362e31580b/pmdplyr/man/join.Rd:73: file link ‘join’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpT5yL4G/R.INSTALL2b362e31580b/pmdplyr/man/pmdplyr.Rd:21: file link ‘join’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpT5yL4G/R.INSTALL2b362e31580b/pmdplyr/man/pmdplyr.Rd:22: file link ‘join’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pmdplyr.Rcheck/00install.out’ for details.
dbm: no visible global function definition for ‘optim’
dbm: no visible global function definition for ‘new’
destat: no visible global function definition for ‘weighted.mean’
local.knn: no visible global function definition for ‘sd’
local.knn: no visible global function definition for ‘optim’
mdpref: no visible global function definition for ‘sd’
mdpref: no visible global function definition for ‘text’
mdpref: no visible global function definition for ‘lines’
phicom: no visible global function definition for ‘optim’
phicom: no visible global function definition for ‘new’
pl: no visible global function definition for ‘optim’
pl: no visible global function definition for ‘new’
rol: no visible global function definition for ‘nlm’
rol: no visible global function definition for ‘new’
wdbm: no visible global function definition for ‘optim’
wdbm: no visible global function definition for ‘new’
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/Rtmpm6zqYV/R.INSTALL2c5d19b30107/pmxTools/man/plot_scm.Rd:108: file link ‘SetNodeStyle’ in package ‘data.tree’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpm6zqYV/R.INSTALL2c5d19b30107/pmxTools/man/plot_scm.Rd:108: file link ‘SetEdgeStyle’ in package ‘data.tree’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpm6zqYV/R.INSTALL2c5d19b30107/pmxTools/man/plot_scm.Rd:119: file link ‘plot.Node’ in package ‘data.tree’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pmxTools.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for ‘pnorm’
pnmtrem1: no visible global function definition for ‘dnorm’
pnmtrem1: no visible global function definition for ‘ginv’
pnmtrem1 : fun: no visible global function definition for ‘pnorm’
pnmtrem1 : derf: no visible global function definition for ‘dnorm’
pnmtrem1 : derf: no visible global function definition for ‘pnorm’
pnmtrem1 : fun: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘TODO.md’
'library' or 'require' call to ‘rgenoud’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
smooth: no visible global function definition for ‘genoud’
Undefined global functions or variables:
  genoud
Found the following significant warnings:
  Rd warning: /tmp/RtmpX9eyya/R.INSTALL3ede1f337c98/poems/man/LatinHypercubeSampler.Rd:11: file link ‘qtri’ in package ‘metRology’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpX9eyya/R.INSTALL3ede1f337c98/poems/man/LatinHypercubeSampler.Rd:232: file link ‘qtri’ in package ‘metRology’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/poems.Rcheck/00install.out’ for details.
bipoilogMLE: no visible global function definition for ‘optim’
bipoilogMLE: no visible global function definition for ‘write.table’
poilogMLE: no visible global function definition for ‘optim’
rbipoilog : sim: no visible global function definition for ‘rnorm’
rbipoilog : sim: no visible global function definition for ‘rpois’
rpoilog : sim: no visible global function definition for ‘rnorm’
rpoilog : sim: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpr5WiEw/R.INSTALL75da554fe806/poio/man/plural_forms.Rd:36: file link ‘ISO_639_2’ in package ‘ISOcodes’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpr5WiEw/R.INSTALL75da554fe806/poio/man/po.Rd:28: file link ‘ngettext’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpr5WiEw/R.INSTALL75da554fe806/poio/man/po.Rd:32: file link ‘R6’ in package ‘R6’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpr5WiEw/R.INSTALL75da554fe806/poio/man/print.po.Rd:12: file link ‘print.tbl_df’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpr5WiEw/R.INSTALL75da554fe806/poio/man/summary.po.Rd:12: file link ‘print.data.frame’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/poio.Rcheck/00install.out’ for details.
approxMargMLE: no visible global function definition for ‘optim’
approxMargMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
approxMargMLECI: no visible global function definition for ‘uniroot’
margMLE: no visible global function definition for ‘optim’
margMLECI: no visible global function definition for ‘optim’
margMLECI : unNormLikeMinusVal: no visible global function definition
  for ‘qchisq’
margMLECI: no visible global function definition for ‘uniroot’
profMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
profMLECI: no visible global function definition for ‘uniroot’
rtbinom: no visible global function definition for ‘rbinom’
rtpois: no visible global function definition for ‘rpois’
waldCI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Packages in Depends field not imported from:
  ‘combinat’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for ‘quantile’
PS.FDR: no visible global function definition for ‘quantile’
Permu.Ind: no visible global function definition for ‘permn’
Permu.Ind: no visible global function definition for ‘hcube’
Trans.Data: no visible global function definition for ‘write.table’
Trans.Data: no visible global function definition for ‘predict’
Trans.Data: no visible global function definition for ‘lm’
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘pow.txt’
Packages in Depends field not imported from:
  ‘MASS’ ‘scatterplot3d’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for ‘layout’
plot.poLCA: no visible global function definition for ‘par’
poLCA: no visible global function definition for ‘model.frame’
poLCA: no visible global function definition for ‘model.response’
poLCA: no visible global function definition for ‘model.matrix’
poLCA: no visible global function definition for ‘runif’
poLCA: no visible global function definition for ‘ginv’
poLCA: no visible global function definition for ‘flush.console’
poLCA.makeplot.dich: no visible global function definition for
  ‘scatterplot3d’
poLCA.makeplot.poly: no visible global function definition for
  ‘scatterplot3d’
poLCA.se: no visible global function definition for ‘ginv’
poLCA.simdata: no visible global function definition for ‘runif’
poLCA.simdata: no visible global function definition for ‘rnorm’
poLCA.table: no visible global function definition for ‘model.frame’
print.poLCA: no visible global function definition for ‘pt’
print.poLCA: no visible global function definition for ‘flush.console’
rmulti: no visible global function definition for ‘runif’
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpdltral/R.INSTALL4088102852d7/PolicyPortfolios/man/pp_measures.Rd:36: file link ‘Gini’ in package ‘ineq’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PolicyPortfolios.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPomlNa/R.INSTALL40ba2b3c4f9e/polite/man/nullcoalesce.Rd:11: file link ‘%||%’ in package ‘purrr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPomlNa/R.INSTALL40ba2b3c4f9e/polite/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/polite.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pollimetrydata’
qPolyaAeppliSingle: no visible global function definition for ‘qgamma’
rPolyaAeppli: no visible global function definition for ‘rpois’
rPolyaAeppli: no visible global function definition for ‘rgeom’
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
Package vignette with placeholder title ‘Vignette Title’:
  ‘polynomials.Rmd’
Found the following files/directories:
  ‘AbsorbedDrugMetabolites’ ‘CorrelationResults’
  ‘EndogenousMetabolites’ ‘HeatMap’ ‘PKresults’
  ‘SecondAbsorbedMetabolites’ ‘preprocessed-data’
Found the following files/directories:
  ‘SPAGfreqExample2.txt’ ‘SpagInputExample.txt’ ‘SpagOutExample.txt’
  ‘SpagTemp.txt’ ‘TetrasatExample.txt’ ‘atetraexample.txt’
  ‘atetratest.txt’ ‘exampleGMoutput.txt’ ‘forPOPDIST.txt’
  ‘genodiveExample.txt’ ‘readGMtest.txt’ ‘strtemp.txt’ ‘structtest.txt’
  ‘testGenoDive2.txt’ ‘testGenoDive3.txt’ ‘testPOPDIST.txt’
  ‘tetrasattest.txt’
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpFz6jyc/R.INSTALL436a36098971/polywog/man/plot.polywog.Rd:35: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/polywog.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmptQe616/R.INSTALL427b6a19fb91/pomdp/man/plot_policy_graph.Rd:49: file link ‘visIgraph’ in package ‘visNetwork’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmptQe616/R.INSTALL427b6a19fb91/pomdp/man/plot_policy_graph.Rd:109: file link ‘visIgraph’ in package ‘visNetwork’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pomdp.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘matrixcalc’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘matrixcalc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for ‘pnorm’
print.pom: no visible global function definition for ‘pnorm’
siteocc : get.mod.matrix: no visible binding for global variable
  ‘na.pass’
siteocc : get.mod.matrix: no visible global function definition for
  ‘formula’
siteocc : get.mod.matrix: no visible global function definition for
  ‘model.matrix’
siteocc: no visible global function definition for ‘nlminb’
siteocc: no visible global function definition for
  ‘is.positive.definite’
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Non-standard file/directory found at top level:
  ‘extdata’
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'popgen.Rd':
  \usage lines wider than 90 characters:
     popgen(datafile, ndigit = 3, freq.overall = T, freq.by.pop = T, genetic.stats = T, pairwise.fst = T)

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘WhopGenome’
asymmetricIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘lm’
bonferroniIntervals: no visible global function definition for
  ‘predict’
bootstrapIntervals: no visible global function definition for ‘stack’
component1a: no visible global function definition for ‘pnorm’
component1b: no visible global function definition for ‘pnorm’
component2: no visible global function definition for ‘dgamma’
eqnForMin: no visible global function definition for ‘pnorm’
eqnForMin: no visible global function definition for ‘integrate’
integrand : <anonymous>: no visible global function definition for
  ‘pnorm’
integrand: no visible global function definition for ‘dnorm’
integrate2: no visible global function definition for ‘integrate’
integrate2a: no visible global function definition for ‘integrate’
integrate2b: no visible global function definition for ‘integrate’
integrate4a: no visible global function definition for ‘integrate’
integrate4b: no visible global function definition for ‘integrate’
optimalCScalar2: no visible global function definition for ‘uniroot’
optimalLambda: no visible global function definition for ‘optimise’
optimalLambdaC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpJPEJJF/R.INSTALL476b59752c65/poptrend/man/poptrend.Rd:17: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/poptrend.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpah6E72/R.INSTALL309b76ea4e69/portalr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/portalr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/BoxPierce.Rd:51: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/BoxPierce.Rd:55: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/BoxPierce.Rd:72: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/Hosking.Rd:65: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/LiMcLeod.Rd:65: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/LjungBox.Rd:53: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/LjungBox.Rd:57: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/LjungBox.Rd:74: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/MahdiMcLeod.Rd:94: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp1vvm7g/R.INSTALL312f20aee3b8/portes/man/portest.Rd:169: file link ‘Box.test’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/portes.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpesSxDz/R.INSTALL1d00bca98a/postGIStools/man/get_postgis_query.Rd:30: file link ‘sp’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/postGIStools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitBvGPD.Rd:121: file link ‘retlev.bvpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitBvGPD.Rd:122: file link ‘convassess.bvpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitGPD.Rd:63: file link ‘plot.uvpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitGPD.Rd:64: file link ‘confint.uvpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitGPD.Rd:67: file link ‘retlev.uvpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitGPD.Rd:68: file link ‘qq.uvpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitGPD.Rd:69: file link ‘pp.uvpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitGPD.Rd:70: file link ‘dens.uvpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitGPD.Rd:71: file link ‘convassess.uvpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitMcGPD.Rd:133: file link ‘retlev.mcpot’ in package ‘POT’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp821YWr/R.INSTALL515318775ed2/POT/man/fitMcGPD.Rd:134: file link ‘convassess.mcpot’ in package ‘POT’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/POT.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
fnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize pnorm points qnorm rexp rnorm uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpo8uhhc/R.INSTALL587e1c1b8d42/ppcc/man/ppccTest.Rd:268: file link ‘qgumbel’ in package ‘VGAM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpo8uhhc/R.INSTALL587e1c1b8d42/ppcc/man/ppccTest.Rd:269: file link ‘qgev’ in package ‘VGAM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ppcc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7px8DA/R.INSTALL47844244e8d9/ppcong/man/P.Rd:10: file link ‘%P%’ in package ‘tfse’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ppcong.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘dev’
Malformed Description field: should contain one or more complete sentences.
TT.test : <anonymous>: no visible global function definition for
  ‘t.test’
TT.test: no visible binding for global variable ‘sd’
TT.test: no visible global function definition for ‘setNames’
kirjelda : combo: no visible binding for global variable ‘sd’
kor.tabel: no visible binding for global variable ‘cor.test’
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpL0TPyR/R.INSTALL345e17ab983f/precisely/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/precisely.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
gausspred: no visible global function definition for ‘qt’
mvapred: no visible global function definition for ‘qt’
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘DESCRIPTION.bck’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘predmixcor/R/firstlib.r’:
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for ‘dbinom’
abs_cor: no visible global function definition for ‘cor’
gen.alpha.IGamma: no visible global function definition for ‘qgamma’
gendata.mix: no visible global function definition for ‘runif’
gendata.mix: no visible global function definition for ‘rbeta’
mh1.unif: no visible global function definition for ‘runif’
train_predict_mix: no visible global function definition for ‘dbinom’
training: no visible global function definition for ‘runif’
training: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCBFgyu/R.INSTALL571d5943ca62/pre/man/coef.gpe.Rd:22: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCBFgyu/R.INSTALL571d5943ca62/pre/man/coef.pre.Rd:22: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCBFgyu/R.INSTALL571d5943ca62/pre/man/corplot.Rd:55: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pre.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
Package suggested but not available for checking: ‘INLA’
basisplot: no visible global function definition for ‘abline’
basisplot: no visible global function definition for ‘text’
basisplot: no visible global function definition for ‘par’
plot.prinsimp: no visible global function definition for ‘screeplot’
plot.simpart: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘strwidth’
simpart.formula: no visible global function definition for ‘terms’
simpart.formula: no visible global function definition for
  ‘model.matrix’
varperc: no visible global function definition for ‘lines’
varperc: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘points’
varsimp: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines model.matrix par points screeplot strwidth terms text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "points", "strwidth",
             "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘priorcd.Rmd’
Found the following files/directories:
  ‘network.html’ ‘network_files’
Packages suggested but not available for checking: 'gurobi', 'rcbc'
Found the following significant warnings:
  Rd warning: /tmp/Rtmp1gA5h2/R.INSTALL4a6f12edcc53/prioritylasso/man/pl_data.Rd:26: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/prioritylasso.Rcheck/00install.out’ for details.
pr.conditional: no visible global function definition for ‘qnorm’
pr.marginal: no visible global function definition for ‘qnorm’
prLogisticDelta: no visible global function definition for ‘glm’
prLogisticDelta: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpVuj5nm/R.INSTALL538b81d41ba/probably/man/reexports.Rd:15: file link ‘as.factor’ in package ‘generics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpVuj5nm/R.INSTALL538b81d41ba/probably/man/reexports.Rd:15: file link ‘as.ordered’ in package ‘generics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/probably.Rcheck/00install.out’ for details.
.pfda.fstep: no visible global function definition for ‘dist’
.pfda.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov dist
Consider adding
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLSikXR/R.INSTALL515972a168bc/prob/man/CharFunc.Rd:108: file link ‘kummerM’ in package ‘fAsianOptions’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLSikXR/R.INSTALL515972a168bc/prob/man/CharFunc.Rd:155: file link ‘kummerU’ in package ‘fAsianOptions’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLSikXR/R.INSTALL515972a168bc/prob/man/CharFunc.Rd:318: file link ‘kummerM’ in package ‘fAsianOptions’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLSikXR/R.INSTALL515972a168bc/prob/man/CharFunc.Rd:319: file link ‘kummerU’ in package ‘fAsianOptions’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/prob.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
GPois: no visible global function definition for ‘dnorm’
GPois: no visible binding for global variable ‘poisson’
GPois: no visible global function definition for ‘predict’
GPois: no visible global function definition for ‘fitted’
GPois: no visible global function definition for ‘residuals’
GPois: no visible global function definition for ‘smooth.spline’
ProDenICA: no visible global function definition for ‘rnorm’
d.gaussmix: no visible global function definition for ‘dnorm’
djordan: no visible global function definition for ‘dt’
djordan: no visible global function definition for ‘dunif’
mixmat: no visible global function definition for ‘rnorm’
mixmat: no visible global function definition for ‘runif’
r.gaussmix: no visible global function definition for ‘rmultinom’
r.gaussmix: no visible global function definition for ‘rnorm’
rjordan: no visible global function definition for ‘rt’
rjordan: no visible global function definition for ‘runif’
rmix.dexp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm dt dunif fitted poisson predict residuals rmultinom rnorm rt
  runif smooth.spline
Consider adding
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  ‘splines’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for ‘survfit’
IndividualPROC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpE63Kn4/R.INSTALL584851851351/projects/man/display_metadata.Rd:81: file link ‘left_join’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE63Kn4/R.INSTALL584851851351/projects/man/export_project.Rd:15: file link ‘zipr’ in package ‘zip’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE63Kn4/R.INSTALL584851851351/projects/man/export_project.Rd:31: file link ‘zipr’ in package ‘zip’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE63Kn4/R.INSTALL584851851351/projects/man/file_management.Rd:82: file link ‘openProject’ in package ‘rstudioapi’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE63Kn4/R.INSTALL584851851351/projects/man/file_management.Rd:116: file link ‘openProject’ in package ‘rstudioapi’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE63Kn4/R.INSTALL584851851351/projects/man/new_edit_delete.Rd:151: file link ‘as_datetime’ in package ‘lubridate’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE63Kn4/R.INSTALL584851851351/projects/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE63Kn4/R.INSTALL584851851351/projects/man/save_session_info.Rd:12: file link ‘dir_create’ in package ‘fs’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/projects.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbEmuFv/R.INSTALL4d673b59419c/projmgr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/projmgr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmX455M/R.INSTALL171274861a1f/projpred/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/projpred.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘SDMTools’
addpi: no visible global function definition for ‘lines’
genPerms: no visible global function definition for ‘combn’
getVar: no visible global function definition for ‘glm’
getVar: no visible global function definition for ‘binomial’
getVar: no visible global function definition for ‘var’
pba: no visible global function definition for ‘glm’
pba: no visible global function definition for ‘binomial’
pba: no visible global function definition for ‘predict’
pba: no visible global function definition for ‘rbinom’
pcr: no visible global function definition for ‘quantile’
plotpi: no visible global function definition for ‘axis’
plotpi: no visible global function definition for ‘abline’
plotpi: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline axis binomial combn glm lines predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addIonSatistics: no visible binding for global variable ‘median’
adjustOne: no visible binding for global variable ‘median’
attachModifications: no visible global function definition for
  ‘na.omit’
avrgLoadingCalculation: no visible binding for global variable ‘median’
channelResponses : estimate: no visible binding for global variable
  ‘var’
responseStatisics : func: no visible global function definition for
  ‘aggregate’
testing: no visible global function definition for ‘aov’
testingOneshot: no visible global function definition for ‘anova’
testingTukey: no visible global function definition for ‘TukeyHSD’
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘class’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘class’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for ‘lines’
addclassifierboundary: no visible global function definition for ‘par’
addclassifierboundary: no visible global function definition for
  ‘contour’
plot.protoclass: no visible global function definition for ‘box’
plot.protoclass: no visible global function definition for ‘rgb2hsv’
plot.protoclass: no visible global function definition for ‘col2rgb’
plot.protoclass: no visible global function definition for ‘points’
plot.protoclass: no visible global function definition for ‘hsv’
predict.protoclass: no visible global function definition for ‘knn1’
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "points")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘doc’
Extract_plant_grapevine_function: no visible global function definition
  for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUgFikz/R.INSTALL52d424f0dc6c/protolite/man/geobuf.Rd:21: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/protolite.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpiykmaU/R.INSTALL258b7d0d7b68/ProTrackR/man/playWave.Rd:25: file link ‘$.audioInstance’ in package ‘audio’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpiykmaU/R.INSTALL258b7d0d7b68/ProTrackR/man/read.module.Rd:22: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpiykmaU/R.INSTALL258b7d0d7b68/ProTrackR/man/read.module.Rd:22: file link ‘url’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpiykmaU/R.INSTALL258b7d0d7b68/ProTrackR/man/resample.Rd:18: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpiykmaU/R.INSTALL258b7d0d7b68/ProTrackR/man/resample.Rd:32: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpiykmaU/R.INSTALL258b7d0d7b68/ProTrackR/man/write.module.Rd:18: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ProTrackR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmphoqeWl/R.INSTALL786d3b52d2d8/protViz/man/mascot.rd:72: file link ‘xmlParse’ in package ‘XML’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/protViz.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package vignette with placeholder title ‘Vignette Title’:
  ‘TargetDecoyFDR_Example.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpzMnEAm/R.INSTALL509953519763/prt/man/formatting.Rd:50: file link ‘tbl_sum’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzMnEAm/R.INSTALL509953519763/prt/man/glimpse.Rd:33: file link ‘glimpse’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzMnEAm/R.INSTALL509953519763/prt/man/glimpse.Rd:39: file link ‘glimpse’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzMnEAm/R.INSTALL509953519763/prt/man/glimpse.Rd:43: file link ‘glimpse’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzMnEAm/R.INSTALL509953519763/prt/man/glimpse.Rd:46: file link ‘glimpse’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzMnEAm/R.INSTALL509953519763/prt/man/subsetting.Rd:28: file link ‘backtick’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/prt.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/hurdle.Rd:81: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/hurdle.Rd:96: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/hurdle.Rd:163: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/hurdle.control.Rd:37: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/predict.hurdle.Rd:67: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/predict.zeroinfl.Rd:67: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/zeroinfl.Rd:77: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/zeroinfl.Rd:90: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/zeroinfl.Rd:155: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp78LySH/R.INSTALL40dc2a951f/pscl/man/zeroinfl.control.Rd:37: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pscl.Rcheck/00install.out’ for details.
mahalanobisComposite: no visible global function definition for
  ‘princomp’
prepareComposite: no visible global function definition for ‘cov’
winsorizor : f: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘PSF_vignette.Rmd’
'library' or 'require' call to ‘numDeriv’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for ‘grad’
test.problem: no visible global function definition for ‘new’
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for ‘new’
show,test.result: no visible global function definition for ‘show’
show,test.result: no visible global function definition for ‘sd’
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for ‘pt’
spearman.test: no visible global function definition for
  ‘complete.cases’
spearman.test: no visible global function definition for ‘cor’
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘orig’
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpsoMhd3/R.INSTALL7d943abf59df/PSSMCOOL/man/Discrete_Cosine_Transform.Rd:17: file link ‘dct’ in package ‘dtt’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpsoMhd3/R.INSTALL7d943abf59df/PSSMCOOL/man/dwt_PSSM.Rd:16: file link ‘dwt.nondyadic’ in package ‘waveslim’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PSSMCOOL.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘EffectsRelBaseline’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable ‘sumSqCat’
compExclusionFraction: no visible global function definition for
  ‘rpois’
compExclusionFraction: no visible global function definition for
  ‘t.test’
compExclusionFraction: no visible global function definition for ‘glm’
compExclusionFraction: no visible global function definition for
  ‘anova’
compPowerCatSelectivity: no visible binding for global variable
  ‘fRatioStat’
compPowerGeneralRespDetection: no visible binding for global variable
  ‘sumSqCat’
compPowerRespDetection: no visible binding for global variable
  ‘sumSqCat’
compRejectionFraction: no visible global function definition for
  ‘rpois’
compRejectionFraction: no visible global function definition for
  ‘t.test’
compRejectionFraction: no visible global function definition for ‘glm’
compRejectionFraction: no visible global function definition for
  ‘anova’
simCatResp: no visible global function definition for ‘rpois’
simNormCatResp: no visible global function definition for ‘rnorm’
testCatEffectBoot: no visible global function definition for ‘boot’
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnLsBb0/R.INSTALL3c614291d644/psychmeta/man/correct_d_bias.Rd:31: file link ‘gamma’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnLsBb0/R.INSTALL3c614291d644/psychmeta/man/correct_glass_bias.Rd:33: file link ‘gamma’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnLsBb0/R.INSTALL3c614291d644/psychmeta/man/print.Rd:19: file link ‘print.tbl’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnLsBb0/R.INSTALL3c614291d644/psychmeta/man/print.Rd:21: file link ‘print.tbl’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpnLsBb0/R.INSTALL3c614291d644/psychmeta/man/print.Rd:23: file link ‘print.tbl’ in package ‘tibble’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/psychmeta.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘multilevel’ ‘nlme’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘README.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3AtLRM/R.INSTALL7f026abd9785/psychomix/man/raschmix.Rd:66: file link ‘RaschModel.fit’ in package ‘psychotools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/psychomix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpHzAjSf/R.INSTALL6a6c432ac2e0/psychotools/man/btmodel.Rd:38: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTP5vNv/Rbuild6efbcff9115/psychotools/man/gpcmodel.Rd:30: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHzAjSf/R.INSTALL6a6c432ac2e0/psychotools/man/pcmodel.Rd:28: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpTP5vNv/Rbuild6efbcff9115/psychotools/man/plmodel.Rd:32: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHzAjSf/R.INSTALL6a6c432ac2e0/psychotools/man/raschmodel.Rd:28: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHzAjSf/R.INSTALL6a6c432ac2e0/psychotools/man/rsmodel.Rd:28: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/psychotools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/bttree.Rd:31: file link ‘na.pass’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/mpttree.Rd:31: file link ‘na.pass’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/pctree.Rd:60: file link ‘plot.modelparty’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/pctree.Rd:60: file link ‘plot.party’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/raschtree.Rd:57: file link ‘plot.modelparty’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/raschtree.Rd:57: file link ‘plot.party’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/rstree.Rd:60: file link ‘plot.modelparty’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/rstree.Rd:60: file link ‘plot.party’ in package ‘partykit’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/psychotree.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpsOntTL/R.INSTALL4825493645ac/psychTools/man/cubits.Rd:25: file link ‘table2df’ in package ‘psych’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpsOntTL/R.INSTALL4825493645ac/psychTools/man/heights.Rd:19: file link ‘table2df’ in package ‘psych’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpsOntTL/R.INSTALL4825493645ac/psychTools/man/psychTools.Rd:7: file link ‘psych’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/psychTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYnqjcn/R.INSTALL57431d9b6014/psymonitor/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/psymonitor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp6iYlUM/R.INSTALL729c63337e78/psyosphere/man/about_common_mistakes.Rd:36: file link ‘wtd.mean’ in package ‘Hmisc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/psyosphere.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpjn4mp2/R.INSTALL1f449d08c71/PtProcess/man/Changes.Rd:89: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjn4mp2/R.INSTALL1f449d08c71/PtProcess/man/makeSOCKcluster.Rd:20: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjn4mp2/R.INSTALL1f449d08c71/PtProcess/man/plot.Rd:8: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PtProcess.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘R.utils’ ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for ‘pchisq’
plot_chase_observed_expected: no visible global function definition for
  ‘meta.MH’
plot_chase_observed_expected: no visible global function definition for
  ‘txtProgressBar’
plot_chase_observed_expected: no visible global function definition for
  ‘setTxtProgressBar’
test.one.treated: no visible global function definition for
  ‘fisher.test’
test_one: no visible global function definition for ‘rbinom’
test_one: no visible global function definition for ‘fisher.test’
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpMkaCOZ/R.INSTALL5f8f18fc90f8/publipha/man/ExtractParameters.Rd:45: file link ‘extract’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/publipha.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
PurBayes: no visible global function definition for ‘update’
PurBayes: no visible global function definition for ‘sd’
plot.PurBayes: no visible global function definition for ‘quantile’
plot.PurBayes: no visible global function definition for ‘lines’
summary.PurBayes : <anonymous>: no visible global function definition
  for ‘quantile’
Undefined global functions or variables:
  lines quantile sd update
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp23VSiq/R.INSTALL611469de6b0a/pushbar/man/pushbar.Rd:21: file link ‘tags’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pushbar.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpFONqXP/R.INSTALL70e95631f70b/pvclust/man/pvclust.Rd:154: file link ‘package_version’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pvclust.Rcheck/00install.out’ for details.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for ‘na.omit’
Committee.getCommittee : <anonymous>: no visible global function
  definition for ‘na.omit’
getAllBios: no visible global function definition for ‘txtProgressBar’
getAllBios: no visible global function definition for
  ‘setTxtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘txtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘setTxtProgressBar’
getAllVotes: no visible global function definition for ‘txtProgressBar’
getAllVotes: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
.grid.matrix: no visible global function definition for ‘slot’
.matrix2grid: no visible global function definition for ‘as’
.poly2grid: no visible global function definition for ‘is’
.poly2grid: no visible global function definition for ‘slot’
.poly2grid: no visible global function definition for ‘as’
.pycno.core : smooth2D : s1d: no visible global function definition for
  ‘filter’
.pycno.core: no visible global function definition for ‘flush.console’
.pycno2matrix: no visible global function definition for ‘slot’
Undefined global functions or variables:
  as filter flush.console is slot
Consider adding
  importFrom("methods", "as", "is", "slot")
  importFrom("stats", "filter")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7ONVCk/R.INSTALLd635dc3a21d/Q7/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Q7.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
csQCAbinTest: no visible global function definition for ‘p.adjust’
fsQCApermTest: no visible global function definition for ‘p.adjust’
mvQCAbinTest: no visible global function definition for ‘p.adjust’
p.threshold.adjust: no visible global function definition for
  ‘p.adjust’
plot.fsQCApt: no visible global function definition for ‘dev.cur’
plot.fsQCApt: no visible global function definition for ‘dev.new’
plot.fsQCApt: no visible global function definition for ‘par’
plot.fsQCApt: no visible global function definition for ‘density’
plot.fsQCApt: no visible global function definition for ‘axis’
plot.fsQCApt: no visible global function definition for ‘polygon’
plot.fsQCApt: no visible global function definition for ‘points’
plot.fsQCApt: no visible global function definition for ‘hist’
summary.csQCAbt: no visible global function definition for
  ‘printCoefmat’
summary.fsQCApt: no visible global function definition for
  ‘printCoefmat’
summary.mvQCAbt: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "points", "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpqGkjQo/R.INSTALL63eb6a03a1b9/QCA/man/chartFunctions.Rd:50: file link ‘translate’ in package ‘admisc’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpqGkjQo/R.INSTALL63eb6a03a1b9/QCA/man/generate.Rd:33: file link ‘expand’ in package ‘admisc’ does not exist and so has been treated as a topic
  Rd warning: /private/var/folders/0z/p7shdp895pvfdqpgnww60_7c0000gp/T/RtmpsUHT8F/Rbuild182e47d306a8/QCA/man/pof.Rd:143: file link ‘translate’ in package ‘admisc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/QCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpfKfoAY/R.INSTALL3ff1538285b2/QCAtools/man/plot.qca.Rd:10: file link ‘eqmcc’ in package ‘QCA’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/QCAtools.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘EWAS_QC_graph_effectsize.png’ ‘EWAS_QC_graph_precision.png’
  ‘EWAS_QC_legend.txt’ ‘sample1.txt.gz’ ‘sample2.txt.gz’
  ‘sample_map.txt.gz’ ‘sample_output.graph_M.png’
  ‘sample_output.graph_QQ.png’ ‘sample_output.graph_p.png’
  ‘sample_output.graph_volcano.png’ ‘sample_output.histo.png’
  ‘sample_output.txt’ ‘sample_output1.graph_M.png’
  ‘sample_output1.graph_QQ.png’ ‘sample_output1.graph_p.png’
  ‘sample_output1.graph_volcano.png’ ‘sample_output1.histo.png’
  ‘sample_output2.graph_M.png’ ‘sample_output2.graph_QQ.png’
  ‘sample_output2.graph_p.png’ ‘sample_output2.graph_volcano.png’
  ‘sample_output2.histo.png’ ‘translation_table.txt’
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘sample_QQ.png’ ‘sample_QQ1.png’ ‘sample_QQ2.png’ ‘sample_QQ3.png’
  ‘sample_distribution.png’ ‘sample_graph_p-correlation.png’
  ‘sample_histogram.png’ ‘sample_histogram1.png’
  ‘sample_histogram2.png’ ‘sample_histogram3.png’
  ‘sample_plots_graph_M.png’ ‘sample_plots_graph_QQ.png’
  ‘sample_precision.png’ ‘sample_regional_association.png’
  ‘sample_skewness_kurtosis.png’
Found the following significant warnings:
  Rd warning: /tmp/RtmpMxUaqH/R.INSTALL41a26a92d3a8/qdapTools/man/id.Rd:26: file link ‘ncol’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMxUaqH/R.INSTALL41a26a92d3a8/qdapTools/man/lookup_e.Rd:97: file link ‘new.env’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMxUaqH/R.INSTALL41a26a92d3a8/qdapTools/man/mtabulate.Rd:41: file link ‘counts2list’ in package ‘qdapTools’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMxUaqH/R.INSTALL41a26a92d3a8/qdapTools/man/split_vector.Rd:24: file link ‘grepl’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMxUaqH/R.INSTALL41a26a92d3a8/qdapTools/man/timeconv.Rd:32: file link ‘times’ in package ‘chron’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qdapTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIjUT33/R.INSTALL4da31daab701/qgraph/man/centrality_auto.Rd:9: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIjUT33/R.INSTALL4da31daab701/qgraph/man/clustcoef_auto.Rd:34: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIjUT33/R.INSTALL4da31daab701/qgraph/man/qgraph.Rd:36: file link ‘cov2cor’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIjUT33/R.INSTALL4da31daab701/qgraph/man/qgraph.Rd:41: file link ‘corr.p’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qgraph.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpS7ZtkB/R.INSTALL56b5dc11244/qiitr/man/qiita_api.Rd:36: file link ‘httr’ in package ‘httr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qiitr.Rcheck/00install.out’ for details.
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.matrix’
chooseMDoubleBootstrap: no visible global function definition for
  ‘as.formula’
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.frame’
chooseMDoubleBootstrap: no visible global function definition for ‘lm’
chooseMDoubleBootstrap: no visible global function definition for
  ‘coef’
chooseMDoubleBootstrap: no visible global function definition for
  ‘quantile’
chooseMDoubleBootstrap: no visible global function definition for
  ‘qnorm’
getModel: no visible global function definition for ‘lm’
getModel: no visible global function definition for ‘model.matrix’
getModel: no visible global function definition for ‘as.formula’
getModel: no visible global function definition for ‘model.frame’
getModel: no visible global function definition for ‘model.response’
getModel: no visible global function definition for ‘coef’
getModel: no visible global function definition for ‘qnorm’
qLearn: no visible global function definition for ‘model.matrix’
qLearn: no visible global function definition for ‘as.formula’
qLearn: no visible global function definition for ‘model.frame’
qLearn: no visible global function definition for ‘coef’
qLearn: no visible global function definition for ‘lm’
qLearn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4KDlM0/R.INSTALL671a24837b1d/qmethod/man/import.easyhtmlq.Rd:9: file link ‘read.csv2’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4KDlM0/R.INSTALL671a24837b1d/qmethod/man/import.htmlq.Rd:9: file link ‘read.csv2’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4KDlM0/R.INSTALL671a24837b1d/qmethod/man/plot.QmethodRes.Rd:18: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4KDlM0/R.INSTALL671a24837b1d/qmethod/man/plot.QmethodRes.Rd:27: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qmethod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpd0oHwY/R.INSTALL67c628cca08c/qmix/man/plot_trace.qmix.Rd:12: file link ‘traceplot’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qmix.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
pcAxisCubeMake: no visible global function definition for ‘aggregate’
pcAxisCubeToCSV: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘datInSFexample6_1pxCube.csv’ ‘datInSFexample6_1pxCubeA0.csv ’
  ‘datInSFexample6_1pxCubeA1.csv ’ ‘datInSFexample6_1pxCubeData.csv ’
  ‘datInSFexample6_1pxCubeVariable.csv’
  ‘datInSFexample6_1pxCubeVariableDomain.csv’
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
Found the following significant warnings:
  Rd warning: /tmp/Rtmps7eE0l/R.INSTALL67964c56578a/qqplotr/man/stat_qq_band.Rd:116: file link ‘s_Qn’ in package ‘robustbase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qqplotr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5TN3nT/R.INSTALL57ce5a8b79db/QRegVCM/man/AHeVT.Rd:82: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5TN3nT/R.INSTALL57ce5a8b79db/QRegVCM/man/AHeVXT.Rd:84: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5TN3nT/R.INSTALL57ce5a8b79db/QRegVCM/man/QRIndiv.Rd:74: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5TN3nT/R.INSTALL57ce5a8b79db/QRegVCM/man/QRSimul.Rd:79: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5TN3nT/R.INSTALL57ce5a8b79db/QRegVCM/man/QRStepwise.Rd:80: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5TN3nT/R.INSTALL57ce5a8b79db/QRegVCM/man/QRWSimul.Rd:81: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5TN3nT/R.INSTALL57ce5a8b79db/QRegVCM/man/simul_shapetest.Rd:101: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp5TN3nT/R.INSTALL57ce5a8b79db/QRegVCM/man/test_variability.Rd:113: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/QRegVCM.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
ci.length: no visible global function definition for ‘qexp’
detectable.bc: no visible global function definition for ‘uniroot’
detectable.f2: no visible global function definition for ‘uniroot’
detectable.ri: no visible global function definition for ‘uniroot’
nu: no visible global function definition for ‘pnorm’
nullinfo: no visible global function definition for ‘qnorm’
nullinfo: no visible global function definition for ‘dnorm’
optselection.bc: no visible global function definition for ‘optimize’
optselection.f2: no visible global function definition for ‘optimize’
optspacing.bc: no visible global function definition for ‘optim’
optspacing.bc: no visible global function definition for ‘optimize’
optspacing.f2: no visible global function definition for ‘optim’
optspacing.f2: no visible global function definition for ‘optimize’
powercalc.bc: no visible global function definition for ‘pchisq’
powercalc.f2: no visible global function definition for ‘pchisq’
samplesize.bc: no visible global function definition for ‘uniroot’
samplesize.f2: no visible global function definition for ‘uniroot’
samplesize.ri: no visible global function definition for ‘uniroot’
tailprob: no visible global function definition for ‘pchisq’
thresh: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCE8ybe/R.INSTALL4086ed2f2a1/qtlnet/man/igraph.Rd:50: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpCE8ybe/R.INSTALL4086ed2f2a1/qtlnet/man/igraph.Rd:66: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qtlnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp10hdeF/R.INSTALL64f73a9c1cbb/qtl/man/addmarker.Rd:28: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qtl.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘Rmpfr’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
quadp: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
alphaf: no visible global function definition for ‘pchisq’
alphaf: no visible global function definition for ‘dbinom’
conout: no visible global function definition for ‘sd’
ibgaout: no visible global function definition for ‘qnorm’
ibgaout: no visible global function definition for ‘pnorm’
plot.qualint: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘rnorm’
powerval: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘pnorm’
print.expplot: no visible global function definition for ‘gray’
print.expplot: no visible binding for global variable ‘coef’
print.outplot: no visible global function definition for ‘gray’
print.outplot: no visible binding for global variable ‘coef’
qualint: no visible global function definition for ‘qnorm’
qualval: no visible global function definition for ‘qnorm’
surout: no visible global function definition for ‘tail’
surout: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef dbinom gray pchisq pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9GQYl0/R.INSTALL2f77526d4d81/qualpalr/man/plot.qualpal.Rd:13: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp9GQYl0/R.INSTALL2f77526d4d81/qualpalr/man/plot.qualpal.Rd:26: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qualpalr.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpE6Smdj/R.INSTALL5f6c38de3b3b/QUALYPSO/man/plotQUALYPSOTotalVarianceByScenario.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE6Smdj/R.INSTALL5f6c38de3b3b/QUALYPSO/man/plotQUALYPSOTotalVarianceDecomposition.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE6Smdj/R.INSTALL5f6c38de3b3b/QUALYPSO/man/plotQUALYPSOeffect.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE6Smdj/R.INSTALL5f6c38de3b3b/QUALYPSO/man/plotQUALYPSOgrandmean.Rd:26: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/QUALYPSO.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpbdpCmS/R.INSTALL5fb542abe58e/qualypsoss/man/plotQUALYPSOSSClimateChangeResponse.Rd:22: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdpCmS/R.INSTALL5fb542abe58e/qualypsoss/man/plotQUALYPSOSSClimateResponse.Rd:21: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdpCmS/R.INSTALL5fb542abe58e/qualypsoss/man/plotQUALYPSOSSTotalVarianceByScenario.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdpCmS/R.INSTALL5fb542abe58e/qualypsoss/man/plotQUALYPSOSSTotalVarianceDecomposition.Rd:23: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdpCmS/R.INSTALL5fb542abe58e/qualypsoss/man/plotQUALYPSOSSeffect.Rd:31: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbdpCmS/R.INSTALL5fb542abe58e/qualypsoss/man/plotQUALYPSOSSgrandmean.Rd:26: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/qualypsoss.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Non-standard file/directory found at top level:
  ‘README.txt’
Rd file 'graph.mod.Rd':
  \usage lines wider than 90 characters:
     graph.mod(ssmod, x, y, data, title = "", xlab = "Centered X", ylab = "Raw Y", ylimit = 1.5, ...)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Judge.pdf’
Found the following significant warnings:
  Rd warning: /tmp/RtmpTqlJCG/R.INSTALL5fc046f1e68d/quantspec/man/ClippedFT-class.Rd:21: file link ‘mvfft’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/quantspec.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpx8hsR1/R.INSTALL43ec45a50800/QuantTools/man/plot_ts.Rd:21: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpx8hsR1/R.INSTALL43ec45a50800/QuantTools/man/plot_ts.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/QuantTools.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Example’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpjta92e/R.INSTALL1f9116643361/questionr/man/addNAstr.Rd:40: file link ‘addNA’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpjta92e/R.INSTALL1f9116643361/questionr/man/wtd.table.Rd:57: file link ‘wtd.table’ in package ‘Hmisc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/questionr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘fastshp’
Found the following significant warnings:
  Rd warning: /tmp/RtmpKnG1BB/R.INSTALL5ae42f4f41c1/quickPlot/man/getSetColors.Rd:130: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKnG1BB/R.INSTALL5ae42f4f41c1/quickPlot/man/getSetColors.Rd:132: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKnG1BB/R.INSTALL5ae42f4f41c1/quickPlot/man/getSetColors.Rd:133: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/quickPlot.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpMXw9RX/R.INSTALL6dd14cd88d25/quickReg/man/reg.Rd:30: file link ‘confint.glm’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXw9RX/R.INSTALL6dd14cd88d25/quickReg/man/reg_x.Rd:30: file link ‘confint.glm’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMXw9RX/R.INSTALL6dd14cd88d25/quickReg/man/reg_y.Rd:25: file link ‘confint.glm’ in package ‘MASS’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/quickReg.Rcheck/00install.out’ for details.
mutualCoherence : .setOneMutualP: no visible global function definition
  for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ReGenesees’
conf2d.default: no visible global function definition for ‘polygon’
conf2d_int: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘R2DGC.Rmd’
'library' or 'require' call to ‘rgdal’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘matrixStats’ ‘rgdal’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘ndvi.rgf’
Found the following files/directories:
  ‘output.html’
Found the following significant warnings:
  Rd warning: /tmp/RtmpQk8FKj/R.INSTALLbfe142e59a8/R2jags/man/attach.jags.Rd:8: file link ‘attach.bugs’ in package ‘R2WinBUGS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpQk8FKj/R.INSTALLbfe142e59a8/R2jags/man/attach.jags.Rd:8: file link ‘detach.bugs’ in package ‘R2WinBUGS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpQk8FKj/R.INSTALLbfe142e59a8/R2jags/man/attach.jags.Rd:32: file link ‘attach.bugs’ in package ‘R2WinBUGS’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R2jags.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmprsstYg/R.INSTALL2e58189ed201/R2OpenBUGS/man/bugs.Rd:92: file link ‘as.mcmc.list’ in package ‘coda’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R2OpenBUGS.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGnl9Fk/Rbuild1cd97c6eb8b/r2sundials/man/r2sundials-package.Rd:40: file link ‘deSolve-package’ in package ‘deSolve’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/r2sundials.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpKGdKOD/R.INSTALL301e46d64f5b/R2SWF/man/dev2swf.Rd:42: file link ‘jpeg’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKGdKOD/R.INSTALL301e46d64f5b/R2SWF/man/dev2swf.Rd:48: file link ‘CairoPNG’ in package ‘Cairo’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKGdKOD/R.INSTALL301e46d64f5b/R2SWF/man/svg2swf.Rd:30: file link ‘svg’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKGdKOD/R.INSTALL301e46d64f5b/R2SWF/man/svg2swf.Rd:31: file link ‘CairoSVG’ in package ‘Cairo’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpKGdKOD/R.INSTALL301e46d64f5b/R2SWF/man/swf.Rd:32: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R2SWF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxDOTcQ/R.INSTALL31fd412dacd2/R2WinBUGS/man/bugs.Rd:76: file link ‘as.mcmc.list’ in package ‘coda’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R2WinBUGS.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpc9l0Lj/R.INSTALL63dd65de4eaa/r3dmol/man/init.Rd:29: file link ‘r3dmolOutput’ in package ‘r3dmol’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpc9l0Lj/R.INSTALL63dd65de4eaa/r3dmol/man/m_grid.Rd:34: file link ‘r3dmolOutput’ in package ‘r3dmol’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/r3dmol.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘r511-intro.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/RtmpLGZSFa/R.INSTALL35773a60b843/R62S3/man/R62Fun.Rd:55: file link ‘isS3stdGeneric’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLGZSFa/R.INSTALL35773a60b843/R62S3/man/R62Fun.Rd:55: file link ‘.S4methods’ in package ‘methods’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLGZSFa/R.INSTALL35773a60b843/R62S3/man/R62S3.Rd:52: file link ‘isS3stdGeneric’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLGZSFa/R.INSTALL35773a60b843/R62S3/man/R62S4.Rd:54: file link ‘.S4methods’ in package ‘methods’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R62S3.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8NbvPO/R.INSTALL588614f4df3f/radarchart/man/renderChartJSRadar.Rd:10: file link ‘shinyRenderWidget’ in package ‘htmlwidgets’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/radarchart.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
getsonde: no visible global function definition for ‘read.table’
plotsonde: no visible global function definition for ‘par’
plotwind: no visible global function definition for ‘mtext’
plotwind: no visible global function definition for ‘abline’
skewt.axis: no visible global function definition for ‘par’
skewt.axis: no visible global function definition for ‘axis’
skewt.axis: no visible global function definition for ‘mtext’
skewt.axis: no visible global function definition for ‘segments’
skewt.axis: no visible global function definition for ‘text’
skewt.axis: no visible global function definition for ‘lines’
skewt.lines: no visible global function definition for ‘lines’
skewt.points: no visible global function definition for ‘points’
station.symbol: no visible global function definition for ‘sd’
station.symbol: no visible global function definition for ‘par’
station.symbol: no visible global function definition for ‘lines’
station.symbol: no visible global function definition for ‘polygon’
station.symbol: no visible global function definition for ‘text’
station.symbol: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis lines mtext par points polygon read.table sd segments
  text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘SondeFile.txt’
Found the following significant warnings:
  Rd warning: /tmp/Rtmpyr0TKS/R.INSTALL8b7204f6df7/RadOnc/man/DVH-class.Rd:82: file link ‘plot.DVH’ in package ‘RadOnc’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpyr0TKS/R.INSTALL8b7204f6df7/RadOnc/man/DVH.list-class.Rd:79: file link ‘plot.DVH.list’ in package ‘RadOnc’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpyr0TKS/R.INSTALL8b7204f6df7/RadOnc/man/zDVH-class.Rd:74: file link ‘plot.DVH’ in package ‘RadOnc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RadOnc.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Rd file 'MDMnMod.Rd':
  \usage lines wider than 90 characters:
     MDMnMod(MDMn.form, data, ID, dist="MDMn", scale.covar=FALSE, est.var=TRUE, calc.resid=TRUE, trace=TRUE)
  \examples lines wider than 100 characters:
     model.nij <- MDMnMod(nij.form, data=n.data, ID=n.data$i, dist="MDMn", scale.covar=TRUE, est.var=FALSE, calc.resid=TRUE, trace=TRUE)

Rd file 'predict.MDMnMod.Rd':
  \examples lines wider than 100 characters:
     model.nij <- MDMnMod(nij.form, data=n.data, ID=n.data$i, dist="MDMn", scale.covar=TRUE, est.var=TRUE, calc.resid=TRUE, trace=TRUE)

Rd file 'truncMod.Rd':
  \usage lines wider than 90 characters:
     truncMod(trunc.form, trunc.pts, data, dist = 'NB', scale.covar=FALSE, est.var = TRUE, trace = TRUE)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpnspvMP/R.INSTALL48d25fddd9b7/radsafer/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/radsafer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSffqDA/R.INSTALL361c79b6ec94/RadTran/man/RnDif.het.Rd:72: file link ‘p.lin’ in package ‘ReacTran’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSffqDA/R.INSTALL361c79b6ec94/RadTran/man/RnDif.het.Rd:73: file link ‘p.exp’ in package ‘ReacTran’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSffqDA/R.INSTALL361c79b6ec94/RadTran/man/RnDif.het.Rd:74: file link ‘p.sig’ in package ‘ReacTran’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RadTran.Rcheck/00install.out’ for details.
RnDif.het: no visible global function definition for ‘runif’
RnDif.hom: no visible global function definition for ‘runif’
RnDifAdv.hom: no visible global function definition for ‘runif’
SoilAdv.hom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmXIQKd/R.INSTALL16866db7b254/rainbow/man/plot.fds.Rd:53: file link ‘lines.fds’ in package ‘rainbow’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmXIQKd/R.INSTALL16866db7b254/rainbow/man/plot.fds.Rd:53: file link ‘points.fds’ in package ‘rainbow’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rainbow.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLo0wRd/R.INSTALL7326148879f3/rAmCharts4/man/amColumn.Rd:17: file link ‘amColorAdapterFromVector’ in package ‘rAmCharts4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLo0wRd/R.INSTALL7326148879f3/rAmCharts4/man/amColumn.Rd:22: file link ‘amColorAdapterFromVector’ in package ‘rAmCharts4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLo0wRd/R.INSTALL7326148879f3/rAmCharts4/man/amSegment.Rd:11: file link ‘amColorAdapterFromVector’ in package ‘rAmCharts4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLo0wRd/R.INSTALL7326148879f3/rAmCharts4/man/rAmCharts4-shapes.Rd:48: file link ‘amColorAdapterFromVector’ in package ‘rAmCharts4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLo0wRd/R.INSTALL7326148879f3/rAmCharts4/man/rAmCharts4-shapes.Rd:57: file link ‘amColorAdapterFromVector’ in package ‘rAmCharts4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rAmCharts4.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘blcs.dot’ ‘ex1.dot’ ‘ex1bridge1.dot’ ‘ex1bridge2.dot’
  ‘ex1bridge3.dot’ ‘ex1effect1.dot’ ‘ex1effect2.dot’ ‘gcmlinear.dot’
  ‘latent.dot’ ‘lcs.dot’ ‘mimic.dot’
Found the following significant warnings:
  Rd warning: /tmp/RtmpM5W2Yz/R.INSTALL49f22a7831/RAM/man/OTU.ord.Rd:12: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RAM.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Found the following significant warnings:
  Rd warning: /tmp/RtmpbifUJs/R.INSTALL4824ea70987/RandomFieldsUtils/man/RFoptions.Rd:116: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbifUJs/R.INSTALL4824ea70987/RandomFieldsUtils/man/RFoptions.Rd:117: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbifUJs/R.INSTALL4824ea70987/RandomFieldsUtils/man/Struve.Rd:38: file link ‘besselI’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpbifUJs/R.INSTALL4824ea70987/RandomFieldsUtils/man/Struve.Rd:55: file link ‘besselI’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RandomFieldsUtils.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘randomGLM/R/randomGLM.R’:
  assign(".randomGLMparallelCluster", cluster, pos = ".GlobalEnv")
Rd file 'predict.randomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

Rd file 'randomGLM.Rd':
  \usage lines wider than 90 characters:
       # Multi-level classification options - only apply to classification with multi-level response

Rd file 'thinRandomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

These lines will be truncated in the PDF manual.
anovaF: no visible global function definition for ‘anova’
anovaF: no visible global function definition for ‘lm’
randInterval: no visible global function definition for ‘quantile’
randInterval : <anonymous>: no visible global function definition for
  ‘quantile’
randPlot: no visible global function definition for ‘par’
randPlot: no visible global function definition for ‘hist’
randPlot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
bartels.rank.test: no visible global function definition for ‘na.omit’
bartels.rank.test: no visible global function definition for ‘pbeta’
bartels.rank.test: no visible global function definition for ‘pnorm’
cox.stuart.test: no visible global function definition for ‘pbinom’
difference.sign.test: no visible global function definition for
  ‘na.omit’
difference.sign.test: no visible global function definition for ‘pnorm’
rank.test: no visible global function definition for ‘na.omit’
rank.test: no visible global function definition for ‘pnorm’
rruns: no visible global function definition for ‘runif’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘na.omit’
runs.test: no visible global function definition for ‘points’
runs.test: no visible global function definition for ‘abline’
runs.test: no visible global function definition for ‘gray’
runs.test: no visible global function definition for ‘pnorm’
turning.point.test: no visible global function definition for ‘embed’
turning.point.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
rank.L2R: no visible global function definition for ‘kmeans’
rank.L2R: no visible global function definition for ‘pnorm’
rank.LN: no visible global function definition for ‘kmeans’
rank.LN: no visible global function definition for ‘pnorm’
rank.gs: no visible global function definition for ‘qnorm’
rank.wald: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8f0iWI/R.INSTALL62566d95230c/rapportools/man/rp.desc.Rd:67: file link ‘melt.data.frame’ in package ‘reshape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8f0iWI/R.INSTALL62566d95230c/rapportools/man/rp.desc.Rd:69: file link ‘cast’ in package ‘reshape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8f0iWI/R.INSTALL62566d95230c/rapportools/man/rp.desc.Rd:29: file link ‘melt.data.frame’ in package ‘reshape’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8f0iWI/R.INSTALL62566d95230c/rapportools/man/rp.desc.Rd:36: file link ‘melt.data.frame’ in package ‘reshape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rapportools.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
freq: no visible global function definition for ‘xtabs’
freq: no visible binding for global variable ‘na.pass’
freq: no visible global function definition for ‘melt’
freq: no visible global function definition for ‘complete.cases’
freq: no visible global function definition for ‘tail’
kurtosis: no visible global function definition for ‘na.omit’
label: no visible global function definition for ‘tail’
name: no visible global function definition for ‘tail’
nvalid : <anonymous>: no visible global function definition for
  ‘na.omit’
rp.desc: no visible global function definition for ‘melt.data.frame’
rp.desc: no visible global function definition for ‘cast’
rp.desc: no visible global function definition for ‘na.omit’
rp.desc : <anonymous>: no visible global function definition for ‘tail’
rp.desc : <anonymous>: no visible global function definition for ‘head’
rp.freq: no visible global function definition for ‘xtabs’
rp.freq: no visible binding for global variable ‘na.pass’
rp.freq: no visible global function definition for ‘melt’
rp.freq: no visible global function definition for ‘complete.cases’
rp.freq: no visible global function definition for ‘tail’
rp.label: no visible global function definition for ‘tail’
rp.name: no visible global function definition for ‘tail’
rp.outlier : lundcrit: no visible global function definition for ‘qf’
rp.outlier: no visible global function definition for ‘lm’
rp.outlier: no visible global function definition for ‘rstandard’
rp.valid : <anonymous>: no visible global function definition for
  ‘na.omit’
skewness: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for ‘chisq.test’
fnRAP: no visible global function definition for ‘combn’
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gurobi’
INT_FIX: no visible global function definition for ‘rbinom’
INT_FIX: no visible global function definition for ‘glm’
INT_FIX: no visible global function definition for ‘as.formula’
INT_FIX: no visible global function definition for ‘residuals’
INT_FIX: no visible global function definition for ‘var’
INT_RAN: no visible global function definition for ‘rbinom’
INT_RAN: no visible global function definition for ‘as.formula’
INT_RAN: no visible global function definition for ‘predict’
JOINT: no visible global function definition for ‘rbinom’
JOINT: no visible global function definition for ‘glm’
JOINT: no visible global function definition for ‘as.formula’
JOINT: no visible global function definition for ‘var’
JOINT: no visible global function definition for ‘residuals’
pKuonen: no visible global function definition for ‘pchisq’
pKuonen: no visible global function definition for ‘uniroot’
pKuonen: no visible global function definition for ‘pnorm’
rareGE: no visible global function definition for ‘rbinom’
rareGE: no visible global function definition for ‘as.formula’
rareGE: no visible global function definition for ‘predict’
rareGE: no visible global function definition for ‘glm’
rareGE: no visible global function definition for ‘residuals’
rareGE: no visible global function definition for ‘var’
rareGE_joint_mc: no visible global function definition for ‘pchisq’
rareGE_joint_mc: no visible global function definition for ‘qchisq’
wuweights: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  as.formula dbeta glm pchisq pnorm predict qchisq rbinom residuals
  uniroot var
Consider adding
  importFrom("stats", "as.formula", "dbeta", "glm", "pchisq", "pnorm",
             "predict", "qchisq", "rbinom", "residuals", "uniroot",
             "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpmwgOXF/R.INSTALL681e4108571f/rareNMtests/man/BiogTest.individual.Rd:75: file link ‘rarecurve’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmwgOXF/R.INSTALL681e4108571f/rareNMtests/man/EcoTest.individual.Rd:62: file link ‘rarecurve’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpmwgOXF/R.INSTALL681e4108571f/rareNMtests/man/rarefaction.individual.Rd:46: file link ‘rarecurve’ in package ‘vegan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rareNMtests.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
BiogTest.individual: no visible global function definition for ‘combn’
BiogTest.individual: no visible global function definition for ‘runif’
BiogTest.individual: no visible global function definition for ‘rlnorm’
BiogTest.individual: no visible global function definition for
  ‘rnbinom’
BiogTest.sample: no visible global function definition for ‘combn’
BiogTest.sample: no visible global function definition for ‘runif’
BiogTest.sample: no visible global function definition for ‘rlnorm’
BiogTest.sample: no visible global function definition for ‘rnbinom’
BiogTest.sample: no visible global function definition for ‘aggregate’
EcoTest.individual: no visible global function definition for ‘xtabs’
plot.BiogTest: no visible global function definition for ‘quantile’
plot.BiogTest: no visible global function definition for ‘combn’
plot.EcoTest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
  importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
             "runif", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp9zbHwf/R.INSTALL43782e7daa19/Rarity/man/corPlot.Rd:40: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rarity.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpclUROZ/R.INSTALLcb31e6d3e55/rasclass/man/classifyRasclass.Rd:43: file link ‘RSNNS’ in package ‘RSNNS’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rasclass.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpo3Idio/R.INSTALL69725521263/rasterDT/man/freqDT.Rd:31: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rasterDT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5x66HA/R.INSTALL7bd971900ef/rasterly/man/reexports.Rd:17: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rasterly.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpzWR9OC/R.INSTALL45de1c39853/rasterpdf/man/dev.off.Rd:14: file link ‘dev.off’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzWR9OC/R.INSTALL45de1c39853/rasterpdf/man/dev.off.Rd:16: file link ‘dev.off’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzWR9OC/R.INSTALL45de1c39853/rasterpdf/man/dev.off.Rd:25: file link ‘dev.off’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzWR9OC/R.INSTALL45de1c39853/rasterpdf/man/raster_pdf.Rd:41: file link ‘cairo_pdf’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzWR9OC/R.INSTALL45de1c39853/rasterpdf/man/raster_pdf.Rd:61: file link ‘cairo_pdf’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzWR9OC/R.INSTALL45de1c39853/rasterpdf/man/raster_pdf.Rd:75: file link ‘cairo_pdf’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rasterpdf.Rcheck/00install.out’ for details.
rateratio.test: no visible global function definition for
  ‘complete.cases’
rateratio.test: no visible global function definition for ‘pbinom’
rateratio.test : p.L: no visible global function definition for ‘qbeta’
rateratio.test : p.U: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
GNU make is a SystemRequirements.
concordance: no visible global function definition for ‘quantile’
concordance : Normal: no visible global function definition for ‘qnorm’
concordance : Normal: no visible global function definition for ‘pnorm’
concordance : MC: no visible global function definition for ‘rmultinom’
concordance : MC: no visible global function definition for ‘quantile’
concordance: no visible global function definition for ‘qnorm’
concordance: no visible global function definition for ‘pnorm’
concordance : Chisq: no visible global function definition for ‘qchisq’
concordance : Chisq: no visible global function definition for ‘pchisq’
concordance : Normal2: no visible global function definition for
  ‘qnorm’
concordance : Normal2: no visible global function definition for
  ‘pnorm’
concordance : MC2: no visible global function definition for
  ‘rmultinom’
concordance : MC2: no visible global function definition for ‘quantile’
wlin.conc: no visible global function definition for ‘quantile’
wlin.conc : MC: no visible global function definition for ‘rmultinom’
wlin.conc : MC: no visible global function definition for ‘quantile’
wquad.conc: no visible global function definition for ‘quantile’
wquad.conc : MC: no visible global function definition for ‘rmultinom’
wquad.conc : MC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpie99xW/R.INSTALL47a36ddc54a6/rationalfun/man/as.character.rationalfun.Rd:24: file link ‘as.character.polynomial’ in package ‘polynom’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpie99xW/R.INSTALL47a36ddc54a6/rationalfun/man/print.rationalfun.Rd:23: file link ‘print.polynomial’ in package ‘polynom’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rationalfun.Rcheck/00install.out’ for details.
.GCD: no visible global function definition for ‘as.polynomial’
.LCM: no visible global function definition for ‘as.polynomial’
.is_zero_polynomial: no visible global function definition for ‘coef’
.poly2expr: no visible global function definition for ‘coef’
integral.rationalfun: no visible global function definition for ‘coef’
integraterf.transcendent: no visible global function definition for
  ‘coef’
rationalfun: no visible global function definition for ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘is.polynomial’
rfun: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘is.polynomial’
simplify: no visible global function definition for ‘coef’
simplify: no visible global function definition for ‘polynomial’
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
Package suggested but not available for checking: ‘rggobi’
Found the following significant warnings:
  Rd warning: /tmp/RtmpkOjlF8/R.INSTALL49184aacc33a/rAverage/man/AIC.Rd:69: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rAverage.Rcheck/00install.out’ for details.
.avisApiBusAvanzada: no visible global function definition for
  ‘read.csv’
.avisRenderMapAdmin: no visible global function definition for ‘points’
.avisRenderMapAdmin: no visible global function definition for ‘rect’
.avisRenderMapPhysical: no visible global function definition for
  ‘points’
avisMap: no visible global function definition for ‘par’
avisMap: no visible global function definition for ‘layout’
Undefined global functions or variables:
  layout par points read.csv rect
Consider adding
  importFrom("graphics", "layout", "par", "points", "rect")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpULTGaY/R.INSTALL4ca75392e76a/Rbeast/man/plot.beast.Rd:13: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rbeast.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpHTMcOc/R.INSTALL6e5827fa7470/rbefdata/man/bef.portal.get.attachments.Rd:27: file link ‘getURLContent’ in package ‘RCurl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHTMcOc/R.INSTALL6e5827fa7470/rbefdata/man/bef.portal.get.dataset.Rd:19: file link ‘getURLContent’ in package ‘RCurl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHTMcOc/R.INSTALL6e5827fa7470/rbefdata/man/bef.portal.get.datasets.for_proposal.Rd:18: file link ‘getURLContent’ in package ‘RCurl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpHTMcOc/R.INSTALL6e5827fa7470/rbefdata/man/bef.portal.get.keywords.Rd:14: file link ‘getURLContent’ in package ‘RCurl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rbefdata.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpaEMABh/R.INSTALL4f823c025820/rbenvo/man/add_BEF.Rd:16: file link ‘st_distance’ in package ‘sf’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaEMABh/R.INSTALL4f823c025820/rbenvo/man/base_benvo.Rd:21: file link ‘Date’ in package ‘lubridate’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpaEMABh/R.INSTALL4f823c025820/rbenvo/man/set_datetime_cols.Rd:23: file link ‘Date’ in package ‘lubridate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rbenvo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpjxyCOE/R.INSTALL4f8757b1319a/RBesT/man/gMAP.Rd:77: file link ‘model.matrix.default’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpjxyCOE/R.INSTALL4f8757b1319a/RBesT/man/gMAP.Rd:343: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RBesT.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpplYVGQ/R.INSTALL6ea324c13a3d/rBeta2009/man/rbeta.Rd:74: file link ‘rbeta’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpplYVGQ/R.INSTALL6ea324c13a3d/rBeta2009/man/rdirichlet.Rd:62: file link ‘rdirichlet’ in package ‘gtools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rBeta2009.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpLhtP9o/R.INSTALL7e941c028c94/rbgm/man/nodeSpatial.Rd:25: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLhtP9o/R.INSTALL7e941c028c94/rbgm/man/nodeSpatial.Rd:22: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLhtP9o/R.INSTALL7e941c028c94/rbgm/man/rbgm-Spatial.Rd:60: file link ‘Spatial’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLhtP9o/R.INSTALL7e941c028c94/rbgm/man/rbgm-Spatial.Rd:45: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLhtP9o/R.INSTALL7e941c028c94/rbgm/man/rbgm-Spatial.Rd:46: file link ‘SpatialLinesDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLhtP9o/R.INSTALL7e941c028c94/rbgm/man/rbgm-Spatial.Rd:47: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLhtP9o/R.INSTALL7e941c028c94/rbgm/man/rbgm-Spatial.Rd:48: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLhtP9o/R.INSTALL7e941c028c94/rbgm/man/rbgm-Spatial.Rd:49: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rbgm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8ruGYq/R.INSTALL6e5be3fc028/rbi/man/optimise.Rd:25: file link ‘optimise’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8ruGYq/R.INSTALL6e5be3fc028/rbi/man/predict.Rd:21: file link ‘optimise’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rbi.Rcheck/00install.out’ for details.
GetHistoricTradeData: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘RBitmoji.Rmd’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZaH3YX/R.INSTALL4b764d2383c0/rbokeh/man/ly_quantile.Rd:34: file link ‘qnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZaH3YX/R.INSTALL4b764d2383c0/rbokeh/man/ly_quantile.Rd:34: file link ‘qunif’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZaH3YX/R.INSTALL4b764d2383c0/rbokeh/man/print_model_json.Rd:14: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rbokeh.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
SumTestSens: no visible global function definition for ‘pnorm’
binarysens: no visible global function definition for ‘dbinom’
hlsens: no visible global function definition for ‘wilcox.test’
iv_sens: no visible global function definition for ‘pnorm’
mcontrol: no visible global function definition for ‘pnorm’
psens: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
find_available_versions: no visible global function definition for
  ‘contrib.url’
find_available_versions: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘contrib.url’
install_version: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘install_url’
load_available_packages: no visible global function definition for
  ‘contrib.url’
validate_installed_package: no visible global function definition for
  ‘installed.packages’
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rcane.Rmd’
Found the following files/directories:
  ‘rcanvec.cache’
RC.read.table: no visible global function definition for ‘type.convert’
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
Found the following files/directories:
  ‘temp.RData’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3IjiB2/R.INSTALL70f93e6698d9/rchallenge/man/plot_activity.Rd:43: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3IjiB2/R.INSTALL70f93e6698d9/rchallenge/man/plot_history.Rd:47: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rchallenge.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
.onAttach: no visible global function definition for
  ‘packageDescription’
rselect.list: no visible global function definition for ‘select.list’
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
Found the following files/directories:
  ‘data.csv’
Malformed Description field: should contain one or more complete sentences.
get_ClinicalCodes: no visible global function definition for ‘read.csv’
get_ClinicalCodes : <anonymous>: no visible global function definition
  for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpxDXWJT/R.INSTALL6ca02fb085ee/rclipboard/man/rclipButton.Rd:15: file link ‘validateCssUnit’ in package ‘shiny’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpxDXWJT/R.INSTALL6ca02fb085ee/rclipboard/man/rclipboardSetup.Rd:12: file link ‘singleton’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rclipboard.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘file1.arp’ ‘file2.arp’ ‘test.txt’ ‘test2.txt’
cmaOptimDP: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following files/directories:
  ‘outcmaesdisp.dat’
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Rd warning: /tmp/RtmpwKJPmr/R.INSTALL7c41450fa8f8/RcmdrPlugin.coin/man/RcmdrPlugin.coin-package.Rd:29: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.coin.Rcheck/00install.out’ for details.
enterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpUpt7Ey/R.INSTALL7dea1d69cd8d/RcmdrPlugin.depthTools/man/RcmdrPlugin.depthTools-package.Rd:29: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.depthTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpqm5hjU/R.INSTALL7e3e54eec0bb/RcmdrPlugin.DoE/man/Menu.Dopt.Rd:83: file link ‘optFederov’ in package ‘AlgDesign’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqm5hjU/R.INSTALL7e3e54eec0bb/RcmdrPlugin.DoE/man/Menu.DoptTab1.rd:15: file link ‘optFederov’ in package ‘AlgDesign’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqm5hjU/R.INSTALL7e3e54eec0bb/RcmdrPlugin.DoE/man/Menu.DoptTab1.rd:45: file link ‘optFederov’ in package ‘AlgDesign’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqm5hjU/R.INSTALL7e3e54eec0bb/RcmdrPlugin.DoE/man/Menu.IAPlot.Rd:24: file link ‘MEPlot’ in package ‘FrF2’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqm5hjU/R.INSTALL7e3e54eec0bb/RcmdrPlugin.DoE/man/Menu.Inspect.rd:15: file link ‘summary.design’ in package ‘DoE.base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqm5hjU/R.INSTALL7e3e54eec0bb/RcmdrPlugin.DoE/man/Menu.Optimal.Rd:48: file link ‘optFederov’ in package ‘AlgDesign’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqm5hjU/R.INSTALL7e3e54eec0bb/RcmdrPlugin.DoE/man/Menu.changecontr.Rd:24: file link ‘change.contr’ in package ‘DoE.base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqm5hjU/R.INSTALL7e3e54eec0bb/RcmdrPlugin.DoE/man/Menu.pickcube.Rd:29: file link ‘pickcube’ in package ‘DoE.base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqm5hjU/R.INSTALL7e3e54eec0bb/RcmdrPlugin.DoE/man/Menu.rsm.Rd:34: file link ‘code.design’ in package ‘DoE.wrapper’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.DoE.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpshrItc/R.INSTALL7f22b9f7e68/RcmdrPlugin.EBM/man/RcmdrPlugin.EBM-package.Rd:40: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.EBM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZhOgcW/R.INSTALL292226d510f/RcmdrPlugin.EcoVirtual/man/RcmdrPlugin.EcoVirtual.package.Rd:33: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.EcoVirtual.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXDu3TJ/R.INSTALL37075a21587/RcmdrPlugin.Export/man/RcmdrPlugin.Export-package.Rd:100: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.Export.Rcheck/00install.out’ for details.
managedata: no visible binding for global variable ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp23eA48/R.INSTALL90a20a7cd3e/RcmdrPlugin.KMggplot2/man/package-RcmdrPlugin.KMggplot2.Rd:15: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp23eA48/R.INSTALL90a20a7cd3e/RcmdrPlugin.KMggplot2/man/package-RcmdrPlugin.KMggplot2.Rd:18: file link ‘RColorBrewer’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp23eA48/R.INSTALL90a20a7cd3e/RcmdrPlugin.KMggplot2/man/package-RcmdrPlugin.KMggplot2.Rd:20: file link ‘scales’ in package ‘scales’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.KMggplot2.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
BOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Found the following significant warnings:
  Rd warning: /tmp/RtmppEZ589/R.INSTALL109534914123/RcmdrPlugin.pointG/man/RcmdrPlugin.pointG-package.Rd:29: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.pointG.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpfYWfDI/R.INSTALL12e27aa4526a/RcmdrPlugin.RMTCJags/man/RcmdrPlugin.RMTCJags-package.Rd:26: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.RMTCJags.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIfQZsW/R.INSTALL146453bb7c26/RcmdrPlugin.ROC/man/RcmdrPlugin.ROC-package.Rd:34: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.ROC.Rcheck/00install.out’ for details.
fncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpChb4fS/R.INSTALL15861fb77b29/RcmdrPlugin.SCDA/man/RcmdrPlugin.SCDA-package.Rd:27: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.SCDA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmparYlyh/R.INSTALL16bc2f763d6c/RcmdrPlugin.SLC/man/RcmdrPlugin.SLC-internal.Rd:10: file link ‘RcmdrPlugin.SLC’ in package ‘RcmdrPlugin.SLC’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.SLC.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmprUvREx/R.INSTALL176b2e2944b4/RcmdrPlugin.sos/man/RcmdrPlugin.sos-package.Rd:19: file link ‘intersectFindFn’ in package ‘sos’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprUvREx/R.INSTALL176b2e2944b4/RcmdrPlugin.sos/man/RcmdrPlugin.sos-package.Rd:32: file link ‘Rcmdr’ in package ‘Rcmdr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.sos.Rcheck/00install.out’ for details.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Rd warning: /tmp/RtmpdTV4vv/R.INSTALL1ec15eb9ffad/RcmdrPlugin.UCA/man/RcmdrPlugin.UCA-internal.Rd:39: file link ‘RcmdrPlugin.UCA’ in package ‘RcmdrPlugin.UCA’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.UCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpRPBhAh/R.INSTALL35a07103344a/Rcmdr/man/RecodeDialog.Rd:51: file link ‘Recode’ in package ‘car’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rcmdr.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
brewer.pal: no visible global function definition for ‘rgb’
display.brewer.all: no visible global function definition for ‘par’
display.brewer.all: no visible global function definition for ‘rect’
display.brewer.all: no visible global function definition for ‘text’
display.brewer.pal: no visible global function definition for ‘image’
Undefined global functions or variables:
  image par rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
addLine: no visible global function definition for ‘abline’
ellipse: no visible global function definition for ‘approx’
ellipse: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYI1NxY/R.INSTALLfe624ae6a47/rcosmo/man/displayPixelBoundaries.Rd:40: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYI1NxY/R.INSTALLfe624ae6a47/rcosmo/man/plot.CMBDataFrame.Rd:58: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYI1NxY/R.INSTALLfe624ae6a47/rcosmo/man/plot.CMBDataFrame.Rd:62: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYI1NxY/R.INSTALLfe624ae6a47/rcosmo/man/plot.CMBWindow.Rd:39: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYI1NxY/R.INSTALLfe624ae6a47/rcosmo/man/plot.HPDataFrame.Rd:63: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rcosmo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSwG5fi/R.INSTALL31b436f72add/RcppAlgos/man/isPrimeRcpp.Rd:46: file link ‘isPrime’ in package ‘numbers’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSwG5fi/R.INSTALL31b436f72add/RcppAlgos/man/primeFactorize.Rd:43: file link ‘factorize’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSwG5fi/R.INSTALL31b436f72add/RcppAlgos/man/primeFactorize.Rd:43: file link ‘primeFactors’ in package ‘numbers’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSwG5fi/R.INSTALL31b436f72add/RcppAlgos/man/primeFactorizeSieve.Rd:42: file link ‘factorize’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSwG5fi/R.INSTALL31b436f72add/RcppAlgos/man/primeFactorizeSieve.Rd:42: file link ‘primeFactors’ in package ‘numbers’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSwG5fi/R.INSTALL31b436f72add/RcppAlgos/man/primeSieve.Rd:51: file link ‘Primes’ in package ‘numbers’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcppAlgos.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpDDt4vk/R.INSTALL5ff07985d719/RcppBigIntAlgos/man/primeFactorizeBig.Rd:47: file link ‘primeFactors’ in package ‘numbers’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcppBigIntAlgos.Rcheck/00install.out’ for details.
Gauss: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCjmLgp/R.INSTALL6a612c96f74f/RcppNumerical/man/fastLR.Rd:64: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcppNumerical.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /tmp/RtmpzEm9rj/R.INSTALL113594e2c13/RCurl/man/binaryBuffer.Rd:15: file link ‘writeBin’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzEm9rj/R.INSTALL113594e2c13/RCurl/man/getCurlErrorClassNames.Rd:25: file link ‘tryCatch’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpzEm9rj/R.INSTALL113594e2c13/RCurl/man/url.exists.Rd:5: file link ‘file.exists’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RCurl.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp79Lc5L/R.INSTALL459d6f0bc278/rDEA/man/dea.Rd:50: file link ‘dea.robust’ in package ‘rDEA’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp79Lc5L/R.INSTALL459d6f0bc278/rDEA/man/dea.Rd:50: file link ‘dea.env.robust’ in package ‘rDEA’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp79Lc5L/R.INSTALL459d6f0bc278/rDEA/man/dea_env_robust.Rd:55: file link ‘dea.robust’ in package ‘rDEA’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp79Lc5L/R.INSTALL459d6f0bc278/rDEA/man/dea_robust.Rd:53: file link ‘dea.env.robust’ in package ‘rDEA’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp79Lc5L/R.INSTALL459d6f0bc278/rDEA/man/rts_test.Rd:59: file link ‘dea.robust’ in package ‘rDEA’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp79Lc5L/R.INSTALL459d6f0bc278/rDEA/man/rts_test.Rd:59: file link ‘dea.env.robust’ in package ‘rDEA’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rDEA.Rcheck/00install.out’ for details.
distimage: no visible binding for global variable ‘terrain.colors’
distimage: no visible global function definition for ‘filled.contour’
distimage: no visible global function definition for ‘title’
distimage: no visible global function definition for ‘axis’
distimage: no visible global function definition for ‘lines’
drawkpc: no visible global function definition for ‘segments’
drawkpc: no visible global function definition for ‘lines’
modelimage: no visible binding for global variable ‘topo.colors’
modelimage: no visible global function definition for ‘filled.contour’
modelimage: no visible global function definition for ‘title’
modelimage: no visible global function definition for ‘axis’
modelimage: no visible global function definition for ‘lines’
sincdata: no visible global function definition for ‘runif’
sincdata: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  axis filled.contour lines rnorm runif segments terrain.colors title
  topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "segments",
             "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpeEgecE/R.INSTALL5a605ca8aca7/R.devices/man/capturePlot.Rd:37: file link ‘replayPlot’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeEgecE/R.INSTALL5a605ca8aca7/R.devices/man/capturePlot.Rd:53: file link ‘replayPlot’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeEgecE/R.INSTALL5a605ca8aca7/R.devices/man/capturePlot.Rd:87: file link ‘recordPlot’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeEgecE/R.INSTALL5a605ca8aca7/R.devices/man/devIsInteractive.Rd:36: file link ‘deviceIsInteractive’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpeEgecE/R.INSTALL5a605ca8aca7/R.devices/man/print.RecordedPlot.Rd:16: file link ‘replayPlot’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R.devices.Rcheck/00install.out’ for details.
sumry_categorical: no visible global function definition for ‘freq’
sumry_continous: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RDieHarder.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIMO4WN/R.INSTALL76f465f319e/Rdistance/man/dfuncSmu.Rd:89: file link ‘bw.nrd0’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIMO4WN/R.INSTALL76f465f319e/Rdistance/man/dfuncSmu.Rd:92: file link ‘bw.nrd’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIMO4WN/R.INSTALL76f465f319e/Rdistance/man/dfuncSmu.Rd:96: file link ‘bw.SJ’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIMO4WN/R.INSTALL76f465f319e/Rdistance/man/dfuncSmu.Rd:98: file link ‘bw.SJ’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIMO4WN/R.INSTALL76f465f319e/Rdistance/man/smu.like.Rd:79: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rdistance.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpGvMvcG/R.INSTALL559346d72773/RDML/man/adpsType.Rd:28: file link ‘assertMatrix’ in package ‘checkmate’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGvMvcG/R.INSTALL559346d72773/RDML/man/loopType.Rd:22: file link ‘assertCount’ in package ‘checkmate’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGvMvcG/R.INSTALL559346d72773/RDML/man/loopType.Rd:24: file link ‘assertCount’ in package ‘checkmate’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpGvMvcG/R.INSTALL559346d72773/RDML/man/mdpsType.Rd:28: file link ‘assertMatrix’ in package ‘checkmate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RDML.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘synchronicity’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘a.desc’ ‘b.desc’ ‘barrnumleft.desc’ ‘barrsense.desc’ ‘c.desc’
  ‘m.desc’ ‘u.desc’ ‘x’ ‘x.desc’
Found the following significant warnings:
  Rd warning: /tmp/RtmpcGxuAN/R.INSTALL4a2a2c801151/RDS/man/control.rds.estimates.Rd:53: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpcGxuAN/R.INSTALL4a2a2c801151/RDS/man/print.summary.svyglm.RDS.Rd:46: file link ‘summary.svyglm’ in package ‘survey’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpcGxuAN/R.INSTALL4a2a2c801151/RDS/man/summary.svyglm.RDS.Rd:32: file link ‘residuals.svyglm’ in package ‘survey’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RDS.Rcheck/00install.out’ for details.
ip2coordinates: no visible global function definition for ‘URLencode’
street2coordinates: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Found the following files/directories:
  ‘example.pdf’
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp8f4IhL/R.INSTALL1aa220f975fa/readr/man/callback.Rd:132: file link ‘ChunkCallback’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8f4IhL/R.INSTALL1aa220f975fa/readr/man/callback.Rd:197: file link ‘ChunkCallback’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8f4IhL/R.INSTALL1aa220f975fa/readr/man/callback.Rd:271: file link ‘ChunkCallback’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8f4IhL/R.INSTALL1aa220f975fa/readr/man/callback.Rd:345: file link ‘ChunkCallback’ in package ‘readr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/readr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmplRNERD/R.INSTALLc375b47d/readsdr/man/read_xmile.Rd:36: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplRNERD/R.INSTALLc375b47d/readsdr/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/readsdr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpxv5VXL/R.INSTALL5e423c043f68/Rearrangement/man/lines.conint.Rd:18: file link ‘lines.default’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpxv5VXL/R.INSTALL5e423c043f68/Rearrangement/man/plot.conint.Rd:7: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpxv5VXL/R.INSTALL5e423c043f68/Rearrangement/man/plot.conint.Rd:29: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpxv5VXL/R.INSTALL5e423c043f68/Rearrangement/man/points.conint.Rd:18: file link ‘points.default’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rearrangement.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp4SmH4g/R.INSTALL25457cb6dc3/rebus.base/man/Backreferences.Rd:82: file link ‘sub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4SmH4g/R.INSTALL25457cb6dc3/rebus.base/man/Backreferences.Rd:83: file link ‘stri_replace_first_regex’ in package ‘stringi’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4SmH4g/R.INSTALL25457cb6dc3/rebus.base/man/Backreferences.Rd:85: file link ‘stri_match_first_regex’ in package ‘stringi’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp4SmH4g/R.INSTALL25457cb6dc3/rebus.base/man/regex.Rd:23: file link ‘paste0’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rebus.base.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmpqsg0h7/R.INSTALL4cc35d499449/rebus.datetimes/man/DateTime.Rd:310: file link ‘Sys.setlocale’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpqsg0h7/R.INSTALL4cc35d499449/rebus.datetimes/man/get_weekdays.Rd:30: file link ‘Sys.setlocale’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rebus.datetimes.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpWcQ7Jq/R.INSTALL4dc22e50a9d/rebus.numbers/man/roman.Rd:32: file link ‘as.roman’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rebus.numbers.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpagCCfY/R.INSTALL777a189fb903/rebus/man/exactly.Rd:7: file link ‘exactly’ in package ‘rebus.base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpagCCfY/R.INSTALL777a189fb903/rebus/man/rebus.Rd:76: file link ‘regexpr’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpagCCfY/R.INSTALL777a189fb903/rebus/man/whole_word.Rd:7: file link ‘whole_word’ in package ‘rebus.base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rebus.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp7UIBPK/R.INSTALL4dc740ac538e/rebus.unicode/man/UnicodeProperty.Rd:283: file link ‘stringi-search-charclass’ in package ‘stringi’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rebus.unicode.Rcheck/00install.out’ for details.
ReCiPa: no visible global function definition for ‘count.fields’
ReCiPa: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYHp0jk/R.INSTALL4e2b3177c222/recmap/man/as.SpatialPolygonsDataFrame.recmap.Rd:25: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYHp0jk/R.INSTALL4e2b3177c222/recmap/man/as.SpatialPolygonsDataFrame.recmap.Rd:39: file link ‘sp’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYHp0jk/R.INSTALL4e2b3177c222/recmap/man/as.recmap.SpatialPolygonsDataFrame.Rd:35: file link ‘sp’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/recmap.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/RtmpWCMt4p/R.INSTALL83a15cacace/REdaS/man/bart_spher.Rd:50: file link ‘KMOS’ in package ‘REdaS’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWCMt4p/R.INSTALL83a15cacace/REdaS/man/freqCI.Rd:14: file link ‘as.table’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpWCMt4p/R.INSTALL83a15cacace/REdaS/man/freqCI.Rd:41: file link ‘as.table’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/REdaS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0Vntg8/R.INSTALL590f42283c1b/redcapAPI/man/exportRecords.Rd:127: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/redcapAPI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpCEAauJ/R.INSTALL78f6739be572/REDCapExporter/man/export_content.Rd:22: file link ‘handle_setform’ in package ‘curl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/REDCapExporter.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpkVwKcO/R.INSTALL59d170e2a3e4/REDCapR/man/kernel_api.Rd:40: file link ‘package_version’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkVwKcO/R.INSTALL59d170e2a3e4/REDCapR/man/kernel_api.Rd:31: file link ‘packageVersion’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkVwKcO/R.INSTALL59d170e2a3e4/REDCapR/man/redcap_read.Rd:104: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkVwKcO/R.INSTALL59d170e2a3e4/REDCapR/man/redcap_read.Rd:107: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkVwKcO/R.INSTALL59d170e2a3e4/REDCapR/man/redcap_read_oneshot.Rd:89: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkVwKcO/R.INSTALL59d170e2a3e4/REDCapR/man/redcap_read_oneshot.Rd:92: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpkVwKcO/R.INSTALL59d170e2a3e4/REDCapR/man/redcap_read_oneshot.Rd:95: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/REDCapR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
Found the following significant warnings:
  Rd warning: /tmp/RtmpVhKpgz/R.INSTALL508169ed6c4f/REEMtree/man/fitted.REEMtree.Rd:20: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/REEMtree.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5exj8K/R.INSTALL690d452fa59d/RefManageR/man/Cite.Rd:131: file link ‘citeNatbib’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RefManageR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmprT9Xe9/R.INSTALL5c5d5a8b190c/refund/man/pffr.Rd:51: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprT9Xe9/R.INSTALL5c5d5a8b190c/refund/man/pffr.Rd:119: file link ‘mrf’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprT9Xe9/R.INSTALL5c5d5a8b190c/refund/man/pffr.Rd:175: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprT9Xe9/R.INSTALL5c5d5a8b190c/refund/man/print.summary.pffr.Rd:28: file link ‘print.summary.gam’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprT9Xe9/R.INSTALL5c5d5a8b190c/refund/man/print.summary.pffr.Rd:31: file link ‘print.summary.gam’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmprT9Xe9/R.INSTALL5c5d5a8b190c/refund/man/smooth.construct.dt.smooth.spec.Rd:46: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/refund.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
cluster.reg: no visible global function definition for ‘rnorm’
cluster.reg: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
Found the following significant warnings:
  Rd warning: /tmp/RtmpE7BZGP/R.INSTALL5b6b2f7fcb34/regressoR/man/rd_model.Rd:41: file link ‘pcr’ in package ‘pls’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE7BZGP/R.INSTALL5b6b2f7fcb34/regressoR/man/rd_model.Rd:41: file link ‘plsr’ in package ‘pls’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE7BZGP/R.INSTALL5b6b2f7fcb34/regressoR/man/rd_type.Rd:21: file link ‘pcr’ in package ‘pls’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE7BZGP/R.INSTALL5b6b2f7fcb34/regressoR/man/rd_type.Rd:21: file link ‘plsr’ in package ‘pls’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpE7BZGP/R.INSTALL5b6b2f7fcb34/regressoR/man/render_table_data.Rd:49: file link ‘renderDT’ in package ‘DT’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/regressoR.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘lars’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
relaxo: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
Rd file 'cvrelaxo.Rd':
  \usage lines wider than 90 characters:
     cvrelaxo(X, Y, K = 5, phi = seq(0, 1, length = 10), max.steps = min( 2* length(Y), 2 * ncol(X)), fast = TRUE, keep.data = TRUE, warn=TR ... [TRUNCATED]

Rd file 'plot.relaxo.Rd':
  \usage lines wider than 90 characters:
     plot(x, type = "l", lty = 1, main = NULL, xlab = "|beta|/max|beta| (phi=1)", ylab = expression("coefficients  " * beta[j]), plotphi = u ... [TRUNCATED]

Rd file 'relaxo.Rd':
  \usage lines wider than 90 characters:
     relaxo(X, Y, phi = seq(0, 1, length = 4), max.steps = min(2*length(Y), 2 * ncol(X)), fast = TRUE,  keep.data = TRUE, warn=TRUE)

These lines will be truncated in the PDF manual.
print.summary.rem: no visible global function definition for
  ‘printCoefmat’
print.summary.rem: no visible global function definition for ‘pnorm’
print.summary.rem: no visible binding for global variable ‘quantile’
print.summary.rem: no visible global function definition for ‘pchisq’
print.summary.rem.dyad: no visible global function definition for
  ‘printCoefmat’
print.summary.rem.dyad: no visible global function definition for
  ‘pnorm’
print.summary.rem.dyad: no visible global function definition for
  ‘pchisq’
rem: no visible global function definition for ‘rnorm’
rem: no visible global function definition for ‘dnorm’
rem: no visible global function definition for ‘runif’
rem: no visible global function definition for ‘rchisq’
rem: no visible global function definition for ‘cov’
rem.dyad: no visible global function definition for ‘rnorm’
rem.dyad: no visible global function definition for ‘optim’
rem.dyad: no visible global function definition for ‘rchisq’
rem.dyad: no visible global function definition for ‘quantile’
rem.dyad: no visible global function definition for ‘sd’
rem.dyad: no visible global function definition for ‘var’
rem.dyad.lprior: no visible global function definition for ‘dnorm’
rem.dyad.lprior: no visible global function definition for ‘dt’
Undefined global functions or variables:
  cov dnorm dt optim pchisq pnorm printCoefmat quantile rchisq rnorm
  runif sd var
Consider adding
  importFrom("stats", "cov", "dnorm", "dt", "optim", "pchisq", "pnorm",
             "printCoefmat", "quantile", "rchisq", "rnorm", "runif",
             "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpluZ2zK/R.INSTALL15f3db04925/reliabilitydiag/man/print.reliabilitydiag.Rd:17: file link ‘print.tbl_df’ in package ‘tibble’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/reliabilitydiag.Rcheck/00install.out’ for details.
duane: no visible global function definition for ‘optim’
duane.plot: no visible global function definition for ‘lines’
duane.plot: no visible global function definition for ‘legend’
duane.plot: no visible global function definition for ‘title’
littlewood.verall: no visible global function definition for ‘optim’
littlewood.verall.plot: no visible global function definition for
  ‘lines’
littlewood.verall.plot: no visible global function definition for
  ‘legend’
littlewood.verall.plot: no visible global function definition for
  ‘title’
moranda.geometric: no visible global function definition for ‘optimize’
moranda.geometric.plot: no visible global function definition for
  ‘lines’
moranda.geometric.plot: no visible global function definition for
  ‘legend’
moranda.geometric.plot: no visible global function definition for
  ‘title’
musa.okumoto: no visible global function definition for ‘optimize’
musa.okumoto.plot: no visible global function definition for ‘lines’
musa.okumoto.plot: no visible global function definition for ‘legend’
musa.okumoto.plot: no visible global function definition for ‘title’
rel.plot: no visible global function definition for ‘lines’
rel.plot: no visible global function definition for ‘segments’
rel.plot: no visible global function definition for ‘legend’
rel.plot: no visible global function definition for ‘title’
total.plot: no visible global function definition for ‘lines’
total.plot: no visible global function definition for ‘legend’
total.plot: no visible global function definition for ‘title’
Undefined global functions or variables:
  legend lines optim optimize segments title
Consider adding
  importFrom("graphics", "legend", "lines", "segments", "title")
  importFrom("stats", "optim", "optimize")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
CapDistSlope: no visible global function definition for ‘coef’
CapDistSlope: no visible global function definition for ‘lm’
EnergyEntropyDecomp: no visible global function definition for ‘legend’
FernholzDecomp: no visible global function definition for ‘legend’
Invest: no visible global function definition for ‘par’
Invest: no visible global function definition for ‘legend’
SimMarketModel: no visible global function definition for ‘rnorm’
plot.capdist: no visible global function definition for ‘abline’
plot.capdist: no visible global function definition for ‘lm’
plot.toymkt: no visible global function definition for ‘par’
plot.toymkt: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline coef legend lm par rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPoX5dK/R.INSTALL4f7b3463b58a/rematch/man/re_match.Rd:29: file link ‘regexpr’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPoX5dK/R.INSTALL4f7b3463b58a/rematch/man/re_match.Rd:20: file link ‘regexpr’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rematch.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmphffa2q/R.INSTALL136262123a1c/remedy/man/chunkr.Rd:21: file link ‘purl’ in package ‘knitr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/remedy.Rcheck/00install.out’ for details.
RearrangeData: no visible global function definition for ‘rainbow’
RearrangeData: no visible global function definition for ‘hclust’
RearrangeData: no visible global function definition for
  ‘as.dendrogram’
RearrangeData: no visible global function definition for ‘heatmap’
RearrangeData: no visible global function definition for ‘pdf’
RearrangeData: no visible global function definition for
  ‘colorRampPalette’
RearrangeData: no visible global function definition for ‘legend’
RearrangeData: no visible global function definition for ‘dev.off’
RearrangeJoseph: no visible global function definition for
  ‘write.table’
RearrangeJoseph: no visible global function definition for
  ‘as.dendrogram’
RearrangeJoseph: no visible global function definition for
  ‘order.dendrogram’
colorDendClass : colLab: no visible global function definition for
  ‘is.leaf’
colorDendClass: no visible global function definition for ‘dendrapply’
testData1: no visible global function definition for ‘runif’
testData1: no visible global function definition for ‘image’
testData2: no visible global function definition for ‘runif’
testData2: no visible global function definition for ‘image’
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf rainbow runif write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘A.txt’ ‘minI.txt’ ‘minJ.txt’
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GlobTestMissing: no visible global function definition for ‘lme’
GlobTestMissing: no visible global function definition for ‘anova’
TestStatSP: no visible global function definition for ‘pf’
TestStatSimple: no visible global function definition for ‘ginv’
TestStatSimple: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
Found the following files/directories:
  ‘PackageCites.bib’
Found the following significant warnings:
  Rd warning: /tmp/RtmpLAIgZ7/R.INSTALL1c69ad7b05b/REPPlab/man/plot.epplab.Rd:28: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpLAIgZ7/R.INSTALL1c69ad7b05b/REPPlab/man/plot.epplab.Rd:66: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/REPPlab.Rcheck/00install.out’ for details.
MBoxtest: no visible global function definition for ‘var’
jrparams: no visible global function definition for ‘prcomp’
jrparams: no visible global function definition for ‘predict’
jrparams: no visible global function definition for ‘qchisq’
jrparams: no visible global function definition for ‘qf’
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
Rd file 'jrparams.Rd':
  \usage lines wider than 90 characters:
     jrparams(BLOCK.1, BLOCK.2, ncomp = min(c(dim(BLOCK.1), dim(BLOCK.2))), Cscrit=0.6, Rscrit=0.6)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmplFb1Fr/R.INSTALL7bafd45677f/reproj/man/reproj.Rd:32: file link ‘ptransform’ in package ‘proj4’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmplFb1Fr/R.INSTALL7bafd45677f/reproj/man/reproj.Rd:49: file link ‘ptransform’ in package ‘proj4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/reproj.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpkOSM1J/R.INSTALL873658e0dbe/repr/man/repr-options.Rd:15: file link ‘getOption’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/repr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp0Fo7J3/R.INSTALL7abc4af46429/repurrrsive/man/wesanderson.Rd:19: file link ‘wesanderson-package’ in package ‘wesanderson’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/repurrrsive.Rcheck/00install.out’ for details.
call.eqs: no visible global function definition for ‘write.table’
read.eqs: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf write.table
Consider adding
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Rd file 'call.eqs.rd':
  \examples lines wider than 100 characters:
     ##res <- call.eqs(EQSpgm = "C:/Program Files/EQS61/WINEQS.EXE", EQSmodel = "c:/eqs61/examples/manul7.eqs", serial = "1234")

Rd file 'run.eqs.rd':
  \examples lines wider than 100 characters:
     ##res <- run.eqs(EQSpgm = "C:/Program Files/EQS61/WINEQS.EXE", EQSmodel = "c:/eqs61/examples/manul7.eqs", serial = "1234")
     ##  res <- run.eqs(EQSpgm = "C:/Program Files/EQS61/WINEQS.EXE", EQSmodel = "c:/eqs61/examples/manul7.eqs", data = X, datname = "manul7 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /tmp/RtmpirKs3v/R.INSTALL5fe56b0b2c45/Require/man/modifyList2.Rd:14: file link ‘Reduce’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Require.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘P.csv’ ‘correct_alpha.csv’ ‘correct_beta.csv’ ‘correct_gamma.csv’
  ‘correct_lambda.csv’ ‘correct_perm_list.csv’ ‘correct_psi.csv’
Found the following significant warnings:
  Rd warning: /tmp/RtmpMnBAch/R.INSTALL22272134c96/resample/man/IfElse.Rd:46: file link ‘if’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMnBAch/R.INSTALL22272134c96/resample/man/cat0.Rd:32: file link ‘paste0’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpMnBAch/R.INSTALL22272134c96/resample/man/colVars.Rd:38: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/resample.Rcheck/00install.out’ for details.
.resampleMakeFunction: no visible global function definition for ‘is’
.resampleSetSeed: no visible global function definition for ‘runif’
CI.bca: no visible global function definition for ‘is’
CI.bca: no visible global function definition for ‘qnorm’
CI.bca: no visible global function definition for ‘pnorm’
CI.t: no visible global function definition for ‘qt’
ExpandProbs: no visible global function definition for ‘pnorm’
ExpandProbs: no visible global function definition for ‘qt’
colVars : f: no visible global function definition for ‘var’
colVars: no visible global function definition for ‘var’
hist.resample: no visible global function definition for ‘density’
hist.resample: no visible global function definition for ‘lines’
hist.resample: no visible global function definition for ‘points’
hist.resample: no visible global function definition for ‘approx’
hist.resample: no visible global function definition for ‘segments’
resample: no visible global function definition for ‘is’
samp.bootknife: no visible global function definition for ‘runif’
samp.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /tmp/RtmpTbQBXu/R.INSTALL51b02f2cf833/reshape2/man/cast.Rd:77: file link ‘.’ in package ‘plyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/reshape2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpW7PxQG/R.INSTALL5551330cbe18/restfulr/man/Media-class.Rd:74: file link ‘XMLAbstractNode-class’ in package ‘XML’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/restfulr.Rcheck/00install.out’ for details.
GUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /tmp/RtmpSipS3c/R.INSTALL7c6667c22e60/reutils/man/xattr.Rd:20: file link ‘xpathApply’ in package ‘XML’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSipS3c/R.INSTALL7c6667c22e60/reutils/man/xname.Rd:18: file link ‘xpathApply’ in package ‘XML’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSipS3c/R.INSTALL7c6667c22e60/reutils/man/xset.Rd:14: file link ‘xpathApply’ in package ‘XML’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpSipS3c/R.INSTALL7c6667c22e60/reutils/man/xvalue.Rd:18: file link ‘xpathApply’ in package ‘XML’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/reutils.Rcheck/00install.out’ for details.
plot.reweight: no visible global function definition for ‘par’
plot.reweight: no visible global function definition for ‘density’
plot.reweight: no visible global function definition for ‘rug’
reweight: no visible global function definition for ‘aggregate’
search.best.h: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate density par quantile rug
Consider adding
  importFrom("graphics", "par", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
FDSNGetTimeSeries: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
fs_author_ids : <anonymous>: no visible global function definition for
  ‘select.list’
fs_download : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  BSD 3-clause License
Packages in Depends field not imported from:
  ‘XML’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
quoteFXTsData : function.fx: no visible global function definition for
  ‘xmlValue’
quoteFundTsData : function.fund: no visible global function definition
  for ‘xmlValue’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlSize’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlValue’
quoteTsData: no visible global function definition for ‘xmlRoot’
quoteTsData: no visible global function definition for ‘htmlTreeParse’
quoteTsData: no visible global function definition for
  ‘xmlErrorCumulator’
quoteTsData: no visible global function definition for ‘xmlSize’
toXts: no visible global function definition for ‘as.xts’
Undefined global functions or variables:
  as.xts htmlTreeParse xmlErrorCumulator xmlRoot xmlSize xmlValue
Found the following significant warnings:
  Rd warning: /tmp/RtmppTNNaT/Rbuilde5c26aba371/RFmerge/man/RFmerge.Rd:84: file link ‘makeForkCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmppTNNaT/Rbuilde5c26aba371/RFmerge/man/RFmerge.Rd:84: file link ‘parRapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmppTNNaT/Rbuilde5c26aba371/RFmerge/man/RFmerge.Rd:85: file link ‘parRapply’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RFmerge.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpXMCWW3/R.INSTALL7fcc507276a6/rfml/man/as.ml.data.frame.Rd:44: file link ‘as.data.frame’ in package ‘rfml’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXMCWW3/R.INSTALL7fcc507276a6/rfml/man/ml.data.frame.Rd:62: file link ‘as.data.frame’ in package ‘rfml’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpXMCWW3/R.INSTALL7fcc507276a6/rfml/man/rm.ml.data.frame.Rd:28: file link ‘as.data.frame’ in package ‘rfml’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rfml.Rcheck/00install.out’ for details.
.testLTS: no visible binding for global variable ‘stackloss’
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
Found the following files/directories:
  ‘interactions.dot’
gabriel.plot: no visible global function definition for ‘barplot’
gabriel.plot: no visible global function definition for ‘arrows’
rgabriel: no visible binding for global variable ‘sd’
rgabriel : psmm_x: no visible global function definition for ‘pnorm’
rgabriel : psmm: no visible global function definition for ‘integrate’
rgabriel : qsmm: no visible global function definition for ‘qnorm’
rgabriel : qsmm: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘gsl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for ‘integrate’
gammaIntegral : <anonymous>: no visible global function definition for
  ‘hyperg_1F1’
gammaMLE: no visible global function definition for ‘weighted.mean’
gammaMME: no visible binding for global variable ‘sd’
gammaMME: no visible binding for global variable ‘var’
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /tmp/RtmphNqrZN/R.INSTALL1b41444b06ff/rgenoud/man/genoud.Rd:450: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rgenoud.Rcheck/00install.out’ for details.
genoud: multiple local function definitions for ‘fn1.bfgs’ with
  different formal arguments
genoud: multiple local function definitions for ‘gr1’ with different
  formal arguments
genoud: multiple local function definitions for ‘hess.fn’ with
  different formal arguments
genoud_transform: multiple local function definitions for ‘fn1.bfgs’
  with different formal arguments
genoud_transform: multiple local function definitions for ‘gr1’ with
  different formal arguments
Found the following significant warnings:
  Rd warning: /tmp/RtmpN4Vz6c/R.INSTALL127138c03eba/rgeos/man/bbox2SP.Rd:14: file link ‘CRS’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4Vz6c/R.INSTALL127138c03eba/rgeos/man/bbox2SP.Rd:19: file link ‘gIntersection’ in package ‘rgeos’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpN4Vz6c/R.INSTALL127138c03eba/rgeos/man/labelpt.Rd:120: file link ‘pointLabel’ in package ‘maptools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rgeos.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/Rtmp3zQT3E/R.INSTALL2e505af47ec1/Rglpk/man/Rglpk_read_file.Rd:43: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3zQT3E/R.INSTALL2e505af47ec1/Rglpk/man/Rglpk_read_file.Rd:45: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp3zQT3E/R.INSTALL2e505af47ec1/Rglpk/man/Rglpk_solve.Rd:93: file link ‘Rsymphony_solve_LP’ in package ‘Rsymphony’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rglpk.Rcheck/00install.out’ for details.