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.
Undeclared package ‘moments’ in Rd xrefs
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘ie2miscdata’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘testit’
  All declared Imports should be used.
Undeclared package ‘matlab’ in Rd xrefs
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
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NB: .First.lib is obsolete and will not be used in R 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.
File ‘ifa/libs/ifa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifctools/libs/ifctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘IFP/libs/IFP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifs/libs/ifs.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘IgorR/R/ReadIgorBinary.R’:
  assign(WaveName, rval, envir = .GlobalEnv)
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.4Mb
Malformed Description field: should contain one or more complete sentences.
File ‘IHSEP/libs/IHSEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ihs.mle: no visible global function definition for ‘as.formula’
pihs: no visible global function definition for ‘pnorm’
qihs: no visible global function definition for ‘qnorm’
rihs: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  as.formula pnorm qnorm rnorm
Consider adding
  importFrom("stats", "as.formula", "pnorm", "qnorm", "rnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘fit.mod6.ps’ ‘res.mod6d.ps’
Undeclared packages ‘bmp’, ‘jpeg’, ‘png’, ‘tiff’ in Rd xrefs
installed size is 51.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.1Mb
    include   3.0Mb
    libs     44.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Undeclared package ‘viridisLite’ in Rd xrefs
IMIS: no visible global function definition for ‘sample.prior’
IMIS: no visible global function definition for ‘var’
IMIS: no visible global function definition for ‘cov’
IMIS: no visible global function definition for ‘prior’
IMIS: no visible global function definition for ‘likelihood’
IMIS : posterior: no visible global function definition for ‘prior’
IMIS : posterior: no visible global function definition for
  ‘likelihood’
IMIS: no visible global function definition for ‘optim’
IMIS: no visible global function definition for ‘rnorm’
IMIS: no visible global function definition for ‘mahalanobis’
IMIS: no visible global function definition for ‘cov.wt’
IMIS: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  cov cov.wt dnorm likelihood mahalanobis optim prior rnorm
  sample.prior var
Consider adding
  importFrom("stats", "cov", "cov.wt", "dnorm", "mahalanobis", "optim",
             "rnorm", "var")
to your NAMESPACE file.
prepare_Rd: IMIS.Rd:26: Dropping empty section \keyword
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Undeclared package ‘mirt’ in Rd xrefs
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.6Mb
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
heter_IV2: no visible global function definition for ‘poly’
heter_IV2: no visible global function definition for ‘lm’
heter_IV2: no visible global function definition for ‘step’
heter_IV2: no visible global function definition for ‘pnorm’
heter_IV2: no visible global function definition for ‘qnorm’
homo_IV1: no visible global function definition for ‘coef’
homo_IV1: no visible global function definition for ‘pnorm’
homo_IV1: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  coef lm pnorm poly qnorm step
Consider adding
  importFrom("stats", "coef", "lm", "pnorm", "poly", "qnorm", "step")
to your NAMESPACE file.
prepare_Rd: heter_IV2.Rd:82-84: Dropping empty section \note
prepare_Rd: heter_IV2.Rd:88-90: Dropping empty section \seealso
prepare_Rd: homo_IV1.Rd:65-67: Dropping empty section \note
prepare_Rd: homo_IV1.Rd:71-73: Dropping empty section \seealso
prepare_Rd: impact.Rd:31-33: Dropping empty section \source
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
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.
File ‘imputeMDR/libs/imputeMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
File ‘imputeMulti/libs/imputeMulti.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Warning: no function found corresponding to methods exports from ‘IM’ for: ‘initialize’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘bmp’ ‘jpeg’ ‘methods’ ‘png’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MultiIm-class.Rd':
  \examples lines wider than 100 characters:
     #create MultiIm object, calculate generalized Pseudo-Zernike moments, invariants, and reconstruction for all images
             #create MultiIm object, calculate discrete Chebyshev moments, invariants, and reconstruction for all images
             #create MultiIm object, calculate continuous Chebyshev - Legendre moments, invariants, and reconstruction for all images

Rd file 'demoPoly.Rd':
  \examples lines wider than 100 characters:
             #display generalized Pseudo-Zernike polynomials of order and repetition (3,2), (4,2), (5,3), (6,3) 

Rd file 'momentObj.Rd':
  \examples lines wider than 100 characters:
             #calculate bivariate Legendre/Gegenbauer moments up to orders 50 and 100 with parameter 1 for Gegenbauer moments.
             #compute Radial Harmonic-Fourier moment invariants of a list of images, using up to order 10 and repetition 10

These lines will be truncated in the PDF manual.
File ‘IM/libs/IM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘V8’ ‘assertive’ ‘shinydashboard’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘IncucyteZoomExport.Rmd’ using rmarkdown
--- finished re-building ‘IncucyteZoomExport.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from /data/gannet/ripley/R/packages/tests-clang/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
/data/gannet/ripley/R/packages/tests-clang/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following file failed:
  ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
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.
Undeclared package ‘gee’ in Rd xrefs
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Undeclared package ‘minfi’ in Rd xrefs
Note: found 151 marked UTF-8 strings
File ‘influenceR/libs/influenceR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
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.
Undeclared package ‘R.methodsS3’ in Rd xrefs
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'library' or 'require' calls to packages already attached by Depends:
  ‘compiler’ ‘deSolve’ ‘lattice’ ‘nlme’
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘insideRODE/R/zzz.r’:
  .First.lib calls:
    require(nlme)
    require(lattice)
    require(deSolve)
    require(compiler)

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

cfLSODE: no visible global function definition for ‘deriv’
cfODE: no visible global function definition for ‘deriv’
cfVODE: no visible global function definition for ‘deriv’
cpLSODE: no visible global function definition for ‘deriv’
cpODE: no visible global function definition for ‘deriv’
cpVODE: no visible global function definition for ‘deriv’
nlmLSODE: no visible global function definition for ‘deriv’
nlmLSODEcp: no visible global function definition for ‘deriv’
nlmODE: no visible global function definition for ‘deriv’
nlmODEcp: no visible global function definition for ‘deriv’
nlmVODE: no visible global function definition for ‘deriv’
nlmVODEcp: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Undeclared package ‘emmeans’ in Rd xrefs
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘flextable’ ‘officer’
  All declared Imports should be used.
Undeclared packages ‘quantreg’, ‘effects’, ‘Hmisc’, ‘rockchalk’, ‘pequod’ in Rd xrefs
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.
File ‘Interact/libs/Interact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
compute_design_performance: no visible global function definition for
  ‘read.csv’
compute_design_performance : get_power: no visible global function
  definition for ‘rnorm’
compute_design_performance : power_curve_plot: no visible global
  function definition for ‘lines’
compute_design_performance : power_curve_plot: no visible global
  function definition for ‘legend’
compute_design_performance : expected_sample_size_plot: no visible
  global function definition for ‘lines’
compute_design_performance : expected_sample_size_plot: no visible
  global function definition for ‘legend’
compute_design_performance : expected_duration_plot: no visible global
  function definition for ‘lines’
compute_design_performance : expected_duration_plot: no visible global
  function definition for ‘legend’
compute_design_performance : boundary_adapt_plot: no visible global
  function definition for ‘matplot’
compute_design_performance : boundary_adapt_plot: no visible global
  function definition for ‘legend’
compute_design_performance : boundary_standard_H0C_plot: no visible
  global function definition for ‘matplot’
compute_design_performance : boundary_standard_H0C_plot: no visible
  global function definition for ‘legend’
compute_design_performance : boundary_standard_H01_plot: no visible
  global function definition for ‘matplot’
compute_design_performance : boundary_standard_H01_plot: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  legend lines matplot read.csv rnorm
Consider adding
  importFrom("graphics", "legend", "lines", "matplot")
  importFrom("stats", "rnorm")
  importFrom("utils", "read.csv")
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.
Undeclared package ‘colorspace’ in Rd xrefs
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘Interpol/R/AAdescriptor.R’:
  data(AAindex)
See section ‘Good practice’ in ‘?data’.
prepare_Rd: AAdescriptor.Rd:25-27: Dropping empty section \details
prepare_Rd: AAdescriptor.Rd:39-41: Dropping empty section \note
prepare_Rd: AAdescriptor.Rd:45-47: Dropping empty section \seealso
prepare_Rd: AAindex.Rd:11-12: Dropping empty section \format
prepare_Rd: AAindex.Rd:1080-1081: Dropping empty section \source
prepare_Rd: AAindex.Rd:1085-1086: Dropping empty section \examples
prepare_Rd: Interpol.Rd:35-37: Dropping empty section \details
prepare_Rd: Interpol.Rd:47-49: Dropping empty section \note
prepare_Rd: Interpol.Rd:53-55: Dropping empty section \seealso
prepare_Rd: V3.Rd:11-12: Dropping empty section \format
prepare_Rd: V3.Rd:13-14: Dropping empty section \details
prepare_Rd: V3.Rd:15-16: Dropping empty section \source
prepare_Rd: V3.Rd:20-21: Dropping empty section \examples
Rd file 'Interpol.Rd':
  \examples lines wider than 100 characters:
             plot(unlist(b), type="l", col="darkgreen", ylim=c(-3,3), ylab="descriptor value", xlab="sequence position", lwd=2)
             lines(seq(1,length(unlist(b)),(length(unlist(b))/length(as.vector(c)))),as.vector(c), col="red", lwd=2)

These lines will be truncated in the PDF manual.
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.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Undeclared packages ‘RcppEigen’, ‘tripack’ in Rd xrefs
icScoreTest: no visible global function definition for ‘pnorm’
icScoreTest: no visible global function definition for ‘pchisq’
icfit.formula: no visible global function definition for ‘terms’
icfit.formula: no visible global function definition for
  ‘model.extract’
icfitBootCI: no visible global function definition for ‘binom.test’
ictest.formula: no visible global function definition for
  ‘model.extract’
plot.icfit: no visible global function definition for ‘gray’
plot.icfit: no visible global function definition for ‘axis’
plot.icfit : polygon.icfit: no visible global function definition for
  ‘polygon’
scoresFromFit: no visible global function definition for ‘dnorm’
scoresFromFit: no visible global function definition for ‘qnorm’
wsrHLYpclt: no visible global function definition for ‘model.matrix’
wsrHLYpclt: no visible global function definition for ‘pchisq’
wsrHLYpclt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis binom.test dnorm gray model.extract model.matrix pchisq pnorm
  polygon qnorm terms
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "polygon")
  importFrom("stats", "binom.test", "dnorm", "model.extract",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
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.
Namespaces in Imports field not imported from:
  ‘EValue’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
Undeclared package ‘nlstools’ in Rd xrefs
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.
Package suggested but not available for checking: ‘iNZightPlots’
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘kableExtra’ ‘markdown’ ‘reshape2’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Note: found 75 marked UTF-8 strings
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.
Note: found 53206 marked UTF-8 strings
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘GlobalOptions’ ‘dplyr’ ‘testthat’
  All declared Imports should be used.
Non-standard file/directory found at top level:
  ‘beta’
Warning: no function found corresponding to methods exports from ‘ipdmeta’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the 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.
ipd.meta.power.base.function : power: no visible global function
  definition for ‘qnorm’
ipd.meta.power.base.function : power: no visible global function
  definition for ‘pnorm’
ipd.meta.power.base.function: no visible global function definition for
  ‘qnorm’
ipdlme.hetero: no visible global function definition for ‘new’
ipdlme.homo: no visible global function definition for ‘new’
plot_ipdlme: no visible global function definition for ‘par’
plot_ipdlme: no visible global function definition for ‘abline’
plot_ipdlme: no visible global function definition for ‘axis’
plot_ipdlme: no visible global function definition for ‘segments’
confint,ipdlme: no visible global function definition for ‘qt’
plot,ipdlme: no visible global function definition for ‘par’
plot,ipdlme: no visible global function definition for ‘abline’
plot,ipdlme: no visible global function definition for ‘axis’
plot,ipdlme: no visible global function definition for ‘segments’
summary,ipdlme: no visible global function definition for ‘pt’
Undefined global functions or variables:
  abline axis new par pnorm pt qnorm qt segments
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "pt", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
File ‘ipfp/libs/ipfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘version’
Undeclared packages ‘randomForest’, ‘party’ in Rd xrefs
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
Note: found 12 marked UTF-8 strings
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
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.
File ‘ISBF/libs/ISBF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Note: found 104 marked UTF-8 strings
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.2Mb
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
File ‘isocir/libs/isocir.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘Unicode’ in Rd xrefs
Note: found 7418 marked UTF-8 strings
Undeclared package ‘multtest’ in Rd xrefs
'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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Undeclared package ‘surveillance’ in Rd xrefs
File ‘ISR3/libs/ISR3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘pangaear’ ‘rcrossref’ ‘rgdal’ ‘stringr’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.6Mb
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.
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.
Undeclared package ‘AER’ in Rd xrefs
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.
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
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.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          21.0Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
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.
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggExtra’ ‘ggplot2’ ‘grid’ ‘gridExtra’ ‘mcmcplots’
  All declared Imports should be used.
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
File ‘JASPAR/libs/JASPAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘version’
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'.
File ‘JavaGD/libs/JavaGD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
getSysinfo: no visible global function definition for ‘sessionInfo’
getVecInfo: no visible global function definition for ‘sd’
isSeriesConstant: no visible global function definition for ‘median’
labelMargins: no visible global function definition for ‘mtext’
plotBG: no visible global function definition for ‘polygon’
plotBG: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘text’
plotImageRotated: no visible global function definition for
  ‘heat.colors’
plotImageRotated: no visible global function definition for ‘par’
plotImageRotated: no visible global function definition for ‘image’
plotImageRotated: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘par’
plotNLines: no visible global function definition for ‘mtext’
plotNLines: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘points’
plotNLines: no visible global function definition for ‘sd’
userCoords: no visible global function definition for ‘par’
Undefined global functions or variables:
  axis heat.colors image median mtext par points polygon sd sessionInfo
  text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "points",
             "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BurStFin’ ‘MASS’ ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
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.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
  ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
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.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   5.0Mb
Undeclared package ‘ordinal’ in Rd xrefs
PKG_CXXFLAGS set in ‘src/Makevars’ without any corresponding files
   PKG_CXXFLAGS set in ‘src/Makevars.win’ without any corresponding files
'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.
Packages in Depends field not imported from:
  ‘Rsolnp’ ‘dglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
File ‘jpeg/libs/jpeg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 176 marked UTF-8 strings
Note: found 188 marked UTF-8 strings
‘configure’: /bin/bash is not portable
File ‘JRF/libs/JRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
‘cleanup’: /bin/bash is not portable
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘survC1’
  All declared Imports should be used.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
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.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.9Mb
Undeclared packages ‘wec’, ‘arm’, ‘interactions’, ‘effects’, ‘piecewiseSEM’ in Rd xrefs
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.
Undeclared package ‘ggplot2’ in Rd xrefs
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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.
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘kaps/libs/kaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
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.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
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.
Note: found 11 marked UTF-8 strings
Found the following files/directories:
  ‘KDVizGroup1.html’ ‘KDVizGroup1_files’
Undeclared packages ‘nor1mix’, ‘ks’, ‘sm’, ‘locfit’, ‘orthopolynom’ in Rd xrefs
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.
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘keras’
  All declared Imports should be used.
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.
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Namespace in Imports field not imported from: ‘quanteda’
  All declared Imports should be used.
‘configure’: /bin/bash is not portable
File ‘KFKSDS/libs/KFKSDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
kissmigDummyS: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
File ‘kissmig/libs/kissmig.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘sapa’
Unknown package ‘sapa’ in Rd xrefs
Running examples in ‘kitagawa-Ex.R’ failed
The error most likely occurred in:

> ### Name: cross_spectrum
> ### Title: Calculate the cross-spectrum of two timeseries
> ### Aliases: cross_spectrum cross_spectrum.mts cross_spectrum.default
> 
> ### ** Examples
> 
> require(stats)
> 
> n <- 1000
> ramp <- seq_len(n)
> parab <- ramp^2
> 
> set.seed(1255)
> X <- ts(rnorm(n) + ramp/2)
> Y <- ts(rnorm(n) + ramp/10 + parab/100)
> 
> # Calculate the cross spectrum, multitaper if K is not NULL
> csd <- cross_spectrum(X, Y, k=20)
calculating sine-multitaper spectra...
Error in loadNamespace(name) : there is no package called ‘sapa’
Calls: cross_spectrum ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
File ‘kknn/libs/kknn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘clustMixType’, ‘randomForest’, ‘ClustVarLV’ in Rd xrefs
Package which this enhances but not available for checking: ‘rkward’
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.
Note: found 8 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘gplots’ ‘wesanderson’
  All declared Imports should be used.
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’.
Malformed Description field: should contain one or more complete sentences.
noe.compute.pv: no visible global function definition for ‘punif’
Undefined global functions or variables:
  punif
Consider adding
  importFrom("stats", "punif")
to your NAMESPACE file.
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 files/directories:
  ‘cld1.Rdata’ ‘main.tex’ ‘myCld.Rdata’ ‘myCld3d.Rdata’ ‘scene.asy’
Warning: no function found corresponding to methods exports from ‘kmlcov’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the 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.
Undeclared package ‘kml3d’ in Rd xrefs
File ‘kml/libs/kml.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘cld1.Rdata’ ‘ld.Rdata’ ‘myCld.Rdata’
File ‘kmlShape/libs/kmlShape.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following files/directories:
  ‘Killed after ’
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dataFiller : central.value: no visible global function definition for
  ‘median’
dataFiller: no visible global function definition for ‘daisy’
dataFiller: no visible global function definition for ‘complete.cases’
knnMCN: no visible global function definition for ‘cov’
knnVCN: no visible global function definition for ‘dist’
Undefined global functions or variables:
  complete.cases cov daisy dist median
Consider adding
  importFrom("stats", "complete.cases", "cov", "dist", "median")
to your NAMESPACE file.
Rd file 'knnMCN.Rd':
  \examples lines wider than 100 characters:
                 ") ", "you have selected is bigger than the capacity of one class in your training data set", 
             stop("\nWarnings:\nsample variance-covariance matrix is singular,\nand larger class sample capacity is required ,\nor you can t ... [TRUNCATED]
                     stop("\nWarnings:\nsample variance-covariance matrix is singular,\nand larger class sample capacity is required ,\nor y ... [TRUNCATED]

Rd file 'knnVCN.Rd':
  \examples lines wider than 100 characters:
                 ") ", "you have selected is bigger than the capacity of one class in your training data set", 

These lines will be truncated in the PDF manual.
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.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared package ‘splancs’ in Rd xrefs
Note: found 9 marked Latin-1 strings
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’
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 52458 marked UTF-8 strings
File ‘kolmim/libs/kolmim.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘linl’ in Rd xrefs
Namespace in Imports field not imported from: ‘mice’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
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.
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
Found the following hidden files and directories:
  .Rbuildindex.10034
  .Rbuildindex.31551
  .Rbuildindex.31678
  .Rbuildindex.9995
  inst/doc/.fr-hy2VZf
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'ROC.graphic.ktsp.Rd':
  \usage lines wider than 90 characters:
     ROC.graphic.ktsp(roc, m = 1, boxplot = TRUE, AUC = TRUE, auc.x = 0.55, auc.y = 0.25, box.col = "yellow", line.col = "red", multiple.col ... [TRUNCATED]

Rd file 'ROC.offset.Rd':
  \usage lines wider than 90 characters:
     ROC.offset(dat, grp, n = 200, healthy = NULL, seed = NULL, para1 = 200, para2 = 1, mult.cutoff = FALSE, length = 40, display = FALSE, m ... [TRUNCATED]

Rd file 'ROC.voting.Rd':
  \usage lines wider than 90 characters:
     ROC.voting(dat, grp, n = 200, healthy = NULL, seed = NULL, para1 = 200, para2 = 1, length = 40, display = FALSE, med = FALSE)

Rd file 'bootstrap.ktsp.Rd':
  \usage lines wider than 90 characters:
     bootstrap.ktsp(dat, grp, k = NULL, seed = NULL, n = 500, length = 40, display = FALSE, med = FALSE)

Rd file 'cv.Rd':
  \usage lines wider than 90 characters:
     cv(dat, grp, cross = 5, display = FALSE, length = 40, seed = NULL, med = FALSE, healthy = NULL)

Rd file 'cv2.Rd':
  \usage lines wider than 90 characters:
     cv2(indice, dat, grp, cross = 5, display = FALSE, length = 40, seed = NULL, med = FALSE, healthy = NULL)

Rd file 'ktspcalc.Rd':
  \usage lines wider than 90 characters:
     ktspcalc(dat, grp, k = NULL, cross = 5, performance = FALSE, healthy = NULL, seed = NULL, display = TRUE, length = 40, med = FALSE)

Rd file 'ktspcalc2.Rd':
  \usage lines wider than 90 characters:
     ktspcalc2(indice, dat, grp, length = 40, cross =5, display = display, med = FALSE, performance = FALSE, seed = NULL, healthy = NULL)

These lines will be truncated in the PDF manual.
S3 methods shown with full name in documentation object 'predict.ktsp':
  ‘predict.ktsp’

S3 methods shown with full name in documentation object 'print.ktsp':
  ‘print.ktsp’

S3 methods shown with full name in documentation object 'summary.ktsp':
  ‘summary.ktsp’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘ktspair/libs/ktspair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
Note: found 95 marked UTF-8 strings
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
Found the following files/directories:
  ‘m.kvh’ ‘test.kvh’
Undeclared package ‘kza’ in Rd xrefs
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'
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  18.0Mb
Undeclared package ‘fso’ in Rd xrefs
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Malformed Description field: should contain one or more complete sentences.
extended.figures: no visible global function definition for ‘par’
extended.figures: no visible global function definition for ‘runif’
extended.figures : figure2: no visible global function definition for
  ‘hist’
extended.figures : figure2: no visible global function definition for
  ‘axis’
extended.figures : figure3 : <anonymous>: no visible global function
  definition for ‘median’
extended.figures : figure3: no visible global function definition for
  ‘barplot’
Undefined global functions or variables:
  axis barplot hist median par runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "median", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Undeclared package ‘rlang’ in Rd xrefs
Undeclared packages ‘carData’, ‘factoextra’, ‘labstatR’ in Rd xrefs
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Undeclared package ‘sampling’ in Rd xrefs
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.
Package suggested but not available for checking: ‘DiceOptim’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
Undeclared package ‘spdep’ in Rd xrefs
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Undeclared package ‘plyr’ in Rd xrefs
File ‘LakeMetabolizer/libs/LakeMetabolizer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Undeclared package ‘gsl’ in Rd xrefs
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').
File ‘LANDD/libs/LANDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘callr’ ‘collections’ ‘desc’ ‘parallel’ ‘repr’
  All declared Imports should be used.
Running ‘testthat.R’ [22s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(lans2r)
  > 
  > test_check("lans2r")
  ── 1. Failure: test that it is possible to load LANS maps (@test-load-data.R#81)
  `... <- NULL` produced warnings.
  
  ── 2. Failure: test that transformation safety checks are in place (@test-transf
  spread_data(bind_rows(a, b)) not equal to full_join(...).
  Names: 2 string mismatches
  Component 3: Mean relative difference: 1.073274
  Component 4: Mean relative difference: 8.788482
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 142 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 2 ]
  1. Failure: test that it is possible to load LANS maps (@test-load-data.R#81) 
  2. Failure: test that transformation safety checks are in place (@test-transformations.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.0Mb
    help   1.1Mb
Found the following files/directories:
  ‘example.llo’
Note: found 6 marked UTF-8 strings
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.
File ‘lars/libs/lars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘glmnet’ in Rd xrefs
File ‘LassoNet/libs/LassoNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘lassoshooting/libs/lassoshooting.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘ggplot2’ in Rd xrefs
Undeclared package ‘zoo’ in Rd xrefs
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Undeclared packages ‘VGAM’, ‘tseries’ in Rd xrefs
Package suggested but not available for checking: ‘texmex’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ReinforcementLearning’ ‘ggplot2’ ‘grDevices’ ‘h2o’ ‘lubridate’
  ‘magrittr’ ‘openssl’ ‘readr’ ‘stringr’
  All declared Imports should be used.
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').
File ‘lbfgs/libs/lbfgs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
File ‘lbiassurv/libs/lbiassurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
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 files/directories:
  ‘fitted.pdf’
File ‘lda/libs/lda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘tm’ in Rd xrefs
Undeclared package ‘RColorBrewer’ in Rd xrefs
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.
Undeclared package ‘Hmisc’ in Rd xrefs
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.
Malformed Description field: should contain one or more complete sentences.
prepare_Rd: HWE2sided.Rd:15-16: Dropping empty section \details
prepare_Rd: HWE2sided.table.Rd:17-18: Dropping empty section \details
prepare_Rd: LD2sided.pvals.Rd:13-14: Dropping empty section \details
File ‘leaderCluster/libs/leaderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Note: found 1096 marked UTF-8 strings
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
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.
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LearningRlab/libs/LearningRlab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘pracma’ in Rd xrefs
Note: found 78 marked UTF-8 strings
Note: found 51 marked UTF-8 strings
Undeclared packages ‘purrr’, ‘dplyr’ in Rd xrefs
Undeclared package ‘MESS’ in Rd xrefs
Note: found 3 marked UTF-8 strings
File ‘lgarch/libs/lgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Undeclared package ‘LiblineaR’ in Rd xrefs
File ‘LiblineaR.ACF/libs/LiblineaR.ACF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LiblineaR/libs/LiblineaR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
‘configure’: /bin/bash is not portable
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   1.2Mb
    libs      8.7Mb
Running ‘testthat.R’ [113s/134s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > rgdal::set_thin_PROJ6_warnings(TRUE)
  > test_check("lidR")
  ── 1. Failure: lastrees supports a LAScatalog (@test-lastrees.R#175)  ──────────
  length(na.omit(unique(las@data$treeID))) not equal to 274.
  1/1 mismatches
  [1] 272 - 274 == -2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1162 | SKIPPED: 0 | WARNINGS: 66 | FAILED: 1 ]
  1. Failure: lastrees supports a LAScatalog (@test-lastrees.R#175) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Undeclared package ‘future’ in Rd xrefs
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.
Note: found 7 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ddpcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
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.
Undeclared package ‘actuar’ in Rd xrefs
Note: found 15 marked UTF-8 strings
File ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘magrittr’ in Rd xrefs
Note: found 1529 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
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.
Undeclared package ‘pinp’ in Rd xrefs
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’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  10.4Mb
‘configure’: /bin/bash is not portable
Note: found 28 marked UTF-8 strings
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.
Undeclared package ‘keras’ in Rd xrefs
File ‘listdtr/libs/listdtr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
Note: found 109 marked UTF-8 strings
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs      20.7Mb
    testdata   1.6Mb
'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.
mq.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for ‘plot.missing’
Undefined global functions or variables:
  plot.missing
Found the following files/directories:
  ‘cross.data.file.csv’ ‘qtl_analysis_reports’
File ‘lmeNBBayes/libs/lmeNBBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lmeNB/libs/lmeNB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
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.
Undeclared packages ‘sfsmisc’, ‘mnormt’ in Rd xrefs
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘lmmlasso’
Packages in Depends field not imported from:
  ‘emulator’ ‘methods’ ‘miscTools’ ‘penalized’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'plot.lmmlasso.Rd':
  \examples lines wider than 100 characters:
     fit <- lmmlasso(x=classroomStudy$X,y=classroomStudy$y,z=classroomStudy$Z,grp=classroomStudy$grp,lambda=15,pdMat="pdIdent")

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
Found the following files/directories:
  ‘basic_1_HOTAIR_MXI1_CD58.pdf’ ‘basic_2_HOTAIR_MXI1_PRKCE.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_exp_test.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_exp_train.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_test_curve.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_test_score.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_train_curve.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_train_score.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_exp_test.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_exp_train.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_test_curve.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_test_score.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_train_curve.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_train_score.pdf’
Found the following files/directories:
  ‘tTestTable.rda’
File ‘localgauss/libs/localgauss.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
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.
File ‘locits/libs/locits.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 23 marked UTF-8 strings
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modules’
  All declared Imports should be used.
Undeclared packages ‘logcondens’, ‘colorspace’ in Rd xrefs
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
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.
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’
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘LogitNet/libs/LogitNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘loglognorm/libs/loglognorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘lokern/libs/lokern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
Found the following files/directories:
  ‘main.tex’ ‘scene.asy’
Note: found 994 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
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.
amendColumns: no visible global function definition for ‘setNames’
fillColumns: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘futile.options’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lowmemtkmeans/libs/lowmemtkmeans.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.2Mb
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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'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.
File ‘LPStimeSeries/libs/LPStimeSeries.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘LRcontrast/libs/LRcontrast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 55 marked UTF-8 strings
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following files/directories:
  ‘homer.bmp’ ‘homer.jpeg’ ‘homer.pdf’ ‘homer.png’ ‘homer.ps’
  ‘homer.tiff’
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.
installed size is 51.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  49.4Mb
Namespace in Imports field not imported from: ‘lavaan’
  All declared Imports should be used.
Undeclared packages ‘etable’, ‘xtable’, ‘tables’ in Rd xrefs
File ‘ltbayes/libs/ltbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘ltsa/libs/ltsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   2.0Mb
Undeclared package ‘shiny’ in Rd xrefs
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 files/directories:
  ‘test’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Undeclared package ‘zoo’ in Rd xrefs
File ‘lxb/libs/lxb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
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.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
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.
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
GNU make is a SystemRequirements.
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.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   7.4Mb
File ‘magree/libs/magree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Malformed Description field: should contain one or more complete sentences.
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  19.5Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
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.
File ‘MAMSE/libs/MAMSE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 328 marked UTF-8 strings
Undeclared package ‘qqman’ in Rd xrefs
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Undeclared package ‘nparLD’ in Rd xrefs
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 47.4Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.0Mb
    libs         42.1Mb
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.
File ‘mapfit/libs/mapfit.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgdal’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
'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.
Undeclared packages ‘rgbif’, ‘htmltools’ in Rd xrefs
Note: found 164 marked UTF-8 strings
Note: found 55 marked UTF-8 strings
Note: found 996 marked UTF-8 strings
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.
Undeclared package ‘plotrix’ in Rd xrefs
Undeclared packages ‘leafsync’, ‘slideview’ in Rd xrefs
Namespace in Imports field not imported from: ‘betareg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
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.
Undeclared package ‘maptools’ in Rd xrefs
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.
Undeclared packages ‘sae’, ‘rsae’, ‘JoSAE’ in Rd xrefs
Error(s) in re-building vignettes:
--- re-building ‘maSAE.Rnw’ using Sweave

Attaching package: ‘maSAE’

The following object is masked from ‘package:stats’:

    predict

--- finished re-building ‘maSAE.Rnw’

--- re-building ‘forestinventory_and_maSAE.Rmd’ using rmarkdown
--- finished re-building ‘forestinventory_and_maSAE.Rmd’

--- re-building ‘A_Taxonomy_of_Estimators.tex’ using tex
Error: processing vignette 'A_Taxonomy_of_Estimators.tex' failed with diagnostics:
Running 'texi2dvi' on 'A_Taxonomy_of_Estimators.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.74 \__kernel_quark_new_conditional:Nn
                                        \__xtemplate_quark_if_nil:N { F }
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.74 ...conditional:Nn \__xtemplate_quark_if_nil:N
                                                   { F }
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘A_Taxonomy_of_Estimators.tex’

SUMMARY: processing the following file failed:
  ‘A_Taxonomy_of_Estimators.tex’

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘mixsqp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs  11.9Mb
Package suggested but not available for checking: ‘WhatIf’
File ‘mateable/libs/mateable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘mathpix-Ex.R’ failed
The error most likely occurred in:

> ### Name: mathpix
> ### Title: Convert an image of an equation to a 'LaTeX' expression
> ### Aliases: mathpix
> 
> ### ** Examples
> 
> mathpix(system.file("extdata", "eq_no_01.png", package = "mathpix"), insert = FALSE)
Using Mathpix APP_ID=jcarroll
Warning: Mathpix says:
Account disabled
Error in if (body == "") { : argument is of length zero
Calls: mathpix -> rmarkdown_block
Execution halted
File ‘matie/libs/matie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
File ‘MAT/libs/MAT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘spdep’, ‘igraph’ in Rd xrefs
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Undeclared packages ‘dplyr’, ‘plyr’, ‘reshape2’, ‘reshape’ in Rd xrefs
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’
Undeclared package ‘tracerer’ in Rd xrefs
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.
File ‘MaXact/libs/MaXact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘dlm’, ‘clue’ in Rd xrefs
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
Note: found 66 marked UTF-8 strings
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.
Undeclared packages ‘logistf’, ‘brglm’ in Rd xrefs
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.
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
Note: found 6 marked Latin-1 strings
Undeclared package ‘gemtc’ in Rd xrefs
Unknown package ‘gemtc’ in Rd xrefs
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
Package suggested but not available for checking: ‘flare’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
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.
File ‘mcclust/libs/mcclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 suggested but not available for checking: ‘cplexAPI’
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.8Mb
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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’
Note: found 28 marked UTF-8 strings
Note: found 46 marked UTF-8 strings
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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
Undeclared packages ‘MCMCpack’, ‘bayesm’, ‘msm’ in Rd xrefs
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.1Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Undeclared package ‘coda’ in Rd xrefs
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘scatterplot3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.nsga2: no visible global function definition for ‘lines’
plot.nsga2: no visible global function definition for ‘pairs’
plot.nsga2.collection: no visible global function definition for
  ‘devAskNewPage’
Undefined global functions or variables:
  devAskNewPage lines pairs
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs")
to your NAMESPACE file.
File ‘mco/libs/mco.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
src/Makevars: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘bayesplot’ ‘methods’ ‘purrr’
  All declared Imports should be used.
Running ‘testthat.R’ [174s/211s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mcp)
  > 
  > test_check("mcp")
  ── 1. Failure: Good variance:
      y ~ 1 + sigma(x + I(x^2)) (@test-runs.R#277)  
  any(stringr::str_starts(attr(gg, "condition")$message, expected_error)) isn't true.
  
  ── 2. Failure: Good variance:
      y ~ 1 + sigma(x + I(x^2)) (@test-runs.R#277)  
  any(stringr::str_starts(attr(gg, "condition")$message, expected_error)) isn't true.
  
  ── 3. Failure: Good variance:
      y ~ 1, 1 + (1 | id) ~ rel(1) + I(x^2) + sigma(
  any(stringr::str_starts(attr(gg, "condition")$message, expected_error)) isn't true.
  
  ── 4. Failure: Good Poisson:
      y ~ 1 (@test-runs.R#277)  ─────────────────────
  any(stringr::str_starts(attr(gg, "condition")$message, expected_error)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1720 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 4 ]
  1. Failure: Good variance:
      y ~ 1 + sigma(x + I(x^2)) (@test-runs.R#277) 
  2. Failure: Good variance:
      y ~ 1 + sigma(x + I(x^2)) (@test-runs.R#277) 
  3. Failure: Good variance:
      y ~ 1, 1 + (1 | id) ~ rel(1) + I(x^2) + sigma(rel(1) + x) (@test-runs.R#277) 
  4. Failure: Good Poisson:
      y ~ 1 (@test-runs.R#277) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘mcr/libs/mcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
Depends: includes the non-default packages:
  'lattice', 'locfit', 'maptools', 'quantreg', 'RANN', 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘car’ ‘spatstat’ ‘spdep’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RANN’ ‘maptools’
  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’.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘covr’ ‘curl’ ‘devtools’ ‘gh’ ‘git2r’ ‘grDevices’ ‘httr’
  ‘knitr’ ‘openssl’ ‘pkgbuild’ ‘rlang’ ‘rmarkdown’ ‘roxygen2’
  ‘spelling’ ‘testthat’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Undeclared package ‘mosaicData’ in Rd xrefs
Note: found 2694 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.3Mb
File ‘meboot/libs/meboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 39.3Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  35.5Mb
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
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.
Undeclared packages ‘reshape’, ‘simba’, ‘labdsv’, ‘Hmisc’, ‘untb’ in Rd xrefs
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.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
Found the following files/directories:
  ‘meme_data2.jpg’
'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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.9Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
Found the following files/directories:
  ‘Absolute Positions.txt’ ‘Epidemics 1.tiff’ ‘Epidemics 1.txt’
  ‘Epidemics 2.tiff’ ‘Epidemics 2.txt’ ‘Epidemics 3.tiff’ ‘Epidemics
  3.txt’ ‘Epidemics 4.tiff’ ‘Epidemics 4.txt’ ‘Epidemics 5.tiff’
  ‘Epidemics 5.txt’ ‘Epidemics 6.tiff’ ‘Epidemics 6.txt’ ‘Epidemics
  7.tiff’ ‘Epidemics 7.txt’ ‘Epidemics 8.tiff’ ‘Epidemics 8.txt’ ‘MAP
  Curve 1.tiff’ ‘MAP Curve 1.txt’ ‘MAP Curve 2.tiff’ ‘MAP Curve 2.txt’
  ‘MAP Curve 3.tiff’ ‘MAP Curve 3.txt’ ‘MAP Curve 4.tiff’ ‘MAP Curve
  4.txt’ ‘MAP Curve 5.tiff’ ‘MAP Curve 5.txt’ ‘MAP Curve 6.tiff’ ‘MAP
  Curve 6.txt’ ‘MAP Curve 7.tiff’ ‘MAP Curve 7.txt’ ‘MAP Curve 8.tiff’
  ‘MAP Curve 8.txt’ ‘MAP Curve Slope 1.tiff’ ‘MAP Curve Slope 1.txt’
  ‘MAP Curve Slope 2.tiff’ ‘MAP Curve Slope 2.txt’ ‘MAP Curve Slope
  3.tiff’ ‘MAP Curve Slope 3.txt’ ‘MAP Curve Slope 4.tiff’ ‘MAP Curve
  Slope 4.txt’ ‘MAP Curve Slope 5.tiff’ ‘MAP Curve Slope 5.txt’ ‘MAP
  Curve Slope 6.tiff’ ‘MAP Curve Slope 6.txt’ ‘MAP Curve Slope 7.tiff’
  ‘MAP Curve Slope 7.txt’ ‘MAP Curve Slope 8.tiff’ ‘MAP Curve Slope
  8.txt’ ‘MEM Model v1.tiff’ ‘MEM Model v1.txt’ ‘MEM Model v2.tiff’
  ‘MEM Model v2.txt’ ‘Moving Epidemics.tiff’ ‘Moving Epidemics.txt’
  ‘Relative Positions.txt’ ‘Summary.txt’ ‘graph 1.tiff’ ‘graph 2.tiff’
  ‘graph 3.tiff’ ‘graph 4.tiff’ ‘graph 5.tiff’ ‘series graph.png’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   6.7Mb
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.
installed size is 137.4Mb
  sub-directories of 1Mb or more:
    libs  136.9Mb
GNU make is a SystemRequirements.
Package required but not available: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’ ‘svglite’
  All declared Imports should be used.
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
File ‘metafolio/libs/metafolio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bcgVaccineData: no visible global function definition for ‘data’
bcgVaccineData: no visible global function definition for ‘qnorm’
hConfidence: no visible global function definition for ‘qchisq’
intervalEstimates_OneSgnf : crt: no visible global function definition
  for ‘qt’
intervalEstimates_OneSgnf: no visible binding for global variable
  ‘qnorm’
metagenGeneralised: no visible binding for global variable ‘quantile’
performancePointH : property: no visible global function definition for
  ‘var’
performancePointR : property: no visible global function definition for
  ‘var’
pfunc : pfun: no visible global function definition for ‘uniroot’
pivotalStream: no visible global function definition for ‘rchisq’
pivotalStream : <anonymous>: no visible global function definition for
  ‘rchisq’
pivotalStream: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rbinom’
rD: no visible global function definition for ‘rchisq’
rY: no visible global function definition for ‘rnorm’
render: no visible global function definition for ‘pdf’
render: no visible global function definition for ‘dev.off’
renderSVG: no visible global function definition for ‘svg’
renderSVG: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  data dev.off pdf qchisq qnorm qt quantile rbinom rchisq rnorm svg
  uniroot var
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "svg")
  importFrom("stats", "qchisq", "qnorm", "qt", "quantile", "rbinom",
             "rchisq", "rnorm", "uniroot", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
File ‘MetaheuristicFPA/libs/MetaheuristicFPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
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.
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘foreign’ ‘gplots’ ‘httr’ ‘jsonlite’ ‘knitr’ ‘lmerTest’
  ‘magrittr’ ‘mgcv’ ‘repmis’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
Running examples in ‘metamicrobiomeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: taxa.compare
> ### Title: Compare taxa relative abundance
> ### Aliases: taxa.compare
> ### Keywords: abundance comparison taxa
> 
> ### ** Examples
> 
> #Load summary tables of bacterial taxa relative abundance from Bangladesh data
> data(taxtab6)
> tl<-colnames(taxtab6)[grep("k__bacteria.p__fusobacteria",colnames(taxtab6))]
> taxacom.ex<-taxa.compare(taxtab=taxtab6[,c("personid","x.sampleid","bf","age.sample",tl)],
+ propmed.rel="gamlss",comvar="bf",adjustvar="age.sample",
+ longitudinal="yes",p.adjust.method="fdr")
Error: Corrupt `grouped_df` using old (< 0.8.0) format.
ℹ Strip off old grouping with `ungroup()`.
Backtrace:
     █
  1. ├─metamicrobiomeR::taxa.compare(...)
  2. │ └─base::as.data.frame(taxtab)
  3. ├─taxtab6[, c("personid", "x.sampleid", "bf", "age.sample", tl)]
  4. └─dplyr:::`[.grouped_df`(...)
  5.   └─dplyr:::group_intersect(x, out)
  6.     ├─generics::intersect(group_vars(x), names(new))
  7.     ├─dplyr::group_vars(x)
  8.     └─dplyr:::group_vars.data.frame(x)
  9.       ├─generics::setdiff(names(group_data(x)), ".rows")
 10.       ├─dplyr::group_data(x)
 11.       └─dplyr:::group_data.grouped_df(x)
 12.         └─dplyr::validate_grouped_df(.data)
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Loading required package: gamlss
Loading required package: splines
Loading required package: gamlss.data

Attaching package: 'gamlss.data'

The following object is masked from 'package:datasets':

    sleep

Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.1-6  ********** 
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.

Warning: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 61-65 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Corrupt `grouped_df` using old (< 0.8.0) format.
ℹ Strip off old grouping with `ungroup()`.
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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 suggested but not available for checking: ‘doSMP’
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘pcaPP:::l1median_HoCr’ ‘pcaPP:::l1median_VaZh’
  See the note in ?`:::` about the use of this operator.
prepare_Rd: DropDupGenes.Rd:29-31: Dropping empty section \details
prepare_Rd: DropDupGenes.Rd:41-43: Dropping empty section \note
prepare_Rd: DropDupGenes.Rd:47-49: Dropping empty section \seealso
prepare_Rd: MetaPCA-package.Rd:29-30: Dropping empty section \seealso
prepare_Rd: MetaPCA.Rd:76-78: Dropping empty section \details
prepare_Rd: MetaPCA.Rd:88-90: Dropping empty section \note
prepare_Rd: MetaPCA.Rd:94-96: Dropping empty section \seealso
prepare_Rd: PlotPC2D.Rd:80-82: Dropping empty section \details
prepare_Rd: PlotPC2D.Rd:92-94: Dropping empty section \note
prepare_Rd: PlotPC2D.Rd:98-100: Dropping empty section \seealso
prepare_Rd: PreprocessMetaAnalysis.Rd:39-41: Dropping empty section \details
prepare_Rd: PreprocessMetaAnalysis.Rd:51-53: Dropping empty section \note
prepare_Rd: PreprocessMetaAnalysis.Rd:57-59: Dropping empty section \seealso
prepare_Rd: requireAll.Rd:19-21: Dropping empty section \details
prepare_Rd: requireAll.Rd:31-33: Dropping empty section \note
prepare_Rd: requireAll.Rd:25-27: Dropping empty section \references
prepare_Rd: requireAll.Rd:37-39: Dropping empty section \seealso
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’ ‘rmarkdown’ ‘testthat’
  All declared Imports should be used.
fishercomb: no visible global function definition for ‘pchisq’
fishercomb: no visible global function definition for ‘p.adjust’
invnorm : <anonymous>: no visible global function definition for
  ‘qnorm’
invnorm: no visible global function definition for ‘pnorm’
invnorm: no visible global function definition for ‘p.adjust’
sim.function : <anonymous>: no visible global function definition for
  ‘rnorm’
sim.function : <anonymous>: no visible global function definition for
  ‘rnbinom’
Undefined global functions or variables:
  p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
             "rnorm")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  ‘SKAT:::Get_Davies_PVal’ ‘SKAT:::Get_Lambda’ ‘SKAT:::Get_Liu_PVal’
  ‘SKAT:::SKAT_Check_Method’ ‘SKAT:::SKAT_Optimal_Each_Q’
  ‘SKAT:::SKAT_Optimal_PValue_Davies’ ‘SKAT:::SKAT_Optimal_PValue_Liu’
  See the note in ?`:::` about the use of this operator.
installed size is 140.5Mb
  sub-directories of 1Mb or more:
    libs  140.0Mb
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.
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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.6Mb
File ‘MEtest/libs/MEtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘R2WinBUGS’ in Rd xrefs
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’
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs  25.6Mb
    misc   1.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Undeclared packages ‘hoa’, ‘evir’ in Rd xrefs
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.
File ‘mewAvg/libs/mewAvg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘ECoL’
  All declared Imports should be used.
Undeclared package ‘refund’ in Rd xrefs
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 ‘mgarchBEKK/libs/mgarchBEKK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Undeclared package ‘gam’ in Rd xrefs
maglm: no visible global function definition for ‘combn’
maglm: no visible global function definition for ‘glm’
maglm: no visible global function definition for ‘logLik’
mamglm: no visible global function definition for ‘combn’
mamglm: no visible global function definition for ‘logLik’
ses.maglm: no visible global function definition for ‘rnorm’
ses.maglm: no visible binding for global variable ‘sd’
ses.mamglm: no visible global function definition for ‘rnorm’
ses.mamglm: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  combn glm logLik rnorm sd
Consider adding
  importFrom("stats", "glm", "logLik", "rnorm", "sd")
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘MGL/libs/MGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘MGSDA/libs/MGSDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  19.7Mb
Undeclared packages ‘McSpatial’, ‘locfit’ 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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
Package suggested but not available for checking: ‘structSSI’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘micEconAids’, ‘micEconSNQP’ in Rd xrefs
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Note: found 9345 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
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’
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mipfp’
  All declared Imports should be used.
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.
.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').
Undeclared package ‘riskRegression’ in Rd xrefs
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
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.
Note: found 5 marked UTF-8 strings
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
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.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
rminimax: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
File ‘minpack.lm/libs/minpack.lm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
.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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
Found the following files/directories:
  ‘GGplots.pdf’ ‘Heatmap.pdf’
Namespace in Imports field not imported from: ‘ecodist’
  All declared Imports should be used.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
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.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   8.2Mb
'library' or 'require' calls in package code:
  ‘rgl’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘canonicalizeAndMergeScene’ ‘colorScene’ ‘t2ve’ ‘vertexNormals’
  ‘vertexTriangles’
Undeclared package ‘scatterplot3d’ in Rd xrefs
Found the following files/directories:
  ‘nmix.off’
Undeclared packages ‘pspline’, ‘lme4’ in Rd xrefs
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Undeclared package ‘maxLik’ in Rd xrefs
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘list’ in Rd xrefs
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.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
AndersonDarling: no visible global function definition for ‘spline’
Hawkins: no visible global function definition for ‘cov’
Hawkins: no visible global function definition for ‘pf’
Impute: no visible global function definition for ‘cov’
Mimpute: no visible global function definition for ‘rnorm’
SimNey: no visible global function definition for ‘runif’
TestMCARNormality: no visible global function definition for ‘cov’
TestMCARNormality: no visible global function definition for ‘pchisq’
TestUNey: no visible global function definition for ‘pchisq’
boxplot.testhomosc: no visible global function definition for ‘par’
boxplot.testhomosc: no visible global function definition for ‘title’
boxplot.testhomosc: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov par pchisq pf rnorm runif spline title
Consider adding
  importFrom("graphics", "abline", "par", "title")
  importFrom("stats", "cov", "pchisq", "pf", "rnorm", "runif", "spline")
to your NAMESPACE file.
‘configure’: /bin/bash is not portable
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'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.
Undeclared package ‘quantmod’ in Rd xrefs
Found the following files/directories:
  ‘imputation.R’ ‘imputation.dat’ ‘imputation.inp’ ‘imputation.sav’
  ‘imputation.sps’ ‘imputation1.dat’ ‘imputation2.dat’
  ‘imputation3.dat’ ‘imputation4.dat’ ‘imputation5.dat’
  ‘imputationlist.dat’
Undeclared package ‘mvtnorm’ in Rd xrefs
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  42.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘mixedMem/libs/mixedMem.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
File ‘mixexp/libs/mixexp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
Undeclared package ‘mvmeta’ in Rd xrefs
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.
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.
File ‘mkde/libs/mkde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
Undeclared package ‘Hmisc’ in Rd xrefs
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.
Undeclared packages ‘rms’, ‘Hmisc’, ‘genefilter’ in Rd xrefs
Undeclared packages ‘genefilter’, ‘MKmisc’ in Rd xrefs
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.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Non-standard file/directory found at top level:
  ‘Data-Administration.R’
File ‘mlbench/libs/mlbench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiscriMiner’ ‘MASS’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘klaR’
  ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
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.
File ‘MLEcens/libs/MLEcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
File ‘mlmmm/libs/mlmmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘mlogitBMA/libs/mlogitBMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Undeclared package ‘htmlwidgets’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.
Depends: includes the non-default packages:
  'mlr3', 'mlr3db', 'mlr3filters', 'mlr3learners', 'mlr3pipelines',
  'mlr3tuning', 'mlr3viz', 'paradox'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘DiceOptim’
Package suggested but not available for checking: ‘FDboost’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
Unknown package ‘FDboost’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringr’
  All declared Imports should be used.
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.
Undeclared package ‘geeM’ in Rd xrefs
Namespace with empty importFrom: ‘gee’
Malformed Description field: should contain one or more complete sentences.
mmm: no visible global function definition for ‘model.frame’
mmm: no visible global function definition for ‘model.matrix’
mmm: no visible global function definition for ‘model.response’
mmm: no visible global function definition for ‘as.formula’
mmm: no visible global function definition for ‘gee’
Undefined global functions or variables:
  as.formula gee 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').
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Checking should be performed on sources prepared by ‘R CMD build’.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
sadmvng: no visible global function definition for ‘cov2cor’
sadmvng: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov2cor pnorm
Consider adding
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
File ‘mnormpow/libs/mnormpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘energy’ in Rd xrefs
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘MoBPSmaps’
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘amap’ ‘fields’ ‘matrixStats’ ‘mco’ ‘miscTools’ ‘plyr’
  ‘reshape2’
  All declared Imports should be used.
Note: found 12 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
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.
File ‘ModelGood/libs/ModelGood.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
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’
Undeclared packages ‘lme4’, ‘rstanarm’, ‘dplyr’ in Rd xrefs
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Undeclared packages ‘ggplot2movies’, ‘openintro’ in Rd xrefs
'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.
Undeclared package ‘roxygen2’ in Rd xrefs
Error(s) in re-building vignettes:
--- re-building ‘modistools-vignette.Rmd’ using rmarkdown
Quitting from lines 41-43 (modistools-vignette.Rmd) 
Error: processing vignette 'modistools-vignette.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘modistools-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘modistools-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2'
Namespaces in Imports field not imported from:
  ‘BioStatR’ ‘ggplot2’
  All declared Imports should be used.
Note: found 20578 marked UTF-8 strings
.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.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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.
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   4.9Mb
Undeclared package ‘sf’ in Rd xrefs
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Warning: no function found corresponding to methods exports from ‘mondate’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the 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.
.date.to.mondate: no visible global function definition for ‘new’
as.character.mondate: no visible global function definition for ‘slot’
Arith,array-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-array: no visible global function definition for
  ‘callGeneric’
Arith,mondate-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-numeric: no visible global function definition for
  ‘callGeneric’
Arith,numeric-mondate: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘getDataPart’
Summary,mondate: no visible global function definition for
  ‘callGeneric’
[,mondate: no visible global function definition for ‘callNextMethod’
[,mondate: no visible global function definition for ‘new’
array,mondate: no visible global function definition for
  ‘callNextMethod’
as.numeric,mondate: no visible global function definition for ‘slot’
c,mondate: no visible global function definition for ‘new’
c,mondate: no visible binding for global variable ‘getDataPart’
c,mondate: no visible global function definition for ‘getDataPart’
matrix,mondate: no visible global function definition for
  ‘callNextMethod’
mondate,Date: no visible global function definition for ‘new’
mondate,POSIXt: no visible global function definition for ‘new’
mondate,missing: no visible global function definition for ‘new’
mondate,mondate: no visible global function definition for ‘new’
mondate,numeric: no visible global function definition for ‘new’
Undefined global functions or variables:
  callGeneric callNextMethod getDataPart new slot
Consider adding
  importFrom("methods", "callGeneric", "callNextMethod", "getDataPart",
             "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package which this enhances but not available for checking: ‘MonetDBLite’
Missing or unexported objects:
  ‘dplyr::base_agg’ ‘dplyr::base_scalar’ ‘dplyr::build_sql’
  ‘dplyr::is.ident’ ‘dplyr::sql_infix’ ‘dplyr::sql_prefix’
  ‘dplyr::sql_translator’ ‘dplyr::sql_variant’ ‘dplyr::src_sql’
  ‘dplyr::tbl_sql’
File ‘MonetDB.R/libs/MonetDB.R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘seewave’ in Rd xrefs
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Found the following files/directories:
  ‘test.csv’ ‘test1.csv’ ‘testsummary.csv’ ‘testsummary1.csv’
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.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   9.9Mb
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’
Mort1Dsmooth: no visible global function definition for ‘time’
Mort1Dsmooth: no visible global function definition for ‘glm’
Mort1Dsmooth: no visible binding for global variable ‘poisson’
Mort1Dsmooth_optimize: no visible global function definition for
  ‘median’
Mort2Dsmooth: no visible global function definition for ‘glm’
Mort2Dsmooth: no visible binding for global variable ‘poisson’
Mort2Dsmooth: no visible global function definition for ‘median’
Mort2Dsmooth_optimize: no visible global function definition for
  ‘median’
plot.Mort1Dsmooth: no visible global function definition for ‘matplot’
plot.Mort2Dsmooth: no visible global function definition for ‘quantile’
predict.Mort1Dsmooth: no visible global function definition for ‘glm’
predict.Mort1Dsmooth: no visible binding for global variable ‘poisson’
predict.Mort2Dsmooth: no visible global function definition for ‘glm’
predict.Mort2Dsmooth: no visible binding for global variable ‘poisson’
print.summary.Mort1Dsmooth: no visible global function definition for
  ‘quantile’
print.summary.Mort2Dsmooth: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  glm matplot median poisson quantile time
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
Undeclared package ‘pracma’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘ggformula’ ‘magrittr’ ‘rlang’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Undeclared package ‘cubature’ in Rd xrefs
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.8Mb
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
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.
Note: found 6 marked UTF-8 strings
File ‘mpbart/libs/mpbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Malformed Title field: should not end in a period.
Undeclared package ‘lme4’ in Rd xrefs
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.
installed size is 82.6Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         78.7Mb
    mathematica   1.5Mb
Dependence on R version ‘3.6.2’ not with patchlevel 0
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
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.
Undeclared package ‘proxy’ in Rd xrefs
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
ppersp: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
installed size is 64.6Mb
  sub-directories of 1Mb or more:
    libs  64.3Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
File ‘MRCE/libs/MRCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.4Mb
File ‘mrfse/libs/mrfse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘MRH_lung’
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   7.2Mb
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.
Malformed Title field: should not end in a period.
MRwarp: no visible global function definition for ‘dev.new’
MRwarp: no visible global function definition for ‘lines’
MRwarp: no visible global function definition for ‘points’
MRwarp: no visible global function definition for ‘hist’
Undefined global functions or variables:
  dev.new hist lines points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "points")
to your NAMESPACE file.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’
File ‘MRwarping/libs/MRwarping.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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').
File ‘msda/libs/msda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 30.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    libs  27.6Mb
installed size is 51.6Mb
  sub-directories of 1Mb or more:
    libs  51.2Mb
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘test.txt’
File ‘msgps/libs/msgps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R   5.3Mb
Undeclared package ‘dr’ in Rd xrefs
MSIseq.classify: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  18.8Mb
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.
Namespace in Imports field not imported from: ‘amap’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘miniUI’
  All declared Imports should be used.
'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.
Note: found 2 marked UTF-8 strings
Found the following files/directories:
  ‘mtkMCDesigner.R’ ‘mtkRegressionTestAnalyser.R’ ‘mtkWWEvaluator.R’
File ‘MTS/libs/MTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Note: found 2632 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
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.
File ‘muhaz/libs/muhaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Undeclared package ‘slam’ in Rd xrefs
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.
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calculate_direction: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
File ‘MultiCNVDetect/libs/MultiCNVDetect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cowsay’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
betas_plot: no visible global function definition for ‘cov2cor’
betas_plot: no visible global function definition for
  ‘colorRampPalette’
betas_plot: no visible global function definition for ‘pdf’
betas_plot: no visible global function definition for ‘dev.off’
mhplot: no visible global function definition for ‘read.table’
mhplot: no visible global function definition for ‘pdf’
mhplot: no visible global function definition for ‘points’
mhplot: no visible global function definition for ‘abline’
mhplot: no visible global function definition for ‘axis’
mhplot: no visible global function definition for ‘dev.off’
multi_meta: no visible global function definition for ‘write.table’
multi_meta: no visible global function definition for ‘read.table’
multi_meta: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘read.table’
qqplotter: no visible global function definition for ‘qchisq’
qqplotter: no visible global function definition for ‘ppoints’
qqplotter: no visible global function definition for ‘median’
qqplotter: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘pdf’
qqplotter: no visible global function definition for ‘abline’
qqplotter: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf points
  ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘Output_from_running_example.txt’
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.
installed size is 98.6Mb
  sub-directories of 1Mb or more:
    libs  98.4Mb
Package suggested but not available for checking: ‘rPorta’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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.
File ‘multinomRob/libs/multinomRob.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
File ‘multispatialCCM/libs/multispatialCCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
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.
Note: found 6 marked UTF-8 strings
Undeclared package ‘lfe’ in Rd xrefs
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.
Undeclared packages ‘AICcmodavg’, ‘bbmle’, ‘glmulti’, ‘arm’, ‘wgeesel’, ‘ape’, ‘bestglm’, ‘leaps’, ‘glmmTMB’, ‘brglm’, ‘quantreg’, ‘maxlike’, ‘RMark’ in Rd xrefs
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
plotFID: no visible global function definition for ‘points’
Undefined global functions or variables:
  points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
Undeclared package ‘tuneR’ in Rd xrefs
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').
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
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.
File ‘MVB/libs/MVB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Checking should be performed on sources prepared by ‘R CMD build’.
File ‘mvcluster/libs/mvcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Undeclared package ‘dosresmeta’ in Rd xrefs
Found the following sources/headers not terminated with a newline:
  src/sitmo/sitmo.hpp
Some compilers warn on such files.
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.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘utils’
  All declared Imports should be used.
Undeclared package ‘VGAM’ in Rd xrefs
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.
File ‘mvrtn/libs/mvrtn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
prepare_Rd: mvsf.Rd:16-17: Dropping empty section \details
Undeclared package ‘mvMORPH’ in Rd xrefs
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.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
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.
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.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
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.
Note: found 50 marked UTF-8 strings
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Package which this enhances but not available for checking: ‘asreml’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
Namespace in Imports field not imported from: ‘mapdata’
  All declared Imports should be used.
Package suggested but not available for checking: ‘re2r’
Malformed Description field: should contain one or more complete sentences.
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    27.4Mb
    models   1.1Mb
Note: found 47936 marked UTF-8 strings
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lifecycle’ ‘lme4’ ‘methods’
  All declared Imports should be used.
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘NanoStringNorm_Example_Plots_All.pdf’
  ‘NanoStringNorm_Interactive_Plot’
NAPPA: no visible binding for global variable ‘sd’
NAPPA: no visible global function definition for ‘sd’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘coef’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘lm’
calibrate.sigmoid.curve: no visible global function definition for
  ‘nls’
calibrate.sigmoid.curve: no visible binding for global variable
  ‘weights’
calibrate.sigmoid.curve: no visible global function definition for
  ‘coef’
calibrate.sigmoid.curve: no visible global function definition for
  ‘rgb’
calibrate.sigmoid.curve: no visible global function definition for
  ‘box’
calibrate.sigmoid.curve: no visible global function definition for
  ‘axis’
calibrate.sigmoid.curve: no visible global function definition for
  ‘abline’
calibrate.sigmoid.curve: no visible global function definition for
  ‘lines’
calibrate.sigmoid.curve: no visible global function definition for
  ‘predict’
calibrate.sigmoid.curve: no visible global function definition for
  ‘smooth.spline’
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for ‘nls’
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable ‘weights’
calibrate.sigmoid.curve: no visible binding for global variable ‘coef’
calibrate.sigmoid.curve: no visible global function definition for ‘pf’
calibrate.sigmoid.curve: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
Undeclared package ‘CBPS’ in Rd xrefs
Note: found 140 marked UTF-8 strings
Undeclared packages ‘sSeq’, ‘PoiClaClu’ in Rd xrefs
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NBPSeq/libs/NBPSeq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
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.
infoNcdfVars: no visible global function definition for ‘na.omit’
modifyNcdfDefAtts: no visible global function definition for ‘na.omit’
plotDatacube: no visible global function definition for ‘runif’
plotDatacube: no visible global function definition for
  ‘colorRampPalette’
plotDatacube: no visible global function definition for ‘dev.cur’
plotDatacube: no visible global function definition for ‘dev.new’
plotDatacube: no visible global function definition for ‘layout’
plotDatacube: no visible global function definition for ‘par’
plotDatacube: no visible global function definition for ‘points’
plotDatacube: no visible global function definition for ‘text’
plotDatacube: no visible global function definition for ‘plot.new’
plotDatacube: no visible global function definition for ‘mtext’
plotDatacube: no visible global function definition for ‘rgb’
plotDatacube: no visible global function definition for ‘legend’
transNcdfRotate: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colorRampPalette dev.cur dev.new layout legend mtext na.omit par
  plot.new points rgb runif text
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.new",
             "rgb")
  importFrom("graphics", "layout", "legend", "mtext", "par", "plot.new",
             "points", "text")
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘test.nc’
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.
Undeclared package ‘reader’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Package suggested but not available for checking: ‘re2r’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Found the following files/directories:
  ‘testNet.dot’ ‘toy_epi_sim.net’
data.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’
File ‘NeatMap/libs/NeatMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Requires orphaned package: ‘bit’
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.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
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.
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’, ‘Rplots.ps’
Please remove them from your package.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
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.
File ‘NetComp/libs/NetComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘buildcmds’
Namespace in Imports field not imported from: ‘mvrtn’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
EnvInd: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fastshp’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘clue’
  All declared Imports should be used.
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   7.0Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
Found the following files/directories:
  ‘map.png’ ‘maze.html’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
simulate.sisnetwork: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
File ‘networksis/libs/networksis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘networkTomography/libs/networkTomography.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 2 marked Latin-1 strings
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.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
Running examples in ‘neuropsychology-Ex.R’ failed
The error most likely occurred in:

> ### Name: describe
> ### Title: Description of dataframes.
> ### Aliases: describe
> 
> ### ** Examples
> 
> require(neuropsychology)
> 
> df <- personality
> 
> describe(df)
Warning: `transmute_()` is deprecated as of dplyr 0.7.0.
Please use `transmute()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: Can't reconstruct data frame.
✖ The `[` method for class <psych/describe/data.frame> must return a data frame.
ℹ It returned a <describe>.
Backtrace:
     █
  1. └─neuropsychology::describe(df)
  2.   └─`%>%`(...)
  3.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         └─neuropsychology:::`_fseq`(`_lhs`)
  7.           └─magrittr::freduce(value, `_function_list`)
  8.             ├─base::withVisible(function_list[[k]](value))
  9.             └─function_list[[k]](value)
 10.               ├─dplyr::transmute_(...)
 11.               └─dplyr:::transmute_.default(...)
 12.                 ├─dplyr::transmute(.data, !!!dots)
 13.                 └─dplyr:::transmute.data.frame(.data, !!!dots)
 14.                   ├─dplyr::mutate(.data, ..., .keep = "none")
 15.                   └
Execution halted
Found the following files/directories:
  ‘correlation_table.csv’ ‘mycorrplot.png’
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.
File ‘neuRosim/libs/neuRosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 4485 marked UTF-8 strings
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’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              6.1Mb
    classic-bugs   1.6Mb
    include        5.7Mb
    libs          17.2Mb
    tests          1.7Mb
Undeclared packages ‘cshapes’, ‘mapdata’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
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.
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
Undeclared packages ‘broom’, ‘mvnfast’ in Rd xrefs
Missing or unexported object: ‘cleanNLP::cnlp_get_token’
Undeclared package ‘tm’ in Rd xrefs
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.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
File ‘nmfgpu4R/libs/nmfgpu4R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘KernelKnn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘uroot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘multicool’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Undeclared packages ‘quadprog’, ‘bvls’ in Rd xrefs
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘arrow’
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.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
File ‘nontarget/libs/nontarget.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘copula’ in Rd xrefs
Note: found 3 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
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.
File ‘norm/libs/norm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NORMT3/libs/NORMT3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Undeclared package ‘bipartite’ in Rd xrefs
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.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
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’
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Undeclared packages ‘logspline’, ‘ks’ in Rd xrefs
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.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
File ‘NPsimex/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

See section ‘Good practice’ in '?.onAttach'.

lambda.select: no visible global function definition for ‘bw.nrd0’
lambda.select: no visible global function definition for ‘bw.nrd’
lambda.select: no visible global function definition for ‘bw.ucv’
lambda.select: no visible global function definition for ‘bw.bcv’
lambda.select: no visible global function definition for ‘bw.SJ’
plot.NPsimex: no visible global function definition for ‘plot.default’
simex.H.density : simex1.est: no visible global function definition for
  ‘lm’
simex.density : simex1.est: no visible global function definition for
  ‘lm’
span.H.select: no visible global function definition for ‘density’
span.H.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
span.select: no visible global function definition for ‘density’
span.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm lm plot.default
Consider adding
  importFrom("graphics", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "lm")
to your NAMESPACE file.
prepare_Rd: lambda.select.Rd:19-20: Dropping empty section \details
prepare_Rd: lambda.select.Rd:21-22: Dropping empty section \value
prepare_Rd: simex.H.density.Rd:28-29: Dropping empty section \details
prepare_Rd: simex.density.Rd:28-29: Dropping empty section \details
prepare_Rd: span.H.select.Rd:28-29: Dropping empty section \details
prepare_Rd: span.H.select.Rd:30-31: Dropping empty section \value
prepare_Rd: span.select.Rd:27-28: Dropping empty section \details
prepare_Rd: span.select.Rd:29-30: Dropping empty section \value
Rd file 'simex.H.density.Rd':
  \examples lines wider than 100 characters:
     set.seed(123); X <- c(rnorm(N/2, mean=-2), rnorm(N/2,mean=2)); U <- rnorm(N,sd=1); msigma <- runif(N,min=0.3,max=0.5)

Rd file 'span.H.select.Rd':
  \usage lines wider than 90 characters:
      span.H.select(W, msigma, span=c(2,4,6,8,10,12,25), approx=FALSE, from=min(W), to=max(W), n.user=128, n.lambda=50, lambda="SJ", bw="SJ" ... [TRUNCATED]
  \examples lines wider than 100 characters:
     set.seed(123); X <- c(rnorm(N/2, mean=-2), rnorm(N/2,mean=2)); U <- rnorm(N,sd=1); msigma <- runif(N,min=0.3,max=0.5)
     X.simex <- simex.H.density(W, msigma=msigma, adjust=1, n.lambda=50, span=spans$span[order(spans$ISE)[1]])
     # X.simex <- simex.H.density(W, msigma=msigma, adjust=1, n.lambda=50, span=spans$span[order(spans$ISE)[1]])

Rd file 'span.select.Rd':
  \usage lines wider than 90 characters:
      span.select(W, msigma, span=c(2,4,6,8,10,12,25), from=min(W), to=max(W), n.user=128, n.lambda=50, lambda="SJ", bw="SJ", adjust=1, na.r ... [TRUNCATED]
  \examples lines wider than 100 characters:
     X.simex <- simex.density(W, msigma=msigma, adjust=1, n.lambda=50, span=spans$span[order(spans$ISE)[1]])

These lines will be truncated in the PDF manual.
File ‘NPsimex/libs/NPsimex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
File ‘npst/libs/npst.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
.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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  20.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.4Mb
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Note: found 6409 marked UTF-8 strings
Note: found 7284 marked UTF-8 strings
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.
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.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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').
obliclus: no visible global function definition for ‘rnorm’
obliclus: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’
File ‘obliclus/libs/obliclus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Requires orphaned package: ‘bit’
Undeclared packages ‘ensurer’, ‘validate’ in Rd xrefs
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.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    doc    2.3Mb
    help   2.7Mb
    libs   4.0Mb
Note: found 1 marked UTF-8 string
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Undeclared package ‘gam’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
installed size is 93.7Mb
  sub-directories of 1Mb or more:
    libs  93.2Mb
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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’.
Note: found 2444 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘oai’ ‘stringr’ ‘utils’
  All declared Imports should be used.
Undeclared package ‘lubridate’ in Rd xrefs
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.
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
Namespaces in Imports field not imported from:
  ‘bayesplot’ ‘ggplot2’
  All declared Imports should be used.
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.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.4Mb
File ‘onemap/libs/onemap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘digest’ ‘dplyr’ ‘miniUI’ ‘text2vec’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.4Mb
Undeclared package ‘mosaicData’ in Rd xrefs
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 220.5Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    210.4Mb
    models    4.7Mb
Undeclared packages ‘ifaTools’, ‘umx’ in Rd xrefs
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
Package suggested but not available for checking: ‘openNLPmodels.en’
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 40 (should be '.', not 'source'):
      source autobrew
  possible bashism in configure line 79 ($(OS|MACH)TYPE):
  case "$OSTYPE" in
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
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').
Namespace in Imports field not imported from: ‘vctrs’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
Package suggested but not available for checking: ‘nbc4va’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      6.3Mb
Package suggested but not available for checking: ‘gurobi’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
prepare_Rd: distance.Rd:21-22: Dropping empty section \details
prepare_Rd: distance.Rd:32-33: Dropping empty section \note
prepare_Rd: filter.Rd:26-27: Dropping empty section \details
prepare_Rd: filter.Rd:28-29: Dropping empty section \value
prepare_Rd: filter.Rd:36-37: Dropping empty section \note
prepare_Rd: findP.Rd:21-22: Dropping empty section \details
prepare_Rd: findP.Rd:34-35: Dropping empty section \note
prepare_Rd: ops-package.Rd:30-31: Dropping empty section \seealso
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’
Malformed Description field: should contain one or more complete sentences.
avg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
File ‘OptHedging/libs/OptHedging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.9Mb
Undeclared packages ‘alabama’, ‘cccp’, ‘nloptr’ in Rd xrefs
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
Undeclared package ‘vegan’ in Rd xrefs
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘orca/libs/orca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Undeclared package ‘VGAM’ in Rd xrefs
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘glmnetcr’
File ‘ordinalpattern/libs/ordinalpattern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Undeclared package ‘microplot’ in Rd xrefs
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’
Undeclared package ‘glmnet’ in Rd xrefs
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’
File ‘OriGen/libs/OriGen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Undeclared package ‘orloca.es’ in Rd xrefs
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.
File ‘ORMDR/libs/ORMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
Namespace in Imports field not imported from: ‘rticles’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
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.
File ‘orQA/libs/orQA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
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.
File ‘osDesign/libs/osDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘maxmatching’ in Rd xrefs
'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.
Note: found 80 marked UTF-8 strings
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   7.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.9Mb
Undeclared package ‘adegenet’ in Rd xrefs
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Found the following files/directories:
  ‘result.txt’
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘praise’ ‘withr’
  All declared Imports should be used.
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘OUwie’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
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.
Malformed Description field: should contain one or more complete sentences.
Non-standard files/directories found at top level:
  ‘DESCRIPTION_EX’ ‘divers’ ‘main.R’ ‘testsDev’
Undeclared package ‘packS4’ in Rd xrefs
[,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'
Undeclared package ‘packClassic’ in Rd xrefs
Undeclared package ‘devtools’ in Rd xrefs
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespace in Imports field not imported from: ‘GenomicAlignments’
  All declared Imports should be used.
Undeclared package ‘pracma’ in Rd xrefs
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.
Namespaces in Imports field not imported from:
  ‘network’ ‘scales’ ‘sna’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
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.
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 files/directories:
  ‘GDPgrowthRESULTS.csv’
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘analogue’ in Rd xrefs
Package which this enhances but not available for checking: ‘CorShrink’
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.
Note: found 1 marked UTF-8 string
Found the following files/directories:
  ‘Dispersion.pdf’
Note: found 9 marked UTF-8 strings
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
Note: found 34 marked UTF-8 strings
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
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.
File ‘PanelCount/libs/PanelCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Undeclared package ‘AER’ in Rd xrefs
Running examples in ‘panelr-Ex.R’ failed
The error most likely occurred in:

> ### Name: are_varying
> ### Title: Check if variables are constant or variable over time.
> ### Aliases: are_varying
> 
> ### ** Examples
> 
> 
> wages <- panel_data(WageData, id = id, wave = t)
Warning: The `add` argument of `group_by()` is deprecated as of dplyr 1.0.0.
Please use the `.add` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
> wages %>% are_varying(occ, ind, fem, blk)
Error in if (get_wave(data) %in% dots) NULL else get_wave(data) : 
  argument is of length zero
Calls: %>% ... freduce -> withVisible -> <Anonymous> -> are_varying
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘reshape.Rmd’ using rmarkdown
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'panelr'

The following object is masked from 'package:stats':

    filter

Quitting from lines 52-67 (reshape.Rmd) 
Error: processing vignette 'reshape.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘reshape.Rmd’

--- re-building ‘wbm.Rmd’ using rmarkdown
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'panelr'

The following object is masked from 'package:stats':

    filter

Quitting from lines 51-53 (wbm.Rmd) 
Error: processing vignette 'wbm.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘wbm.Rmd’

SUMMARY: processing the following files failed:
  ‘reshape.Rmd’ ‘wbm.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
Undeclared package ‘emmeans’ in Rd xrefs
Namespace in Imports field not imported from: ‘survey’
  All declared Imports should be used.
Undeclared package ‘Familias’ in Rd xrefs
Undeclared package ‘knitr’ in Rd xrefs
Found the following files/directories:
  ‘example.csv’ ‘example.tsv’ ‘example.xlsx’
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tibble’
  All declared Imports should be used.
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.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘NUL’
Note: found 16 marked UTF-8 strings
File ‘parma/libs/parma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Calls with DUP:
   .C("aracne", as.double(t(mis)), as.integer(n), as.double(eps), 
       as.double(eta), res = double(n * n), PACKAGE = "parmigene", 
       DUP = FALSE)
   .C("clr", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
   .C("mrnet", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘parmigene/libs/parmigene.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
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.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.8Mb
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’
Warning: no function found corresponding to methods exports from ‘partsm’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Undeclared package ‘randomForest’ in Rd xrefs
Undeclared package ‘randomForest’ in Rd xrefs
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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘PATHChange’
Undeclared package ‘pathfindR’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘R6’ ‘glue’ ‘logging’ ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Checking should be performed on sources prepared by ‘R CMD build’.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.8Mb
GNU make is a SystemRequirements.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘KernSmooth’ ‘Mfuzz’ ‘SelectBoost’ ‘animation’ ‘c060’
  ‘cluster’ ‘gplots’ ‘grid’ ‘jetset’
  All declared Imports should be used.
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.
File ‘pauwels2014/libs/pauwels2014.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘future’ in Rd xrefs
Warning: no function found corresponding to methods exports from ‘PAWL’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘foreach’ ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘foreach’ ‘ggplot2’ ‘methods’ ‘mvtnorm’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'createAdaptiveRandomWalkProposal.Rd':
  \usage lines wider than 90 characters:
         createAdaptiveRandomWalkProposal(nchains, targetdimension, adaptiveproposal, adaptationrate, sigma_init)

These lines will be truncated in the PDF manual.
File ‘PAWL/libs/PAWL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pbdNCDF4/libs/pbdNCDF4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    lib   9.9Mb
Found the following sources/headers with CR or CRLF line endings:
  src/zmqsrc/src/condition_variable.hpp
Some Unix compilers require LF line endings.
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      3.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
Undeclared packages ‘tibble’, ‘data.table’ in Rd xrefs
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   7.6Mb
Undeclared packages ‘combinat’, ‘unifDAG’ in Rd xrefs
Undeclared package ‘robustbase’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
PCDReg.wf: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Undeclared package ‘spatstat’ in Rd xrefs
installed size is 172.8Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  169.2Mb
GNU make is a SystemRequirements.
File ‘PCICt/libs/PCICt.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
Found the following files/directories:
  ‘AbsolutePlot_Absolute Risk.pdf’ ‘ContrastPlot_OR.pdf’
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
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.
Note: found 11 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘cycling-potential-uk.Rmd’ using rmarkdown
Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 6.3.2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘cycling-potential-uk.Rmd’

--- re-building ‘pct-international.Rmd’ using rmarkdown
--- finished re-building ‘pct-international.Rmd’

--- re-building ‘pct.Rmd’ using rmarkdown
--- finished re-building ‘pct.Rmd’

--- re-building ‘pct_training.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

tmap mode set to interactive viewing
Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 6.3.2
Legend for line widths not available in view mode.
Warning in plot.sf(l_top_cycling, add = TRUE, lwd = 5, col = "green") :
  ignoring all but the first attribute
Quitting from lines 270-290 (pct_training.Rmd) 
Error: processing vignette 'pct_training.Rmd' failed with diagnostics:
Must extract column with a single valid subscript.
✖ Subscript `setdiff(names(x), attr(x, "sf_column"))` has size 0 but must be size 1.
--- failed re-building ‘pct_training.Rmd’

SUMMARY: processing the following file failed:
  ‘pct_training.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘sm’, ‘spdep’ in Rd xrefs
File ‘PDFEstimator/libs/PDFEstimator.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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.
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').
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
Undeclared packages ‘mlbench’, ‘foreach’, ‘ICEbox’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
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.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
peacf: no visible global function definition for ‘is.ts’
peacf: no visible global function definition for ‘cycle’
peacf: no visible global function definition for ‘ts.intersect’
peacf: no visible global function definition for ‘lag’
peacf: no visible global function definition for ‘ts’
peacf: no visible global function definition for ‘pchisq’
peacf.plot: no visible global function definition for ‘segments’
peacf.plot: no visible global function definition for ‘title’
pear: no visible global function definition for ‘cycle’
pear: no visible global function definition for ‘pchisq’
peboxplot: no visible global function definition for ‘cycle’
peboxplot: no visible global function definition for ‘boxplot’
peboxplot: no visible global function definition for ‘title’
peplot: no visible global function definition for ‘par’
peplot: no visible global function definition for ‘cycle’
peplot: no visible global function definition for ‘identify’
peplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq segments title ts
  ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
The following files should probably not be installed:
  ‘addendum.tex’, ‘slplot.tex’, ‘table1.tex’, ‘table3.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
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.
File ‘PedCNV/libs/PedCNV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘pedigree/libs/pedigree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘A.txt’ ‘Ainv.txt’
Undeclared packages ‘Hmisc’, ‘vcd’, ‘VecStatGraphs2D’, ‘mvtsplot’, ‘matrixStats’, ‘RandomFields’, ‘automap’, ‘spsann’ in Rd xrefs
Undeclared packages ‘ade4’, ‘vegan’ in Rd xrefs
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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘lhs’
  All declared Imports should be used.
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'library' or 'require' calls in package code:
  ‘CoxBoost’ ‘codetools’ ‘locfit’ ‘penalized’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
complexity.LASSO: no visible global function definition for ‘profL1’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘locfit’
complexity.mincv.CoxBoost: no visible global function definition for
  ‘cv.CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘locfit’
extract: no visible global function definition for ‘findGlobals’
fit.CoxBoost: no visible global function definition for ‘CoxBoost’
fit.LASSO: no visible global function definition for ‘penalized’
Undefined global functions or variables:
  CoxBoost cv.CoxBoost findGlobals locfit penalized profL1
Rd file 'aggregation.brier.Rd':
  \usage lines wider than 90 characters:
     aggregation.brier(full.data=NULL, response, x, model, cplx=NULL,  type=c("apparent", "noinf"), 

Rd file 'aggregation.misclass.Rd':
  \usage lines wider than 90 characters:
     aggregation.misclass(full.data=NULL, response, x, model, cplx=NULL,  type=c("apparent", "noinf"), 

These lines will be truncated in the PDF manual.
File ‘peperr/libs/peperr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘PARMA21del1_ident’
File ‘perccal/libs/perccal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘PerfMeas/libs/PerfMeas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘timeSeries’, ‘tseries’, ‘car’, ‘gplots’ in Rd xrefs
Package suggested but not available for checking: ‘dendextendRcpp’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
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.
hasMethod: no visible global function definition for ‘getS3method’
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 63777 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘SnowballC’ ‘cluster’ ‘graph’
  All declared Imports should be used.
Found the following files/directories:
  ‘neural_network-s0000r1000.html’ ‘neural_network-s1000r1000.html’
  ‘neural_network-s2000r1000.html’ ‘neural_network-s3000r1000.html’
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘classInt’, ‘PMCMR’, ‘agricolae’, ‘plotrix’, ‘AICcmodavg’ in Rd xrefs
Found the following files/directories:
  ‘Myfile.txt’
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
pGLS: no visible global function definition for ‘model.response’
pGLS: no visible global function definition for ‘model.matrix’
pGLS: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
prepare_Rd: data_fs.Rd:11: Dropping empty section \source
prepare_Rd: var_fs.Rd:12-14: Dropping empty section \references
File ‘pGMGM/libs/pGMGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘animation.gif’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   1.6Mb
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.
Undeclared package ‘phase1RMD’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data       2.3Mb
    examples   2.6Mb
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.
File ‘phenmod/libs/phenmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘memoise’
  All declared Imports should be used.
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
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.
File ‘pheno/libs/pheno.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
Undeclared package ‘vowels’ in Rd xrefs
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Undeclared package ‘photobiologyLEDs’ in Rd xrefs
Note: found 1 marked Latin-1 string
Undeclared packages ‘fishmethods’, ‘photobiologyWavebands’ in Rd xrefs
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘photosynthesis’
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘photosynthesis-introduction.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: units
udunits system database from /usr/share/udunits

Attaching package: 'purrr'

The following object is masked from 'package:magrittr':

    set_names

New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
Quitting from lines 100-129 (photosynthesis-introduction.Rmd) 
Error: processing vignette 'photosynthesis-introduction.Rmd' failed with diagnostics:
no applicable method for 'units<-' applied to an object of class "NULL"
--- failed re-building ‘photosynthesis-introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘photosynthesis-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Package suggested but not available for checking: ‘OutbreakTools’
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
Found the following files/directories:
  ‘output_values’
Found the following significant warnings:
  Note: possible error in 'plotGMPhyloMorphoSpace(phy, ': unused arguments (phy, A, ancStates = FALSE) 
See ‘/data/gannet/ripley/R/packages/tests-clang/phylocurve.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
fast.geomorph.physignal: possible error in plotGMPhyloMorphoSpace(phy,
  A, ancStates = FALSE): unused arguments (phy, A, ancStates = FALSE)
File ‘phyloland/libs/phyloland.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘surface’, ‘bayou’, ‘future’, ‘geiger’, ‘caper’ in Rd xrefs
Unknown packages ‘surface’, ‘bayou’ in Rd xrefs
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
File ‘PhyloMeasures/libs/PhyloMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘picante’ in Rd xrefs
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  14.8Mb
Found the following files/directories:
  ‘subj_slp_sum.csv’ ‘wa_ps_V811043_sum.csv’
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
Undeclared package ‘BsMD’ in Rd xrefs
File which contains pragma(s) suppressing diagnostics:
  ‘src/pijavski.cpp’
File ‘Pijavski/libs/Pijavski.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 2048 marked UTF-8 strings
Undeclared package ‘rticles’ in Rd xrefs
Note: found 36 marked UTF-8 strings
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.
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ggsubplot’
File ‘PivotalR/libs/PivotalR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘Hmisc’ in Rd xrefs
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.
Undeclared package ‘processx’ in Rd xrefs
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘usethis’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Undeclared packages ‘pkgdown’, ‘htmlwidgets’ in Rd xrefs
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘multiplot.Rmd’ using rmarkdown
--- finished re-building ‘multiplot.Rmd’

--- re-building ‘noncompartmental-analysis.Rmd’ using rmarkdown
Quitting from lines 69-71 (noncompartmental-analysis.Rmd) 
Error: processing vignette 'noncompartmental-analysis.Rmd' failed with diagnostics:
Can't convert a NULL to a quosure.
--- failed re-building ‘noncompartmental-analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘noncompartmental-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
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’
Package suggested but not available for checking: ‘BradleyTerryScalable’
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘sp’ in Rd xrefs
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
File ‘planar/libs/planar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 150 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.7Mb
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
Undeclared package ‘curl’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
File ‘plgp/libs/plgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
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.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   8.1Mb
nrmlepln: no visible global function definition for ‘pchisq’
nrmlerasch: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Undeclared package ‘ltm’ in Rd xrefs
File ‘pln/libs/pln.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.7Mb
plotAuto: no visible global function definition for ‘window’
plotAuto: no visible global function definition for ‘title’
plotAuto: no visible global function definition for ‘axis’
plotAuto: no visible global function definition for ‘box’
plotCumu: no visible global function definition for ‘title’
plotCumu: no visible global function definition for ‘axis’
plotCumu: no visible global function definition for ‘box’
plotDens : panel.dens: no visible global function definition for ‘var’
plotDens : panel.dens: no visible global function definition for
  ‘quantile’
plotDens : panel.dens: no visible global function definition for
  ‘median’
plotDens: no visible global function definition for ‘tail’
plotQuant: no visible global function definition for ‘par’
plotQuant: no visible binding for global variable ‘quantile’
plotQuant: no visible global function definition for ‘lines’
plotQuant: no visible global function definition for ‘bxp’
plotQuant: no visible global function definition for ‘matplot’
plotQuant: no visible global function definition for ‘axis’
plotQuant: no visible global function definition for ‘box’
plotQuant: no visible global function definition for ‘title’
plotSplom: no visible global function definition for ‘pairs’
plotTrace : panel.trace: no visible global function definition for
  ‘var’
plotTrace : panel.trace: no visible global function definition for
  ‘median’
plotTrace: no visible global function definition for ‘tail’
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par quantile tail title var
  window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
Undeclared package ‘scape’ in Rd xrefs
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.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
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’
Undeclared package ‘sm’ in Rd xrefs
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
File ‘plugdensity/libs/plugdensity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘glue’ in Rd xrefs
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.
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.
Package suggested but not available for checking: ‘MSnbase’
Note: found 62 marked UTF-8 strings
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').
File ‘png/libs/png.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Note: found 7256 marked UTF-8 strings
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.
File ‘poilog/libs/poilog.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
Undeclared package ‘ISOcodes’ in Rd xrefs
Note: found 8 marked UTF-8 strings
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 ‘poisDoubleSamp/libs/poisDoubleSamp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/poismf.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
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’
rpoistweedie: no visible global function definition for ‘runif’
testOmegaPT: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: poistweedie.Rd:51: Dropping empty section \references
prepare_Rd: ppoistweedie.Rd:37: Dropping empty section \references
prepare_Rd: qpoistweedie.Rd:40: Dropping empty section \references
prepare_Rd: rpoistweedie.Rd:36: Dropping empty section \references
prepare_Rd: varpt.Rd:31: Dropping empty section \references
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘formattable’ ‘rlang’
  All declared Imports should be used.
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.
Undeclared package ‘flexmix’ in Rd xrefs
File ‘poLCA/libs/poLCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘Table.Output.html’
Undeclared package ‘purrr’ in Rd xrefs
Note: found 9 marked UTF-8 strings
Package suggested but not available for checking: ‘pollimetrydata’
Package required but not available: ‘RcppCWB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
File ‘polyfreqs/libs/polyfreqs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   4.0Mb
Namespace in Imports field not imported from: ‘combinat’
  All declared Imports should be used.
Found the following files/directories:
  ‘AbsorbedDrugMetabolites’ ‘CorrelationResults’
  ‘EndogenousMetabolites’ ‘HeatMap’ ‘PKresults’
  ‘SecondAbsorbedMetabolites’ ‘preprocessed-data’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      3.3Mb
Undeclared package ‘BSgenome’ in Rd xrefs
Namespace in Imports field not imported from: ‘regtools’
  All declared Imports should be used.
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’
Undeclared package ‘Rcmdr’ in Rd xrefs
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Undeclared package ‘nloptr’ in Rd xrefs
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
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’
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘ecodist’ in Rd xrefs
Undeclared package ‘bnpsd’ in Rd xrefs
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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Undeclared packages ‘rags2ridges’, ‘ragt2ridges’ in Rd xrefs
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'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:
  ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘portfolioSim/R/AllClasses.R’:
  .onLoad calls:
    require(methods)

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

contributionSummaryDf,simResult : <anonymous>: no visible global
  function definition for ‘aggregate’
getSimTrades,stiFromSignal-orderable-portfolio-simData-logical: no
  visible binding for global variable ‘shares’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.freq’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.errors’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.type’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.summary.interface’
loadIn,simResultSinglePeriod-character-missing: no visible binding for
  global variable ‘x’
plot,simResult-missing: no visible global function definition for
  ‘xyplot’
runSim,portfolioSim-logical: no visible binding for global variable
  ‘id’
runSim,portfolioSim-logical: no visible global function definition for
  ‘updateSummary’
securityPerfSummaryDf,simResult: no visible global function definition
  for ‘aggregate’
summary,simResult: no visible global function definition for ‘sd’
summary,simResult: no visible global function definition for ‘head’
summary,simResult: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head id master.errors master.freq master.summary.interface
  master.type sd shares tail updateSummary x xyplot
Consider adding
  importFrom("stats", "aggregate", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘StanHeaders’ ‘dplyr’ ‘ggplot2’ ‘gridExtra’ ‘rstan’ ‘tibble’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'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.
Undeclared package ‘emmeans’ in Rd xrefs
Undeclared package ‘cosa’ in Rd xrefs
Undeclared package ‘advclust’ in Rd xrefs
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Found the following files/directories:
  ‘Quad1.RData’ ‘Sp Env Data.RData’ ‘Sp PPM Data.RData’
  ‘SpEnvData.RData’ ‘Test.RData’ ‘TestPPM.RData’ ‘TestSP.RData’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc  11.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
pps1: no visible global function definition for ‘runif’
ppss: no visible global function definition for ‘runif’
ppswr: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: calif.Rd:5-6: Dropping empty section \arguments
prepare_Rd: calif.Rd:8-9: Dropping empty section \examples
prepare_Rd: califcty.Rd:5-6: Dropping empty section \arguments
prepare_Rd: califcty.Rd:8-9: Dropping empty section \examples
prepare_Rd: sizesok.Rd:12-13: Dropping empty section \examples
prepare_Rd: stratumsizes.Rd:11-12: Dropping empty section \examples
Malformed Description field: should contain one or more complete sentences.
LDA.Tree : Find.proj: no visible binding for global variable ‘var’
LDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
LDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘var’
PDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.Tree : Find.proj: no visible binding for global variable ‘var’
PP.Tree : Find.proj: no visible binding for global variable ‘median’
PP.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.optimize.Huber: no visible binding for global variable ‘sd’
PP.optimize.anneal: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible global function definition for ‘hist’
PP.optimize.plot: no visible global function definition for ‘text’
PP.optimize.plot: no visible global function definition for ‘par’
PP.optimize.plot: no visible global function definition for ‘colors’
PP.optimize.plot: no visible global function definition for ‘pairs’
PP.optimize.random: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  IQR colors hist median pairs par sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
File ‘PPtree/libs/PPtree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’
  All declared Imports should be used.
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.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
PKG_CXXFLAGS set in ‘src/Makevars.win’ without any corresponding files
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinycssloaders’ ‘shinythemes’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R.cache’ ‘docopt’ ‘here’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
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.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ROCR’ ‘ada’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘randomForest’ ‘rattle’ ‘rpart’
  ‘shinyAce’ ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’
  ‘xgboost’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘here’ ‘tidyr’
  All declared Imports should be used.
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.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
Undeclared package ‘colorspace’ in Rd xrefs
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
Note: found 42966 marked UTF-8 strings
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘lubridate’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
File ‘primes/libs/primes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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.
Found the following files/directories:
  ‘network.html’ ‘network_files’
Package suggested but not available for checking: ‘gurobi’
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  16.8Mb
Namespace in Imports field not imported from: ‘exactextractr’
  All declared Imports should be used.
Undeclared packages ‘ipflasso’, ‘mvtnorm’ in Rd xrefs
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Note: found 2 marked UTF-8 strings
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.
.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.
prepare_Rd: ProbForecastGOP-package.Rd:42-43: Dropping empty section \seealso
Rd file 'Emp.variog.Rd':
  \usage lines wider than 90 characters:
     Emp.variog(day, obs, forecast, id, coord1, coord2, cut.points=NULL, max.dist=NULL, nbins=300)

Rd file 'EmpDir.variog.Rd':
  \usage lines wider than 90 characters:
     EmpDir.variog(day, obs, forecast, id, coord1, coord2, tol.angle1=45, tol.angle2=135, cut.points=NULL, max.dist=NULL, nbins=300, type) 
  \examples lines wider than 100 characters:
     plot(dir.variog$bin.midpoints,dir.variog$dir.variog,xlab="Distance",ylab="Semi-variance",main="Empirical Directional variogram")

Rd file 'Field.sim.Rd':
  \usage lines wider than 90 characters:
     Field.sim(obs, forecast, coord1.grid, coord2.grid, forecast.grid,variog.model="exponential", param.est, n.sim=99, n.displ=4, 

Rd file 'avg.variog.Rd':
  \examples lines wider than 100 characters:
     variogram <- avg.variog(day=day, coord1=coord1,coord2=coord2,id=id,variable=obs,cut.points=NULL,max.dist=NULL,nbins=NULL) 
     plot(variogram$bin.midpoints,variogram$empir.variog,xlab="Distance", ylab="Semi-variance",main="Empirical variogram")

Rd file 'avg.variog.dir.Rd':
  \examples lines wider than 100 characters:
     dir.variog <- avg.variog.dir(day,coord1,coord2,id,variable=obs, tol.angle1=NULL,tol.angle2=NULL,cut.points=NULL,max.dist=NULL, nbins=NU ... [TRUNCATED]
     plot(dir.variog$bin.midpoints,dir.variog$dir.variog,xlab="Distance", ylab="Semi-variance",main="Empirical Directional variogram")

Rd file 'linesmodel.Rd':
  \examples lines wider than 100 characters:
     lines(variogram$bin.midpoints,linesmodel(distance=variogram$bin.midpoints,variog.model="exponential",param=c(param.variog$nugget,

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.6Mb
Error(s) in re-building vignettes:
--- re-building ‘processcheckr.Rmd’ using rmarkdown
Quitting from lines 58-67 (processcheckr.Rmd) 
Error: processing vignette 'processcheckr.Rmd' failed with diagnostics:
Column name `r2` must not be duplicated.
--- failed re-building ‘processcheckr.Rmd’

SUMMARY: processing the following file failed:
  ‘processcheckr.Rmd’

Error: Vignette re-building failed.
Execution halted
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
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.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      6.3Mb
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.
File ‘proj4/libs/proj4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘distcrete’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Undeclared package ‘purrr’ in Rd xrefs
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared packages ‘binom’, ‘PropCIs’, ‘BlakerCI’, ‘prevalence’ in Rd xrefs
Package suggested but not available for checking: ‘SDMTools’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   3.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
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 suggested but not available for checking: ‘resemble’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
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.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.6Mb
Undeclared package ‘XML’ in Rd xrefs
Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
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.
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.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Malformed Description field: should contain one or more complete sentences.
candidate.overlap: no visible global function definition for
  ‘write.table’
fisher: no visible global function definition for ‘fisher.test’
fisher.iteration: no visible global function definition for
  ‘download.file’
fisher.iteration: no visible global function definition for
  ‘read.table’
pSI.list: no visible global function definition for ‘write.table’
specificity.index: no visible global function definition for ‘png’
specificity.index: no visible global function definition for ‘par’
specificity.index: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘gene_count_1.csv’
Note: found 26 marked Latin-1 strings
'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.
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘orig’
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.
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.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 53.6Mb
  sub-directories of 1Mb or more:
    libs  52.6Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘performance’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ptstem)
  > 
  > test_check("ptstem")
  ── 1. Failure: Stemming Hunspell Works (@test-ptstem.R#15)  ────────────────────
  ptstem(texts, algorithm = "hunspell") not equal to c("coma frutas pois elas fazem bem para a saúde", "não coma doces, elas fazem mal para os dentes").
  2/2 mismatches
  x[1]: "elas coma saúde não elas elas fazem a frutas"
  y[1]: "coma frutas pois elas fazem bem para a saúde"
  
  x[2]: "pois elas não, para elas pois fazem os saúde"
  y[2]: "não coma doces, elas fazem mal para os dentes"
  
  ── 2. Failure: Stemming Hunspell Works (@test-ptstem.R#19)  ────────────────────
  ptstem(words, algorithm = "hunspell") not equal to c("balões", "aviões", "aviões", "gostou", "gostou", "gostou").
  5/6 mismatches
  x[2]: "balões"
  y[2]: "aviões"
  
  x[3]: "balões"
  y[3]: "aviões"
  
  x[4]: "gostaram"
  y[4]: "gostou"
  
  x[5]: "gostaram"
  y[5]: "gostou"
  
  x[6]: "gostaram"
  y[6]: "gostou"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Stemming Hunspell Works (@test-ptstem.R#15) 
  2. Failure: Stemming Hunspell Works (@test-ptstem.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Note: found 28898 marked UTF-8 strings
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
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.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is 60.3Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
File ‘pullword/libs/pullword.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘itsadug’ ‘mgcv’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
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.
Undeclared packages ‘vctrs’, ‘httr’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Undeclared package ‘concurve’ in Rd xrefs
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.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PWEALL/libs/PWEALL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PWFSLSmoke)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: maps
  Loading required package: MazamaCoreUtils
  Loading required package: MazamaSpatialUtils
  Loading required package: sp
  
  Attaching package: 'PWFSLSmoke'
  
  The following objects are masked from 'package:MazamaCoreUtils':
  
      loadDataFile, parseDatetime
  
  > 
  > test_check("PWFSLSmoke")
  ── 1. Failure: arguments are validated (@test-timeinfo.R#19)  ──────────────────
  `timeInfo <- timeInfo(datetime, longitude, latitude)` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 41 | SKIPPED: 2 | WARNINGS: 16 | FAILED: 1 ]
  1. Failure: arguments are validated (@test-timeinfo.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
.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').
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Running examples in ‘PythonInR-Ex.R’ failed
The error most likely occurred in:

> ### Name: pyGet
> ### Title: Gets Python objects by name and transforms them into R objects
> ### Aliases: pyGet
> 
> ### ** Examples
> 
> ## Don't show: 
> PythonInR:::pyCranConnect()
R is already connected to Python!
> ## End(Don't show)
> ## get a character of length 1
> pyGet("__name__")
[1] "__main__"
> ## get a character of length 1 > 1
> pyGet("sys.path")
[1] ""                                   "/usr/lib64/python38.zip"           
[3] "/usr/lib64/python3.8"               "/usr/lib64/python3.8/lib-dynload"  
[5] "/usr/lib64/python3.8/site-packages" "/usr/lib/python3.8/site-packages"  
[7] "."                                 
> ## get a list
> pyGet("sys.path", simplify = FALSE)
[[1]]
[1] ""

[[2]]
[1] "/usr/lib64/python38.zip"

[[3]]
[1] "/usr/lib64/python3.8"

[[4]]
[1] "/usr/lib64/python3.8/lib-dynload"

[[5]]
[1] "/usr/lib64/python3.8/site-packages"

[[6]]
[1] "/usr/lib/python3.8/site-packages"

[[7]]
[1] "."

> ## get a PythonInR_List
> x <- pyGet("sys.path", autoTypecast = FALSE)
> x
['', '/usr/lib64/python38.zip', '/usr/lib64/python3.8', '/usr/lib64/python3.8/lib-dynload', '/usr/lib64/python3.8/site-packages', '/usr/lib/python3.8/site-packages', '.']
> class(x)
[1] "PythonInR_List"   "PythonInR_Object" "R6"              
> 
> ## get an object where no specific transformation to R is defined
> ## this example also shows the differnces between pyGet and pyGet0
> pyExec("import datetime")
Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/usr/lib64/python3.8/datetime.py", line 8, in <module>

    
import math as _math
ImportError
: 
/usr/lib64/python3.8/lib-dynload/math.cpython-38-x86_64-linux-gnu.so: undefined symbol: PyFloat_Type
Error in pyExec("import datetime") : 
  An error has occured while executing Python code. See traceback above.
Execution halted
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’
Undeclared package ‘HURDAT’ in Rd xrefs
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.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    gui          1.7Mb
    libs         2.8Mb
    staticdocs   3.4Mb
GNU make is a SystemRequirements.
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’
Undeclared package ‘qdap’ in Rd xrefs
Undeclared package ‘gplots’ in Rd xrefs
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 76102 marked UTF-8 strings
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.
installed size is 107.2Mb
  sub-directories of 1Mb or more:
    libs  106.9Mb
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’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘qrNLMM’ in Rd xrefs
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.4Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘msm’
  All declared Imports should be used.
Package suggested but not available for checking: ‘qtl2’
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
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.
Undeclared package ‘qtl’ in Rd xrefs
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       3.0Mb
    libs      1.6Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
'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').
File ‘QuACN/libs/QuACN.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
quadp: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
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.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  13.6Mb
Note: found 2 marked UTF-8 strings
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   6.9Mb
Note: found 35707 marked UTF-8 strings
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
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’
Undeclared package ‘dynlm’ in Rd xrefs
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   6.0Mb
Found the following sources/headers with CR or CRLF line endings:
  inst/include/BackTest.h
Some Unix compilers require LF line endings.
Found the following files/directories:
  ‘Example’
Namespace in Imports field not imported from: ‘haven’
  All declared Imports should be used.
Undeclared package ‘Hmisc’ in Rd xrefs
Note: found 4145 marked UTF-8 strings
Package suggested but not available for checking: ‘fastshp’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Undeclared package ‘PredictABEL’ in Rd xrefs
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
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’
File ‘QUIC/libs/QUIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘quint’
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
Note: found 12928 marked UTF-8 strings
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’
File ‘qVarSel/libs/qVarSel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘chk1_1.dat’ ‘chk1_1.mem’ ‘chk1_1.noisy’
mutualCoherence : .setOneMutualP: no visible global function definition
  for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Note: found 89912 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
Undeclared package ‘fields’ in Rd xrefs
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.
Undeclared package ‘gplots’ in Rd xrefs
Note: found 32 marked UTF-8 strings
Namespace in Imports field not imported from: ‘vctrs’
  All declared Imports should be used.
'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’
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
Found the following files/directories:
  ‘output.html’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘RAbHIT-vignette.Rmd’ using rmarkdown
Loading required package: ggplot2
RAbHIT version: 0.1.4
Quitting from lines 198-200 (RAbHIT-vignette.Rmd) 
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
Can't combine `..1$SUBJECT` <logical> and `..2$SUBJECT` <character>.
--- failed re-building ‘RAbHIT-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RAbHIT-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.2Mb
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
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’
Note: found 3 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
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.
File ‘RAD/libs/RAD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘hexbin’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
Undeclared packages ‘longitudinal’, ‘gRbase’ in Rd xrefs
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   7.1Mb
Package suggested but not available for checking: ‘xcms’
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘stringi’
  All declared Imports should be used.
Found the following sources/headers not terminated with a newline:
  inst/include/ramcmc.h
Some compilers warn on such files.
Found the following files/directories:
  ‘blcs.dot’ ‘blcs.pdf’ ‘ex1.dot’ ‘ex1.pdf’ ‘ex1bridge1.dot’
  ‘ex1bridge1.pdf’ ‘ex1bridge2.dot’ ‘ex1bridge2.pdf’ ‘ex1bridge3.dot’
  ‘ex1bridge3.pdf’ ‘ex1effect1.dot’ ‘ex1effect1.pdf’ ‘ex1effect2.dot’
  ‘ex1effect2.pdf’ ‘gcmlinear.dot’ ‘gcmlinear.pdf’ ‘latent.dot’
  ‘latent.pdf’ ‘lcs.dot’ ‘lcs.pdf’ ‘mimic.dot’ ‘mimic.pdf’
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
File ‘randaes/libs/randaes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   5.2Mb
Undeclared packages ‘spam’, ‘RandomFields’ in Rd xrefs
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.
Undeclared package ‘WGCNA’ in Rd xrefs
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.
File ‘randomUniformForest/libs/randomUniformForest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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.
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RJDBC’
  All declared Imports should be used.
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.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
File ‘rappdirs/libs/rappdirs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs  13.1Mb
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.
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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.6Mb
Undeclared package ‘arm’ in Rd xrefs
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘glmnet’ in Rd xrefs
Undeclared package ‘maptools’ in Rd xrefs
File ‘rasterKernelEstimates/libs/rasterKernelEstimates.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘crosstalk’ in Rd xrefs
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   7.7Mb
Undeclared packages ‘gstat’, ‘fields’ in Rd xrefs
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
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.
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.
Package suggested but not available for checking: ‘arrow’
.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.
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    etc    1.9Mb
    po     1.2Mb
Note: found 12 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘raustats_introduction.Rmd’ using rmarkdown
Loading required package: readxl
Attaching package: 'raustats'
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Mar%202020?OpenDocument
Quitting from lines 204-205 (raustats_introduction.Rmd) 
Error: processing vignette 'raustats_introduction.Rmd' failed with diagnostics:
arguments imply differing number of rows: 0, 1
--- failed re-building ‘raustats_introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘raustats_introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
.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.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  37.4Mb
GNU make is a SystemRequirements.
Undeclared packages ‘MCMCpack’, ‘gtools’ in Rd xrefs
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘PZ.bi’ ‘mu_sigma.nc’
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.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/Rblpapi.Rcheck/00install.out’ for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   8.6Mb
‘configure’: /bin/bash is not portable
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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.
File ‘rbvs/libs/rbvs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 26334 marked UTF-8 strings
Found the following files/directories:
  ‘rcanvec.cache’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
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.
File ‘RCassandra/libs/RCassandra.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘rCAT-Ex.R’ failed
The error most likely occurred in:

> ### Name: ConBatch
> ### Title: Batch process, preliminary conservation assessments
> ### Aliases: ConBatch
> 
> ### ** Examples
> 
> mydata <- read.csv(system.file("extdata","multiple_species.csv",package="rCAT"))
> resultdf <- ConBatch(mydata$scientificname,mydata$latitude,mydata$longitude,2000,FALSE)
[1] "Processing species x"
Error in showSRID(uprojargs, format = "PROJ", multiline = "NO") : 
  Can't parse PROJ.4-style parameter string
+proj=cea +lon_0=24.5446916866314+lat_ts=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs
Calls: ConBatch -> simProjWiz -> CRS -> <Anonymous> -> showSRID
Execution halted
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following files/directories:
  ‘temp.RData’
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
Found the following sources/headers not terminated with a newline:
  inst/include/cereal/types/memory.hpp
Some compilers warn on such files.
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’
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
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 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’
Undeclared package ‘processx’ in Rd xrefs
Undeclared package ‘car’ in Rd xrefs
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'rqubic',
  'BicARE', 's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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.
Namespace with empty importFrom: ‘tcltk’
'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
computeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
'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.
Undeclared packages ‘BsMD’, ‘rsm’, ‘AlgDesign’, ‘lhs’ in Rd xrefs
managedata: no visible binding for global variable ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Undeclared packages ‘car’, ‘leaps’, ‘latticeExtra’, ‘rgl’ in Rd xrefs
'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.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  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 ‘getRcmdr’
.onAttach: no visible global function definition for ‘closeCommander’
.onAttach: no visible global function definition for ‘Commander’
mosaicMenuItem: no visible global function definition for
  ‘mosaicSelectDialog’
mosaicMenuItem: no visible global function definition for ‘Message’
Undefined global functions or variables:
  Commander Message closeCommander getRcmdr mosaicSelectDialog
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
Namespaces with empty importFrom:
  ‘stats’ ‘tcltk’
Malformed Description field: should contain one or more complete sentences.
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.
'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.
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.
Undeclared packages ‘e1071’, ‘RcmdrMisc’ in Rd xrefs
Package suggested but not available for checking: ‘ROpenOffice’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.4Mb
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.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
Found the following sources/headers not terminated with a newline:
  inst/include/Rcpp/traits/static_max_int.h
Some compilers warn on such files.
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.0Mb
    libs      1.9Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
File ‘RcppBDT/libs/RcppBDT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘RcppExamples’ in Rd xrefs
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    lib    5.0Mb
    libs   1.6Mb
‘cleanup’: /bin/bash is not portable
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppCWB.Rcheck/00install.out’ for details.
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     24.1Mb
Gauss: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
File ‘RcppFaddeeva/libs/RcppFaddeeva.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
‘configure’: /bin/bash is not portable
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
installed size is 58.3Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      43.1Mb
    libs     13.1Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       3.1Mb
GNU make is a SystemRequirements.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.4Mb
    libs      5.5Mb
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    jsonexamples   3.8Mb
    libs           2.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Found the following sources/headers not terminated with a newline:
  inst/include/pflineart.h
Some compilers warn on such files.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
‘cleanup’: /bin/bash is not portable
Undeclared package ‘inline’ in Rd xrefs
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 ‘RcppXts/libs/RcppXts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
‘cleanup’: /bin/bash is not portable
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/rCRM.h
  inst/include/rCRM_RcppExports.h
Some Unix compilers require LF line endings.
GNU make is a SystemRequirements.
Note: found 6543 marked UTF-8 strings
Running examples in ‘rcv-Ex.R’ failed
The error most likely occurred in:

> ### Name: rcv_tally
> ### Title: Determines RCV round results in a dataframe
> ### Aliases: rcv_tally
> 
> ### ** Examples
> 
> rcv_tally(image = sf_bos_clean, rcvcontest = "Board of Supervisors, District 7")
Error: Problem with `summarise()` input `total`.
✖ could not find function "n"
ℹ Input `total` is `n()`.
ℹ The error occured in group 1: candidate = "BEN MATRANGA".
Backtrace:
     █
  1. └─rcv::rcv_tally(image = sf_bos_clean, rcvcontest = "Board of Supervisors, District 7")
  2.   └─`%>%`(...)
  3.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         └─rcv:::`_fseq`(`_lhs`)
  7.           └─magrittr::freduce(value, `_function_list`)
  8.             └─function_list[[i]](value)
  9.               ├─dplyr::summarise(., total = n())
 10.               └─dplyr:::summarise.grouped_df(., total = n())
 11.                 └─dplyr:::summarise_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
█
Execution halted
Namespace in Imports field not imported from: ‘roxygen2’
  All declared Imports should be used.
Undeclared package ‘Rglpk’ in Rd xrefs
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.
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.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Undeclared package ‘Rtsne’ in Rd xrefs
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
Undeclared package ‘gbutils’ in Rd xrefs
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
'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’
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.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
File ‘Rdtq/libs/Rdtq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘example.pdf’
Undeclared packages ‘readMzXmlData’, ‘MALDIquantForeign’ in Rd xrefs
File ‘read.dbc/libs/read.dbc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
Undeclared package ‘MALDIquantForeign’ in Rd xrefs
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
GNU make is a SystemRequirements.
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Non-standard file/directory found at top level:
  ‘devel’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘mgcv’
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
prepare_Rd: bestmods.Rd:47-49: Dropping empty section \note
prepare_Rd: bestmods.Rd:43-44: Dropping empty section \references
prepare_Rd: cic.Rd:24-26: Dropping empty section \details
prepare_Rd: cic.Rd:40-42: Dropping empty section \note
prepare_Rd: cvic.Rd:49-51: Dropping empty section \note
prepare_Rd: eic.Rd:31-33: Dropping empty section \details
prepare_Rd: eic.Rd:50-52: Dropping empty section \note
prepare_Rd: eic.Rd:56-58: Dropping empty section \seealso
prepare_Rd: ic.min.Rd:22-24: Dropping empty section \details
prepare_Rd: ic.min.Rd:47-49: Dropping empty section \note
prepare_Rd: ic.min.Rd:53-55: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:16-17: Dropping empty section \references
prepare_Rd: reams-package.Rd:19-20: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:21-22: Dropping empty section \examples
prepare_Rd: scoremods.Rd:26-28: Dropping empty section \details
prepare_Rd: scoremods.Rd:43-45: Dropping empty section \note
prepare_Rd: xy.Rd:46-48: Dropping empty section \note
prepare_Rd: xy.Rd:52: Dropping empty section \seealso
Note: found 8 marked UTF-8 strings
Undeclared package ‘rebus.unicode’ in Rd xrefs
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.8Mb
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.
Note: found 1036 marked UTF-8 strings
Undeclared package ‘car’ in Rd xrefs
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   6.0Mb
‘configure’: /bin/bash is not portable
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/rEDM.Rcheck/00install.out’ for details.
‘configure’: /bin/bash is not portable
AutoCorrelationLRtest: no visible global function definition for
  ‘logLik’
AutoCorrelationLRtest: no visible global function definition for
  ‘pchisq’
REEMtree: no visible global function definition for ‘terms’
REEMtree: no visible binding for global variable ‘SubsetVector’
REEMtree: no visible global function definition for ‘predict’
REEMtree: no visible global function definition for ‘logLik’
fitted.REEMtree: no visible global function definition for ‘fitted’
predict.REEMtree: no visible global function definition for ‘predict’
residuals.REEMtree: no visible global function definition for
  ‘residuals’
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq predict residuals terms
Consider adding
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
Rd file 'REEMtree.Rd':
  \usage lines wider than 90 characters:
                     ErrorTolerance=0.001, MaxIterations=1000, verbose=FALSE, tree.control=rpart.control(), 
                     lme.control=lmeControl(returnObject=TRUE), method="REML", correlation=NULL)

These lines will be truncated in the PDF manual.
S3 methods shown with full name in documentation object 'fitted.REEMtree':
  ‘fitted.REEMtree’

S3 methods shown with full name in documentation object 'logLik':
  ‘logLik.REEMtree’

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

S3 methods shown with full name in documentation object 'predict':
  ‘predict.REEMtree’

S3 methods shown with full name in documentation object 'print':
  ‘print.REEMtree’

S3 methods shown with full name in documentation object 'ranef.REEMtree':
  ‘ranef.REEMtree’

S3 methods shown with full name in documentation object 'residuals.REEMtree':
  ‘residuals.REEMtree’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
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’
Namespaces in Imports field not imported from:
  ‘glue’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
  Note: found 3134 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’
  All declared Imports should be used.
Undeclared package ‘monomvn’ in Rd xrefs
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.8Mb
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘ROCR’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’ ‘gbm’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘rattle’ ‘rpart’ ‘shinyWidgets’
  ‘shinydashboardPlus’ ‘shinyjs’ ‘xgboost’ ‘zip’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Non-standard files/directories found at top level:
  ‘prebuild.sh’ ‘regtest-Ex.R’
Warning in fun(libname, pkgname) :
  package regtest is under development and still may change considerably

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
binregtest: no visible global function definition for ‘str’
binregtest: no visible binding for global variable ‘str’
binregtest: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif str
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Rd file 'binregtest.rd':
  \usage lines wider than 90 characters:
     binregtest(FUN1, FUN2, ..., PARS = NULL, PAR1 = NULL, PAR2 = NULL, WHICH = sample(1:n), TRYALL = TRUE, COMP = is.all.equal, NAME = "UNN ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Undeclared package ‘care’ in Rd xrefs
Package which this enhances but not available for checking: ‘Rcplex’
Undeclared package ‘graph’ in Rd xrefs
'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.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
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.
File ‘relevent/libs/relevent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
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.
Undeclared package ‘magrittr’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
File ‘remMap/libs/remMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rEMM/libs/rEMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘remote/libs/remote.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.5Mb
Undeclared package ‘pls’ in Rd xrefs
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.
File ‘ReorderCluster/libs/ReorderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Undeclared package ‘ggplot2’ in Rd xrefs
Note: found 25 marked UTF-8 strings
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 files/directories:
  ‘P.csv’ ‘correct_alpha.csv’ ‘correct_beta.csv’ ‘correct_gamma.csv’
  ‘correct_lambda.csv’ ‘correct_perm_list.csv’ ‘correct_psi.csv’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.7Mb
PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
Found the following files/directories:
  ‘forest.out’
.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').
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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.
File ‘restrictedMVN/libs/restrictedMVN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs      4.2Mb
    swagger   1.4Mb
Namespace in Imports field not imported from: ‘Rserve’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.4Mb
Malformed Description field: should contain one or more complete sentences.
Warning: no function found corresponding to methods exports from ‘retimes’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the 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.
dexgauss: no visible global function definition for ‘pnorm’
loglik: no visible global function definition for ‘pnorm’
mexgauss: no visible global function definition for ‘sd’
rexgauss: no visible global function definition for ‘rnorm’
rexgauss: no visible global function definition for ‘rexp’
timefit: no visible global function definition for ‘optim’
timefit: no visible global function definition for ‘sd’
timefit: no visible global function definition for ‘par’
timefit: no visible global function definition for ‘hist’
timefit: no visible global function definition for ‘density’
timefit: no visible global function definition for ‘curve’
timefit: no visible global function definition for ‘new’
plot,timefit: no visible global function definition for ‘density’
plot,timefit: no visible global function definition for ‘par’
plot,timefit: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘retimes/libs/retimes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘purrr’ ‘readr’ ‘tibble’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Undeclared package ‘robustbase’ in Rd xrefs
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.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
installed size is 65.8Mb
  sub-directories of 1Mb or more:
    libs  64.5Mb
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    data   1.9Mb
    help   1.0Mb
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
Note: found 44 marked UTF-8 strings
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
Found the following files/directories:
  ‘Test.txt’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
.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’
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘prob’ ‘titanic’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
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.
Undeclared package ‘curl’ in Rd xrefs
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       2.2Mb
    extdata   2.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   2.9Mb
Malformed Description field: should contain one or more complete sentences.
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
Undeclared package ‘Matching’ in Rd xrefs
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      2.1Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:34: warning: 'GTypeDebugFlags' is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: 'GTimeVal' is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/rggobi.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
Undeclared packages ‘lpSolve’, ‘ROI’, ‘Rsymphony’ in Rd xrefs
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    2.7Mb
Undeclared package ‘heplots’ in Rd xrefs
Found the following files/directories:
  ‘MD_display.csv’ ‘kola.c_COUNTRY_Cu.csv’
  ‘kola.c_COUNTRY_Cu_fences.txt’ ‘ogrady.mvalloc_mvalloc.csv’
  ‘sind.mat2open_NGR_summary.csv’ ‘sind.save_PC-loadings.csv’
  ‘sind.save_PC-scores.csv’ ‘test.save.mvalloc_mvalloc.csv’
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.6Mb
    libs   9.1Mb
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’
File ‘RGtk2/libs/RGtk2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘DBI’ in Rd xrefs
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb
.quick_fetch: no visible global function definition for ‘POST’
.quick_fetch: no visible global function definition for ‘add_headers’
.quick_fetch: no visible global function definition for
  ‘stop_for_status’
.quick_fetch: no visible global function definition for ‘content’
fetch_healthdata: no visible binding for global variable ‘resources’
fetch_healthdata : <anonymous>: no visible binding for global variable
  ‘filters’
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for ‘new’
ECLDataset: no visible global function definition for ‘new’
ECLDedUp: no visible global function definition for ‘new’
ECLDistribute: no visible global function definition for ‘new’
ECLIterate: no visible global function definition for ‘new’
ECLJoin: no visible global function definition for ‘new’
ECLOutput: no visible global function definition for ‘new’
ECLProject: no visible global function definition for ‘new’
ECLRecord: no visible global function definition for ‘new’
ECLRollUp: no visible global function definition for ‘new’
ECLSort: no visible global function definition for ‘new’
ECLTOPN: no visible global function definition for ‘new’
ECLTable: no visible global function definition for ‘new’
ECLTransform: no visible global function definition for ‘new’
eclDirectCall: no visible global function definition for ‘postForm’
parseResults: no visible global function definition for ‘xmlRoot’
parseResults: no visible global function definition for ‘xmlTreeParse’
parseResults: no visible global function definition for ‘getNodeSet’
parseResults: no visible global function definition for ‘xmlGetAttr’
parseResults: no visible global function definition for ‘xmlValue’
parseResults: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Undeclared packages ‘tseries’, ‘TSA’ in Rd xrefs
Unknown package ‘TSA’ in Rd xrefs
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for ‘cov’
RHT.2samp : get.lambda : get.para: no visible global function
  definition for ‘optimize’
RHT.2samp : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.2samp : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.2samp : <anonymous>: no visible global function definition for
  ‘cov’
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for ‘cov’
RHT.fun : get.lambda : get.para: no visible global function definition
  for ‘optimize’
RHT.fun : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.fun : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.fun : <anonymous>: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FusedQDA : <anonymous>: no visible global function definition for ‘cov’
RidgeFused: no visible binding for global variable ‘cov2cor’
RidgeFusedCV : <anonymous>: no visible global function definition for
  ‘cov’
SSRidgeFused : <anonymous>: no visible global function definition for
  ‘cov’
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
ridit.raw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Undeclared package ‘fastcluster’ in Rd xrefs
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Undeclared package ‘fastcluster’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
R2ngon: no visible global function definition for ‘approx’
plotR2pre: no visible global function definition for ‘points’
plotR2pre: no visible global function definition for ‘gray’
plotR2pre: no visible global function definition for ‘legend’
plotR2pre: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  approx gray legend points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
plot.ijzip: no visible global function definition for ‘axis’
read.ijzip: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  axis unzip
Consider adding
  importFrom("graphics", "axis")
  importFrom("utils", "unzip")
to your NAMESPACE file.
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘methods’ ‘readr’
  All declared Imports should be used.
Found the following files/directories:
  ‘mtcars.txt’
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
desmat.sanitize: no visible global function definition for ‘aggregate’
dispdist: no visible global function definition for ‘quantile’
dispdist: no visible global function definition for ‘hist’
dispdist: no visible global function definition for ‘lines’
estate: no visible global function definition for ‘weighted.mean’
estate: no visible global function definition for ‘lm’
genperms: no visible global function definition for ‘combn’
genprobexact: no visible global function definition for ‘ave’
invert.ci: no visible global function definition for ‘quantile’
invert.ci: no visible global function definition for ‘uniroot’
omni.ate: no visible global function definition for ‘hist’
omni.ate: no visible global function definition for ‘lines’
omni.ate: no visible global function definition for ‘quantile’
resresplot: no visible global function definition for ‘lm’
resresplot: no visible global function definition for ‘symbols’
resresplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline aggregate ave combn hist lines lm quantile symbols uniroot
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "symbols")
  importFrom("stats", "aggregate", "ave", "lm", "quantile", "uniroot",
             "weighted.mean")
  importFrom("utils", "combn")
to your NAMESPACE file.
Rd file 'genperms.custom.Rd':
  \examples lines wider than 100 characters:
                     teststat <- pf(fstat[1],fstat[2],fstat[3],lower.tail=FALSE)  # extract F-test p-value

Rd file 'genprob.Rd':
  \examples lines wider than 100 characters:
                     teststat <- pf(fstat[1],fstat[2],fstat[3],lower.tail=FALSE)  # extract F-test p-value

These lines will be truncated in the PDF manual.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.9Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
KM.plot: no visible global function definition for ‘lines’
SchoenSmooth: no visible global function definition for ‘lm’
llCoxReg: no visible binding for global variable ‘time’
risksetAUC: no visible global function definition for ‘abline’
risksetROC: no visible global function definition for ‘abline’
weightedKM: no visible binding for global variable ‘time’
Undefined global functions or variables:
  abline lines lm time
Consider adding
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Alg2: no visible global function definition for ‘uniroot’
Alg3: no visible global function definition for ‘optim’
NVCopula: no visible global function definition for ‘rnorm’
NVCopula: no visible global function definition for ‘rgamma’
NVCopula: no visible global function definition for ‘var’
NVCopula: no visible global function definition for ‘cov’
NVCopula: no visible global function definition for ‘qnorm’
NVCopulaMT: no visible global function definition for ‘rnorm’
NVCopulaMT: no visible global function definition for ‘rgamma’
NVCopulaMT: no visible global function definition for ‘var’
NVCopulaMT: no visible global function definition for ‘cov’
NVCopulaMT: no visible global function definition for ‘qnorm’
R2X: no visible global function definition for ‘write.table’
ReturnCopula: no visible global function definition for ‘qt’
ReturnCopula: no visible global function definition for ‘pt’
SISCopula: no visible global function definition for ‘runif’
SISCopula: no visible global function definition for ‘qnorm’
SISCopula: no visible global function definition for ‘rnorm’
SISCopula: no visible global function definition for ‘qgamma’
SISCopula: no visible global function definition for ‘var’
SISCopula: no visible global function definition for ‘cov’
SISCopulaMT: no visible global function definition for ‘runif’
SISCopulaMT: no visible global function definition for ‘qnorm’
SISCopulaMT: no visible global function definition for ‘rnorm’
SISCopulaMT: no visible global function definition for ‘qgamma’
SISCopulaMT: no visible global function definition for ‘var’
SISCopulaMT: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Note: found 12 marked UTF-8 strings
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
Undeclared package ‘utility’ in Rd xrefs
Packages in Depends field not imported from:
  ‘compiler’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for ‘pchip’
NumConv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘pchip’
NumDeconv : error_function: no visible global function definition for
  ‘pchip’
NumDeconv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘optim’
RivivcA: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
Rd file 'NumConv.Rd':
  \usage lines wider than 90 characters:
     NumConv(impulse.matrix, input.matrix, conv.timescale = NULL, explicit.interpolation = 1000)

Rd file 'RivivcA.Rd':
  \examples lines wider than 100 characters:
     result<-RivivcA(input_mtx,impulse_mtx,resp_mtx,explicit.interp=accur_explic,implicit.interp=accur_implic)

These lines will be truncated in the PDF manual.
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘install-sh’ ‘jri’ ‘version’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  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'.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Found the following files/directories:
  ‘Barplot’ ‘Boxplot’ ‘BubblePlot’ ‘CircularFV’ ‘DataTable’
  ‘Dendrogram’ ‘DensityPlot’ ‘Heatmap’ ‘HivePlot’ ‘Network’ ‘Piechart’
  ‘Scatter3d’ ‘ScatterPlot’ ‘Surface3d’ ‘SymHeatmap’ ‘WordCloud’
installed size is  8.5Mb
File
  LICENSE
is not mentioned in the DESCRIPTION file.
'library' or 'require' call to ‘rJava’ which was already attached by Depends.
  Please remove these calls from your code.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
cv.coef: no visible global function definition for ‘sd’
normalize.softmax: no visible global function definition for ‘plogis’
plot.rknnSupport: no visible global function definition for ‘dotchart’
predicted: no visible global function definition for ‘influence’
predicted: no visible global function definition for ‘fitted’
predicted: no visible global function definition for ‘resid’
pressresid: no visible global function definition for ‘influence’
pressresid: no visible global function definition for ‘resid’
Undefined global functions or variables:
  dotchart fitted influence plogis resid sd
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘stringi’
  All declared Imports should be used.
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
':::' calls which should be '::':
  ‘stats:::dexp’ ‘stats:::dgamma’ ‘stats:::dweibull’ ‘stats:::pexp’
  ‘stats:::pgamma’ ‘stats:::pweibull’ ‘stats:::qexp’ ‘stats:::qgamma’
  ‘stats:::qweibull’ ‘stats:::rexp’ ‘stats:::rgamma’ ‘stats:::rweibull’
  See the note in ?`:::` about the use of this operator.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Undeclared package ‘httpuv’ in Rd xrefs
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Undeclared package ‘rgdal’ in Rd xrefs
installed size is 70.6Mb
  sub-directories of 1Mb or more:
    libs  69.9Mb
GNU make is a SystemRequirements.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
File ‘Rlof/libs/Rlof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Found the following files/directories:
  ‘file.out’
Package in Depends field not imported from: ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘EMSRb_internal’ ‘EM_internal’ ‘PD_internal’
EMSRb_internal: no visible global function definition for ‘qnorm’
EM_internal: no visible global function definition for ‘dnorm’
EM_internal: no visible global function definition for ‘pnorm’
PD_internal: no visible global function definition for ‘qtnorm’
PD_internal: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'EMSRb_internal.Rd':
  \usage lines wider than 90 characters:
     EMSRb_internal(Fare = Fare, Mean = Mean, Var = Var, p_up = numeric(length(Fare)), cap = cap)

These lines will be truncated in the PDF manual.
ma.filter: no visible global function definition for ‘par’
ma.filter: no visible global function definition for ‘lines’
ma.filter: no visible global function definition for ‘abline’
qn: no visible global function definition for ‘lm’
qn: no visible global function definition for ‘var’
qn: no visible global function definition for ‘resid’
ss.filter: no visible global function definition for ‘smooth.spline’
ss.filter: no visible global function definition for ‘par’
ss.filter: no visible global function definition for ‘lines’
ss.filter: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Note: found 31 marked UTF-8 strings
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    rmd   8.3Mb
Found the following files/directories:
  ‘dipper.inp’ ‘mark001.inp’ ‘mark001.out’ ‘mark001.res’ ‘mark001.vcv’
  ‘mark002.inp’ ‘mark002.out’ ‘mark002.res’ ‘mark002.vcv’ ‘mark003.inp’
  ‘mark003.out’ ‘mark003.res’ ‘mark003.vcv’ ‘mark004.inp’ ‘mark004.out’
  ‘mark004.res’ ‘mark004.vcv’ ‘mark005.inp’ ‘mark005.out’ ‘mark005.res’
  ‘mark005.vcv’ ‘mark006.inp’ ‘mark006.out’ ‘mark006.res’ ‘mark006.vcv’
  ‘mark007.inp’ ‘mark007.out’ ‘mark007.res’ ‘mark007.vcv’ ‘mark008.inp’
  ‘mark008.out’ ‘mark008.res’ ‘mark008.vcv’ ‘mark009.inp’ ‘mark009.out’
  ‘mark009.res’ ‘mark009.vcv’ ‘mark010.inp’ ‘mark010.out’ ‘mark010.res’
  ‘mark010.vcv’ ‘mark010V.tmp’ ‘mark010X.tmp’ ‘mark010Y.tmp’
  ‘mark011.inp’ ‘mark011.out’ ‘mark011.res’ ‘mark011.vcv’ ‘mark012.inp’
  ‘mark012.out’ ‘mark012.res’ ‘mark012.vcv’ ‘mark013.inp’ ‘mark013.out’
  ‘mark013.res’ ‘mark013.vcv’
installed size is 72.6Mb
  sub-directories of 1Mb or more:
    libs  71.8Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘blogdown’ ‘bookdown’ ‘bookdownplus’ ‘citr’ ‘pagedown’ ‘rticles’
  ‘tinytex’ ‘xaringan’
  All declared Imports should be used.
Undeclared package ‘R.oo’ in Rd xrefs
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   7.1Mb
CI: no visible global function definition for ‘sd’
CI: no visible global function definition for ‘qt’
L: no visible global function definition for ‘sd’
L: no visible global function definition for ‘residuals’
Qa: no visible global function definition for ‘logLik’
Qb: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘logLik’
STDERR: no visible global function definition for ‘sd’
group.UCL: no visible global function definition for ‘aggregate’
lr.glover: no visible binding for global variable ‘logLik’
lr.glover: no visible binding for global variable ‘update’
lr.glover : nobs0: no visible binding for global variable ‘nobs’
lr.glover : nobs0 : nobs2: no visible global function definition for
  ‘residuals’
lr.glover : tlab: no visible global function definition for ‘terms’
lr.glover : name: no visible global function definition for ‘formula’
lr.glover : modelUpdate: no visible global function definition for
  ‘as.formula’
lr.glover: no visible global function definition for ‘model.frame’
lr.glover: no visible binding for global variable ‘AIC’
lr.glover: no visible binding for global variable ‘BIC’
summarySE : <anonymous>: no visible global function definition for ‘sd’
summarySE: no visible global function definition for ‘qt’
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for ‘new’
barplotMixCluster: no visible global function definition for ‘is’
barplotMixCluster: no visible global function definition for ‘par’
barplotMixCluster: no visible global function definition for ‘lines’
barplotMixCluster: no visible global function definition for ‘text’
barplotMixCluster: no visible global function definition for ‘title’
barplotMixCluster: no visible global function definition for ‘mtext’
histMixCluster: no visible global function definition for ‘is’
histMixCluster: no visible global function definition for ‘par’
histMixCluster: no visible global function definition for ‘dnorm’
histMixCluster: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘par’
mixmodEntPlot: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘axis’
mixmodEntPlot: no visible global function definition for ‘title’
mixmodEntPlot: no visible binding for global variable ‘par’
plot,MixmodCombi: no visible global function definition for ‘par’
plot,MixmodCombi: no visible global function definition for ‘plot.new’
plot,MixmodCombi: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  39.6Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
.pLGP_qvec: no visible global function definition for ‘ppois’
.qLGP_pvec: no visible global function definition for ‘qpois’
.rLGP.failsafe: no visible global function definition for ‘runif’
.subdmg: no visible global function definition for ‘dbinom’
dnegbin: no visible global function definition for ‘dnbinom’
pLGP: no visible global function definition for ‘ppois’
qLGP: no visible global function definition for ‘qpois’
rLGP: no visible global function definition for ‘rpois’
rLGP: no visible global function definition for ‘rnorm’
rLGP: no visible global function definition for ‘runif’
rbinegbin: no visible global function definition for ‘rnbinom’
rmanaclash: no visible global function definition for ‘rbinom’
rmanaclash: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Undeclared packages ‘dfoptim’, ‘pracma’ in Rd xrefs
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
Undeclared package ‘fortunes’ in Rd xrefs
rms.pval: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Undeclared package ‘multiwayvcov’ in Rd xrefs
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
dWishartSpike: no visible global function definition for ‘dnorm’
pWishartSpike: no visible global function definition for ‘pnorm’
qWishartSpike: no visible global function definition for ‘qnorm’
rWishartSpike: no visible global function definition for ‘qnorm’
rmp: no visible global function definition for ‘runif’
rtw: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
GNU make is a SystemRequirements.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
Running ‘testthat.R’ [18s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(rmweather)
  > 
  > test_check("rmweather")
  ── 1. Failure: Test training function (@test_02_rmw_functions.R#72)  ───────────
  model$r.squared not equal to 0.1620433.
  1/1 mismatches
  [1] 0.436 - 0.162 == 0.274
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 40 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Test training function (@test_02_rmw_functions.R#72) 
  
  Error: testthat unit tests failed
  Execution halted
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  ‘DESeq’ ‘seqinr’ ‘topGO’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Note: found 133 marked Latin-1 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
Note: found 7 marked Latin-1 strings
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Undeclared packages ‘fossil’, ‘raster’ in Rd xrefs
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running ‘spelling.R’
  Running ‘test-all.R’ [76s/93s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > 
  > test_check("RNeXML")
  Loading required package: RNeXML
  Loading required package: ape
  ── 1. Failure: coalesce_() works correctly (@test_01_utils.R#129)  ─────────────
  `dplyr::coalesce(dta$col1, dta$col3, last)` did not throw an error.
  
  ── 2. Failure: coalesce_() works correctly (@test_01_utils.R#130)  ─────────────
  `dplyr::coalesce(dta$col3, last)` did not throw an error.
  
  Done simulation(s).
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 303 | SKIPPED: 42 | WARNINGS: 2 | FAILED: 2 ]
  1. Failure: coalesce_() works correctly (@test_01_utils.R#129) 
  2. Failure: coalesce_() works correctly (@test_01_utils.R#130) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
well19937.validate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘rngwell19937/libs/rngwell19937.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doxygen   1.6Mb
    libs      3.6Mb
installed size is 92.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     90.5Mb
Nnls.trimW : fun1: no visible global function definition for ‘runif’
initM: no visible global function definition for ‘runif’
rnmf: no visible global function definition for ‘txtProgressBar’
rnmf: no visible global function definition for ‘setTxtProgressBar’
see: no visible global function definition for ‘heat.colors’
see: no visible global function definition for ‘colorRampPalette’
see: no visible global function definition for ‘grey’
see: no visible global function definition for ‘par’
see: no visible global function definition for ‘image’
see: no visible global function definition for ‘mtext’
simtum: no visible global function definition for ‘runif’
simtum: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘abind’ ‘foreach’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  16.2Mb
Undeclared packages ‘mvoutlier’, ‘StatDA’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘robustbase’ ‘sfsmisc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for ‘as.formula’
.BuildPartial: no visible global function definition for ‘residuals’
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for ‘na.omit’
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable ‘median’
.PairwiseCorrelation: no visible global function definition for
  ‘complete.cases’
.yw: no visible global function definition for ‘toeplitz’
FastQn: no visible global function definition for ‘median’
FastQn: no visible global function definition for ‘mad’
fqn: no visible global function definition for ‘median’
fqn: no visible global function definition for ‘mad’
psdcor: no visible global function definition for ‘posdefify’
psdcor: no visible global function definition for ‘nearcor’
robar: no visible global function definition for ‘frequency’
robcor: no visible global function definition for ‘covMcd’
s_FastQn: no visible global function definition for ‘median’
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
File ‘robcp/libs/robcp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Undeclared package ‘ggm’ in Rd xrefs
Undeclared package ‘distrEx’ in Rd xrefs
Undeclared package ‘ROptEst’ in Rd xrefs
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Undeclared package ‘svdvisual’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DEoptimR’ ‘DT’ ‘PerformanceAnalytics’ ‘ggplot2’ ‘graphics’
  ‘gridExtra’ ‘methods’ ‘shinyjs’ ‘utils’ ‘xts’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
Undeclared packages ‘matrixStats’, ‘robustX’, ‘quantreg’, ‘rrcov’, ‘Hmisc’ in Rd xrefs
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘mgcv’ ‘robustbase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for ‘integrate’
QM.poisson: no visible global function definition for ‘ppois’
QM.poisson: no visible global function definition for ‘dpois’
expect.poisson: no visible global function definition for ‘dpois’
expect.poisson: no visible global function definition for ‘ppois’
pred.robustgam: no visible global function definition for
  ‘Predict.matrix’
robust.sigma: no visible global function definition for ‘median’
robustgam: no visible global function definition for ‘s’
robustgam: no visible global function definition for
  ‘smooth.construct.tp.smooth.spec’
robustgam: no visible global function definition for
  ‘smooth.construct.cr.smooth.spec’
robustgam: no visible global function definition for
  ‘smooth.construct.ps.smooth.spec’
robustgam : w.fun: no visible global function definition for ‘covMcd’
robustgam.GIC.optim: no visible global function definition for ‘optim’
robustgam.crossval : w.fun: no visible global function definition for
  ‘covMcd’
robustgam.crossval: no visible global function definition for
  ‘integrate’
smooth.construct.tr.smooth.spec: no visible global function definition
  for ‘quantile’
w.binomial: no visible global function definition for ‘pbinom’
w.poisson: no visible global function definition for ‘ppois’
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
File ‘robustgam/libs/robustgam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
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.
aggregateRanks: no visible binding for global variable ‘median’
aggregateRanks: no visible global function definition for ‘pnorm’
betaScores: no visible global function definition for ‘pbeta’
correctBetaPvaluesExact: no visible binding for global variable ‘qbeta’
thresholdBetaScore: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
PKG_CXXFLAGS set in ‘src/Makevars.win’ without any corresponding files
Undeclared package ‘pcaPP’ in Rd xrefs
Undeclared packages ‘mvtnorm’, ‘scatterplot3d’, ‘HH’ in Rd xrefs
Malformed Title field: should not end in a period.
NPROCwoGS: no visible global function definition for ‘quantile’
NPROCwoGS : rdirichlet: no visible global function definition for
  ‘rgamma’
NPROCwoGS: no visible global function definition for ‘rbinom’
NPROCwoGS: no visible global function definition for ‘rbeta’
NPROCwoGS: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
prepare_Rd: score.Rd:20-22: Dropping empty section \details
prepare_Rd: score.Rd:23-25: Dropping empty section \source
prepare_Rd: score.Rd:26-28: Dropping empty section \references
Rd file 'NPROCwoGS.Rd':
  \examples lines wider than 100 characters:
     AUC<- sum((ROC.est$T.Se[1,-1]+ROC.est$T.Se[1,-(ncutoff+2)])*(ROC.est$T.Sp[1,-1]-ROC.est$T.Sp[1,-(ncutoff+2)])/2)
     plot(1-ROC.est$T.Sp[1,],ROC.est$T.Se[1,],"l", xlab="1-Specificities",ylab="Sensitivities", main=paste("AUC=", format(AUC, digits=4),

Rd file 'ROCwoGS-package.Rd':
  \examples lines wider than 100 characters:
     AUC<- sum((ROC.est$T.Se[1,-1]+ROC.est$T.Se[1,-(ncutoff+2)])*(ROC.est$T.Sp[1,-1]-ROC.est$T.Sp[1,-(ncutoff+2)])/2)
     plot(1-ROC.est$T.Sp[1,],ROC.est$T.Se[1,],"l", xlab="1-Specificities",ylab="Sensitivities", main=paste("AUC=", format(AUC, digits=4),

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Note: found 59 marked UTF-8 strings
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RODBC’
A package should be listed in only one of these fields.
'library' or 'require' call to ‘RODBC’ which was already attached by Depends.
  Please remove these calls from your code.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
File ‘Rook/libs/Rook.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘ROptimizely’
ROSE.eval: no visible global function definition for ‘methods’
ROSE.eval: no visible binding for global variable ‘model.frame’
ROSE.eval: no visible binding for global variable ‘predict’
adj.formula: no visible global function definition for ‘terms’
adj.formula: no visible global function definition for ‘as.formula’
omnibus.balancing: no visible binding for global variable ‘model.frame’
ou.sampl: no visible global function definition for ‘rbinom’
over.sampl: no visible global function definition for ‘rbinom’
roc.curve: no visible global function definition for ‘lines’
roc.curve: no visible global function definition for ‘abline’
rose.real: no visible binding for global variable ‘sd’
rose.real: no visible global function definition for ‘sd’
rose.real: no visible global function definition for ‘rnorm’
rose.sampl: no visible global function definition for ‘rbinom’
under.sampl: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  abline as.formula lines methods model.frame predict rbinom rnorm sd
  terms
Consider adding
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
Undeclared packages ‘DMwR’, ‘pROC’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘methods’
  All declared Imports should be used.
Undeclared package ‘userfriendlyscience’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘rstudioapi’ ‘tinytex’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   6.3Mb
bestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
.computeValueReduct: no visible global function definition for ‘combn’
.findAllReductsFromCore: no visible global function definition for
  ‘combn’
.findFirstReductsFromCore: no visible global function definition for
  ‘combn’
.findSmallestReductFamilyFromCore: no visible global function
  definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
royston.test: no visible global function definition for ‘shapiro.test’
royston.test: no visible global function definition for ‘cor’
royston.test: no visible global function definition for ‘qnorm’
royston.test: no visible global function definition for ‘pnorm’
royston.test: no visible global function definition for ‘cov’
royston.test: no visible global function definition for ‘mahalanobis’
royston.test: no visible global function definition for ‘qqplot’
royston.test: no visible global function definition for ‘qchisq’
royston.test: no visible global function definition for ‘ppoints’
royston.test: no visible global function definition for ‘abline’
royston.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    2.5Mb
    tests   1.3Mb
License components which are templates and need '+ file LICENSE':
  MIT
Package in Depends field not imported from: ‘hash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for ‘has.key’
get_rand_int: no visible global function definition for ‘runif’
last: no visible global function definition for ‘tail’
rand_partitions: no visible global function definition for ‘hash’
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘rpartitions/libs/rpartitions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘tree’ in Rd xrefs
evalMedian: no visible global function definition for ‘xtabs’
evalMode: no visible global function definition for ‘xtabs’
rpartScore: no visible global function definition for ‘model.extract’
rpartScore: no visible global function definition for ‘var’
rpartScore: no visible binding for global variable ‘var’
splitAbs: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘RODBC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for ‘sqlSave’
rpart.rules.table : <anonymous>: no visible global function definition
  for ‘setNames’
rpart.subrules.table : <anonymous>: no visible global function
  definition for ‘setNames’
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Read-and-delete-me’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘survival’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for ‘mvrnorm’
GetVarImp : FitPenalizedModel: no visible global function definition
  for ‘clogit’
Undefined global functions or variables:
  clogit mvrnorm
Rd file 'GetVarImp.Rd':
  \examples lines wider than 100 characters:
     hist(MyResults, breaks=6, col="orange", xlab="Importance score", ylab="Number of features", main="Histogram of R-PCLR variable importan ... [TRUNCATED]
     ## Sort from most important (highest importance score) to least important feature (lowest importance score)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Rpdb.pdb’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
‘configure’: /bin/bash is not portable
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Undeclared packages ‘geomorph’, ‘phylocurve’ in Rd xrefs
Found the following files/directories:
  ‘mygraph.eps’ ‘mygraph.png’ ‘mygraph.tex’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/libpq/Makefile.win
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'.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Found the following files/directories:
  ‘Datasample.mads.txt’ ‘Datasample.medians.txt’ ‘control_plot.pdf’
  ‘correlation_plot.pdf’ ‘dataIII_qqplot.pdf’ ‘kruskalBoxplot.pdf’
  ‘plotQC.pdf’ ‘simpleBoxplot.pdf’ ‘wilcoxonBoxplot.pdf’
Undeclared package ‘htmlwidgets’ in Rd xrefs
GNU make is a SystemRequirements.
but_last: no visible global function definition for ‘head’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
preview_frames: no visible global function definition for ‘str’
print.EprimeFrame: no visible global function definition for ‘str’
print.FrameList: no visible global function definition for ‘str’
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
Non-standard file/directory found at top level:
  ‘rpsychi-Ex.R’
Rd file 'ind.prop.Rd':
  \examples lines wider than 100 characters:
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=1)    #Odds for not relapse is higher in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=1)    #Odds for relapse is lower in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=2)    #Odds for not relapse is lower in control than treatment condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=2)    #Odds for relapse is higher in control than treatment condition.

Rd file 'ind.prop.second.Rd':
  \examples lines wider than 100 characters:
     ind.prop.second(x=tab[,1], n = rowSums(tab))             #Risk for relapse is lower in treatment than control condition.
     ind.prop.second(x=tab[,1], n = rowSums(tab), ref.ind=2)  #Risk for relapse is higher in control than treatment condition.

These lines will be truncated in the PDF manual.
Undeclared package ‘scalreg’ in Rd xrefs
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
File ‘rredis/libs/rredis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘glasso’ ‘matrixcalc’ ‘mvoutlier’ ‘pcaPP’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rrest: no visible binding for global variable ‘glasso’
rrest: no visible global function definition for ‘pcout’
rrest: no visible global function definition for ‘var’
rrest: no visible global function definition for ‘mahalanobis’
rrlda : centerObservations: no visible global function definition for
  ‘l1median_NLM’
rrlda : df.L2glasso: no visible global function definition for
  ‘duplication.matrix’
rrlda : alt.df.L2glasso: no visible global function definition for
  ‘lower.triangle’
Undefined global functions or variables:
  duplication.matrix glasso l1median_NLM lower.triangle mahalanobis
  pcout var
Consider adding
  importFrom("stats", "mahalanobis", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
File ‘rr/libs/rr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘robustbase’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.computekappa: no visible global function definition for ‘pnorm’
.computekappa: no visible global function definition for ‘dnorm’
.initmethod : <anonymous>: no visible global function definition for
  ‘median’
.initmethod: no visible global function definition for ‘model.matrix’
.mspe: no visible global function definition for ‘rnorm’
.mspe : <anonymous>: no visible global function definition for ‘rnorm’
makedata: no visible global function definition for ‘rnorm’
makedata : addraneff: no visible global function definition for ‘rnorm’
plot.meanssaemodel: no visible global function definition for ‘par’
plot.meanssaemodel: no visible global function definition for ‘lines’
plot.meanssaemodel: no visible global function definition for ‘axis’
plot.meanssaemodel: no visible global function definition for ‘grid’
plot.meanssaemodel: no visible global function definition for ‘box’
plot.meanssaemodel: no visible global function definition for ‘legend’
plot.meanssaemodel: no visible global function definition for ‘arrows’
saemodel: no visible global function definition for ‘model.frame’
saemodel: no visible global function definition for ‘model.response’
saemodel: no visible global function definition for ‘model.matrix’
summary.fitsaemodel: no visible global function definition for ‘pt’
summary.fitsaemodel: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
File ‘rsae/libs/rsae.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘sp’ in Rd xrefs
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Undeclared package ‘AICcmodavg’ in Rd xrefs
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘rscimark/libs/rscimark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSclient/libs/RSclient.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Undeclared packages ‘keras’, ‘tensorflow’, ‘devtools’ in Rd xrefs
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘labelled’
  All declared Imports should be used.
convexhull: no visible global function definition for ‘chull’
convexhull: no visible global function definition for ‘rnorm’
drawcompletegraph: no visible global function definition for ‘segments’
getbag: no visible global function definition for ‘chull’
getbag: no visible global function definition for ‘polygon’
getbag: no visible global function definition for ‘points’
inflate: no visible global function definition for ‘rnorm’
rsmed: no visible global function definition for ‘runif’
rsplot: no visible global function definition for ‘chull’
rsplot: no visible global function definition for ‘polygon’
rsplot: no visible global function definition for ‘points’
rsrings: no visible global function definition for ‘chull’
rsrings: no visible global function definition for ‘polygon’
rsrings: no visible global function definition for ‘points’
rstinterval: no visible global function definition for ‘runif’
rstinterval: no visible global function definition for ‘rnorm’
rstinterval: no visible global function definition for ‘chull’
rstinterval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  chull points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘Rcompression’
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  Rserv.c:2150:17: warning: 'RSA_generate_key' is deprecated [-Wdeprecated-declarations]
  oc.c:47:33: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/00install.out’ for details.
Non-standard files/directories found at top level:
  ‘aclocal.m4’ ‘clients’ ‘clients.txt’ ‘version’
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
addNoisyCopies: no visible global function definition for ‘rnorm’
eta: no visible global function definition for ‘var’
gaussClassifier: no visible global function definition for ‘runif’
getSigma: no visible global function definition for ‘sd’
getSigma: no visible binding for global variable ‘sd’
sfaClassify: no visible global function definition for ‘rainbow’
sfaClassify: no visible global function definition for ‘par’
sfaClassify: no visible global function definition for ‘points’
sfaClassify: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Note: found 467 marked UTF-8 strings
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘methods’ ‘tcltk’ ‘tools’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.5Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
negbin.pow : negbin.disp: no visible global function definition for
  ‘rpois’
negbin.pow : negbin.disp: no visible global function definition for
  ‘rnbinom’
negbin.pow : inner.fcn: no visible global function definition for
  ‘na.omit’
negbin.pow : inner.fcn: no visible global function definition for
  ‘quantile’
negbin.pow: no visible global function definition for ‘txtProgressBar’
negbin.pow: no visible global function definition for
  ‘setTxtProgressBar’
poiss.pow : inner.fcn: no visible global function definition for
  ‘rpois’
poiss.pow : inner.fcn: no visible global function definition for
  ‘quantile’
poiss.pow: no visible global function definition for ‘txtProgressBar’
poiss.pow: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Found the following files/directories:
  ‘Database’ ‘rSQM.yaml’ ‘rSQM_Sample_Project’ ‘sample_script.R’
installed size is 258.1Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  251.4Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
Undeclared packages ‘gamm4’, ‘shiny’, ‘biglm’ in Rd xrefs
GNU make is a SystemRequirements.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
GNU make is a SystemRequirements.
installed size is 192.0Mb
  sub-directories of 1Mb or more:
    libs  189.2Mb
Undeclared packages ‘coda’, ‘rstanarm’ in Rd xrefs
GNU make is a SystemRequirements.
installed size is 122.8Mb
  sub-directories of 1Mb or more:
    libs  121.4Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
Undeclared packages ‘gridExtra’, ‘rstanarm’ in Rd xrefs
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  14.9Mb
Undeclared packages ‘survPen’, ‘flexsurv’ in Rd xrefs
Undeclared packages ‘shiny’, ‘Rook’, ‘opencpu’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Malformed Title field: should not end in a period.
File ‘RSvgDevice/libs/RSvgDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘Rplots.svg’
File ‘RSVGTipsDevice/libs/RSVGTipsDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘svgplot1.svg’ ‘svgplot10.svg’ ‘svgplot11.svg’ ‘svgplot12.svg’
  ‘svgplot13.svg’ ‘svgplot2.svg’ ‘svgplot3.svg’ ‘svgplot4.svg’
  ‘svgplot5.svg’ ‘svgplot6.svg’ ‘svgplot7.svg’ ‘svgplot8.svg’
  ‘svgplot9.svg’
Note: found 18627 marked UTF-8 strings
Found the following files/directories:
  ‘mapCH2017.rda’
Undeclared packages ‘lpSolve’, ‘Rglpk’ in Rd xrefs
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab

Found the following assignments to the global environment:
File ‘rSymPy/R/sympy.R’:
  assign(".Jython", .jnew("org.python.util.PythonInterpreter"), 
    .GlobalEnv)
  assign(".Jython", rJython(modules = system.file("Lib", package = "rSymPy")), 
    .GlobalEnv)
Undeclared package ‘spacyr’ in Rd xrefs
Malformed Title field: should not end in a period.
barplot.rtconnect: no visible global function definition for ‘rainbow’
barplot.rtconnect: no visible global function definition for ‘text’
plot.rtconnect: no visible global function definition for ‘par’
plot.rtconnect: no visible global function definition for ‘axis.Date’
rtconnect: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis.Date par rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
File ‘RTextTools/libs/RTextTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
plotGLCM: 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:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.9Mb
    projects   2.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘quantmod’ ‘sp’ ‘timetk’
  All declared Imports should be used.
Note: found 17315 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 30.7Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  21.9Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RQuantLib’
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
Found the following files/directories:
  ‘Tsttwalk.dat’
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 113868 marked UTF-8 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.4Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   8.0Mb
Undeclared package ‘magrittr’ in Rd xrefs
Found the following files/directories:
  ‘results’
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Rd file 'Runiversal-package.Rd':
  \examples lines wider than 100 characters:
     #Getting estimates from regression object as Java variables that be directly interpretable by Bean Shell.

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘somefile.xml’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Undeclared packages ‘labdsv’, ‘ape’, ‘RGCCA’, ‘cramer’, ‘FSA’, ‘npsm’, ‘mvnormtest’, ‘EMT’, ‘statmod’ in Rd xrefs
installed size is 58.6Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘rvgtest/libs/rvgtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
HapMendlianCheck: no visible global function definition for
  ‘write.table’
rvPDT.test.sub: no visible global function definition for ‘pnorm’
whap.prehap: no visible global function definition for ‘write.table’
whap.prehap: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
installed size is 57.6Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     53.3Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/RVowpalWabbit.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
lc_TDT: no visible global function definition for ‘pchisq’
rvTDT: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for ‘lm’
LASSO: no visible global function definition for ‘anova’
LASSO: no visible global function definition for ‘glm’
LASSO: no visible global function definition for ‘pchisq’
LASSO : <anonymous>: no visible global function definition for
  ‘extractAIC’
PCR : <anonymous>: no visible global function definition for ‘cor’
PLS : <anonymous>: no visible global function definition for ‘cor’
RR : RRscore: no visible binding for global variable ‘sd’
SPLS: no visible global function definition for ‘lm’
SPLS: no visible global function definition for ‘anova’
SPLS : <anonymous>: no visible global function definition for
  ‘extractAIC’
VTWOD : getScores: no visible global function definition for ‘sd’
VTWOD : getScores: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable ‘NoAm_country’
check_ISO_code: no visible binding for global variable ‘SoAm_country’
check_ISO_code: no visible binding for global variable ‘Oceana_country’
check_ISO_code: no visible binding for global variable ‘Africa_country’
check_ISO_code: no visible binding for global variable ‘Asia_country’
check_ISO_code: no visible binding for global variable ‘Eur_country’
climate_map: no visible binding for global variable ‘data’
date_correct: no visible global function definition for ‘tail’
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for ‘na.omit’
RWBP.default: no visible global function definition for ‘kmeans’
RWBP.formula: no visible global function definition for ‘model.extract’
predict.RWBP: no visible global function definition for ‘head’
Undefined global functions or variables:
  head kmeans model.extract na.omit
Consider adding
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Found the following files/directories:
  ‘RWebLogo.pdf’ ‘RWebLogo.png’
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 3619 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
File
  LICENSE
is not mentioned in the DESCRIPTION file.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Undeclared package ‘tm’ in Rd xrefs
Note: found 2016 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
.dwt: no visible global function definition for ‘median’
.udwt: no visible global function definition for ‘median’
plotSignalTransformation: no visible global function definition for
  ‘box’
plotSignalTransformation: no visible global function definition for
  ‘axis’
plotSignalTransformation: no visible global function definition for
  ‘lines’
plotSignalTransformation: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  axis box legend lines median
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines")
  importFrom("stats", "median")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'SnakeCharmR', 'installr'
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs    8.7Mb
    yacas   1.5Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs    9.4Mb
    yacas   1.6Mb
Undeclared package ‘rym’ in Rd xrefs
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
flemming.plot: no visible global function definition for ‘par’
flemming.plot: no visible global function definition for ‘segments’
flemming.plot: no visible global function definition for ‘text’
flemming.plot : triax.segments: no visible global function definition
  for ‘segments’
legend.bubbles: no visible global function definition for ‘quantile’
legend.bubbles: no visible global function definition for ‘legend’
other.methods: no visible global function definition for ‘quantile’
pejrup.plot: no visible global function definition for ‘par’
pejrup.plot: no visible global function definition for ‘segments’
pejrup.plot: no visible global function definition for ‘text’
pejrup.plot : triax.segments: no visible global function definition for
  ‘segments’
pejrup.plot: no visible global function definition for ‘legend’
rysgran.plot: no visible global function definition for ‘par’
rysgran.plot: no visible global function definition for ‘text’
rysgran.plot: no visible global function definition for ‘points’
rysgran.plot: no visible global function definition for ‘abline’
rysgran.plot: no visible global function definition for ‘mtext’
rysgran.ternary: no visible global function definition for ‘par’
rysgran.ternary: no visible global function definition for ‘points’
rysgran.ternary: no visible global function definition for ‘text’
shepard.plot: no visible global function definition for ‘par’
shepard.plot: no visible global function definition for ‘segments’
shepard.plot: no visible global function definition for ‘text’
shepard.plot : triax.segments: no visible global function definition
  for ‘segments’
shepard.plot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend mtext par points quantile segments text
Consider adding
  importFrom("graphics", "abline", "legend", "mtext", "par", "points",
             "segments", "text")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Note: found 841 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘sentiment.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 90-104 (sentiment.Rmd) 
Error: processing vignette 'sentiment.Rmd' failed with diagnostics:
Corrupt `grouped_df` using old (< 0.8.0) format.
ℹ Strip off old grouping with `ungroup()`.
--- failed re-building ‘sentiment.Rmd’

SUMMARY: processing the following file failed:
  ‘sentiment.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 40 (should be '.', not 'source'):
      source autobrew
Undeclared package ‘sf’ in Rd xrefs
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
calculate.summary: no visible global function definition for ‘sd’
detect.saccades: no visible global function definition for ‘median’
diagnostic.plot: no visible global function definition for ‘dev.new’
diagnostic.plot: no visible global function definition for ‘par’
diagnostic.plot: no visible global function definition for ‘recordPlot’
diagnostic.plot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
CV.Epidemic.Vn: no visible global function definition for ‘uniroot’
CV.Epidemic.Wn: no visible global function definition for ‘uniroot’
G.alfa: no visible global function definition for ‘dchisq’
Graf.Diagnostic: no visible global function definition for ‘stepfun’
Graf.Diagnostic: no visible global function definition for ‘title’
Graf.Diagnostic: no visible global function definition for ‘quantile’
Graf.Diagnostic: no visible global function definition for ‘legend’
Graf.Diagnostic: no visible global function definition for ‘arrows’
Graf.Diagnostic: no visible global function definition for ‘par’
Plot.ll: no visible global function definition for ‘segments’
Plot.ll: no visible global function definition for ‘axis’
SemiparChangePoint: no visible global function definition for ‘glm’
SemiparChangePoint: no visible binding for global variable ‘binomial’
SemiparChangePoint: no visible global function definition for
  ‘glm.control’
SemiparChangePoint: no visible global function definition for ‘coef’
Sn.alfa : tempfun: no visible global function definition for ‘dchisq’
Sn.alfa : d.tempfun: no visible global function definition for ‘dchisq’
Zn.alfa : tempfun: no visible global function definition for ‘dchisq’
Zn.alfa : d.tempfun: no visible global function definition for ‘dchisq’
cumsum.test: no visible global function definition for ‘var’
p.OneChange : tempfun: no visible global function definition for
  ‘dchisq’
p.OneChange: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  arrows axis binomial coef dchisq glm glm.control legend par quantile
  segments stepfun title uniroot var
Consider adding
  importFrom("graphics", "arrows", "axis", "legend", "par", "segments",
             "title")
  importFrom("stats", "binomial", "coef", "dchisq", "glm", "glm.control",
             "quantile", "stepfun", "uniroot", "var")
to your NAMESPACE file.
prepare_Rd: BootsModelTest.Rd:28-29: Dropping empty section \details
prepare_Rd: BootsModelTest.Rd:43: Dropping empty section \note
prepare_Rd: CriticalValues.Rd:38: Dropping empty section \note
prepare_Rd: Pvalues.Rd:24-25: Dropping empty section \details
prepare_Rd: Pvalues.Rd:38: Dropping empty section \note
prepare_Rd: cumsum.test.Rd:16-17: Dropping empty section \details
prepare_Rd: cumsum.test.Rd:28: Dropping empty section \note
Undeclared package ‘strucchange’ in Rd xrefs
fit.saery.AR1: no visible global function definition for ‘qnorm’
fit.saery.MA1: no visible global function definition for ‘qnorm’
fit.saery.indep: no visible global function definition for ‘qnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘write.table’
plot.saery: no visible global function definition for ‘devAskNewPage’
plot.saery: no visible global function definition for ‘par’
plot.saery: no visible global function definition for ‘abline’
plot.saery: no visible global function definition for ‘title’
plot.saery: no visible global function definition for ‘axis’
plot.saery: no visible global function definition for ‘lines’
plot.saery: no visible global function definition for ‘legend’
pvalue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par pnorm qnorm rnorm title
  write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Undeclared packages ‘magrittr’, ‘rlang’ in Rd xrefs
Package in Depends field not imported from: ‘lpSolveAPI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable ‘gaussian’
glm: no visible global function definition for ‘glm.control’
glm: no visible global function definition for ‘model.response’
glm: no visible global function definition for ‘is.empty.model’
glm: no visible global function definition for ‘model.matrix’
glm: no visible global function definition for ‘model.weights’
glm: no visible global function definition for ‘model.offset’
glm: no visible global function definition for ‘model.extract’
glm: no visible global function definition for ‘glm.fit’
glm: no visible global function definition for ‘.getXlevels’
separator: no visible global function definition for ‘make.lp’
separator: no visible global function definition for ‘set.column’
separator: no visible global function definition for ‘set.rhs’
separator: no visible global function definition for ‘set.constr.type’
separator: no visible global function definition for ‘set.objfn’
separator: no visible global function definition for ‘set.bounds’
separator: no visible global function definition for ‘lp.control’
separator: no visible global function definition for ‘get.variables’
separator: no visible global function definition for ‘set.basis’
separator: no visible global function definition for
  ‘get.dual.solution’
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘shinybusy’
  All declared Imports should be used.
File ‘SALES/libs/SALES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  13.6Mb
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘methods’
  All declared Imports should be used.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Rd file 'mudiff.acc.Rd':
  \usage lines wider than 90 characters:
     mudiff.acc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, equal = TRUE, m = 10000, mcs = 3)

Rd file 'mudiff.alc.Rd':
  \usage lines wider than 90 characters:
     mudiff.alc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, equal = TRUE, m = 10000, mcs = 3)

Rd file 'mudiff.mblmodwoc.Rd':
  \usage lines wider than 90 characters:
     mudiff.mblmodwoc(len, alpha1, beta1, alpha2, beta2, level = 0.95, worst.level = 0.95, m = 50000, mcs = 3)

Rd file 'mudiff.mblmodwoc.equalvar.Rd':
  \usage lines wider than 90 characters:
     mudiff.mblmodwoc.equalvar(len, alpha, beta, level = 0.95, worst.level = 0.95, m = 50000, mcs = 3)

Rd file 'mudiff.modwoc.Rd':
  \usage lines wider than 90 characters:
     mudiff.modwoc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, worst.level = 0.95, equal = TRUE, m = 50000, mcs = 3)

Rd file 'mudiff.modwoc.equalvar.Rd':
  \usage lines wider than 90 characters:
     mudiff.modwoc.equalvar(len, alpha, beta, n01, n02, level = 0.95, worst.level = 0.95, equal = TRUE)

These lines will be truncated in the PDF manual.
propdiff.acc: no visible global function definition for ‘rbeta’
propdiff.acc: no visible global function definition for ‘rbinom’
propdiff.acc: no visible global function definition for ‘pbeta’
propdiff.alc: no visible global function definition for ‘rbeta’
propdiff.alc: no visible global function definition for ‘rbinom’
propdiff.alc: no visible global function definition for ‘qbeta’
propdiff.freq: no visible global function definition for ‘qnorm’
propdiff.mblacc: no visible global function definition for ‘rbeta’
propdiff.mblacc: no visible global function definition for ‘rbinom’
propdiff.mblacc: no visible global function definition for ‘pbeta’
propdiff.mblalc: no visible global function definition for ‘rbeta’
propdiff.mblalc: no visible global function definition for ‘rbinom’
propdiff.mblalc: no visible global function definition for ‘qbeta’
propdiff.mblmodwoc: no visible global function definition for ‘qchisq’
propdiff.mblmodwoc: no visible global function definition for ‘pbeta’
propdiff.mblwoc: no visible global function definition for ‘pbeta’
propdiff.modwoc: no visible global function definition for ‘qchisq’
propdiff.modwoc: no visible global function definition for ‘pbeta’
propdiff.woc: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
File ‘sampling/libs/sampling.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
‘cleanup’: /bin/bash is not portable
GraphBinaryForestPlot: no visible global function definition for
  ‘abline’
GraphBinaryForestPlot: no visible global function definition for ‘text’
GraphContinuousForestPlot: no visible global function definition for
  ‘abline’
GraphContinuousForestPlot: no visible global function definition for
  ‘text’
ImputeBinaryEvents: no visible global function definition for ‘rbinom’
ImputeSMD: no visible global function definition for ‘rnorm’
funnelplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.9Mb
generate.sample.core: no visible global function definition for
  ‘predict’
mdh: no visible global function definition for ‘model.frame’
mdh: no visible binding for global variable ‘na.fail’
mdh: no visible global function definition for ‘.getXlevels’
mdh: no visible global function definition for ‘quantile’
mdh: no visible global function definition for ‘hist’
predict.mdh: no visible global function definition for ‘model.frame’
samur: no visible global function definition for ‘predict’
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mixer’
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Note: found 826 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘saotd.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Selecting by n
Selecting by n
Selecting by n
Selecting by n
Selecting by n
Selecting by n
Joining, by = "word"
Quitting from lines 259-264 (saotd.Rmd) 
Error: processing vignette 'saotd.Rmd' failed with diagnostics:
only 0's may be mixed with negative subscripts
--- failed re-building ‘saotd.Rmd’

SUMMARY: processing the following file failed:
  ‘saotd.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 4 marked UTF-8 strings
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is 63.0Mb
  sub-directories of 1Mb or more:
    extdata  62.6Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for ‘download.file’
generate.sas7bdat.source: 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.
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Rd file 'read.SAScii.Rd':
  \usage lines wider than 90 characters:
     read.SAScii( fn, sas_ri, beginline = 1, buffersize = 50, zipped = F , n = -1 , intervals.to.print = 1000 , lrecl = NULL , skip.decimal. ... [TRUNCATED]
  \examples lines wider than 100 characters:
                     paste( "http://smpbff2.dsd.census.gov/pub/sipp/2004/l04puw" , i , ".zip" , sep = "" )

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
SASPECT: no visible global function definition for ‘dbinom’
my.SOnePro: missing arguments not allowed in calls to ‘c’
my.ttest: no visible global function definition for ‘var’
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘SASPECT.result.txt’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘stateLung-R01.pdf’ ‘stateLung-R01.txt’
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SAVE/libs/SAVE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
loads: no visible global function definition for ‘untar’
saves: no visible global function definition for ‘tar’
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
Found the following significant warnings:
  sbfc.cpp:752:3: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:754:3: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:756:3: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:780:3: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:871:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:876:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:879:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:883:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:885:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:1050:3: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
  sbfc.cpp:1063:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/sbfc.Rcheck/00install.out’ for details.
File ‘sbfc/libs/sbfc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
K: no visible global function definition for ‘dnorm’
sBF: no visible global function definition for ‘density’
sBF: no visible global function definition for ‘txtProgressBar’
sBF: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbioPN/libs/sbioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbmSDP/libs/sbmSDP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘insulin_receptor_IR_beta_pY1146_stats.csv’
  ‘insulin_receptor_exp_dataset.csv’ ‘pe_datasets’ ‘pe_plots’
  ‘ps1_datasets’ ‘ps1_plots’ ‘ps2_datasets’ ‘ps2_plots’ ‘sim_datasets’
  ‘sim_datasets_sum’ ‘sim_plots’
Malformed Title field: should not end in a period.
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 Description field: should contain one or more complete sentences.
fitSBSA: no visible binding for global variable ‘var’
fitSBSA: no visible global function definition for ‘var’
fitSBSA: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
File ‘SBSA/libs/SBSA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
Missing or unexported objects:
  ‘Rmosek::mosek_lptoprob’ ‘Rmosek::mosek_qptoprob’
Non-standard file/directory found at top level:
  ‘src-java’
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘Scale’
ChooseBest: no visible global function definition for ‘head’
GetScores: no visible global function definition for ‘write.table’
ReportTable: no visible binding for global variable ‘sd’
ReportTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
Undeclared package ‘plyr’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘MASS’ ‘methods’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.scair: no visible global function definition for ‘par’
plot.scair: no visible global function definition for ‘points’
plot.scar: no visible global function definition for ‘par’
plot.scar: no visible global function definition for ‘points’
predict.scair: no visible global function definition for ‘approx’
predict.scar: no visible global function definition for ‘approx’
scair: no visible global function definition for ‘gaussian’
scair: no visible global function definition for ‘runif’
scair: no visible global function definition for ‘rnorm’
scar: no visible global function definition for ‘gaussian’
scar: no visible global function definition for ‘glm.fit’
scar: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx gaussian glm.fit par points rnorm runif
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
Undeclared packages ‘Iso’, ‘scam’, ‘gam’ in Rd xrefs
File ‘scar/libs/scar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘spData’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘schoolmath/R/prime.factor.R’:
  data(primlist)
See section ‘Good practice’ in ‘?data’.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringi’ ‘stringr’ ‘tibble’ ‘tidyr’ ‘tidytext’
  All declared Imports should be used.
Note: found 464 marked UTF-8 strings
File ‘scio/libs/scio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
score.GGUM: no visible global function definition for ‘dnorm’
score.GGUM: no visible global function definition for ‘hist’
score.GGUM: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘EAP_est1.txt’
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
License components which are templates and need '+ file LICENSE':
  MIT License
Note: found 1 marked UTF-8 string
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘RCurl’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for ‘getURLAsynchronous’
scrape: no visible global function definition for ‘runif’
scrape: no visible global function definition for ‘capture.output’
scrape: no visible binding for global variable ‘xmlParse’
scrape: no visible binding for global variable ‘htmlParse’
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following files/directories:
  ‘untitled_consensus_cluster’
Note: found 57 marked UTF-8 strings
GNU make is a SystemRequirements.
Note: found 27 marked UTF-8 strings
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Undeclared package ‘care’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
Namespace in Imports field not imported from: 'lpSolveAPI'
  All declared Imports should be used.
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘flush.console’
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘flush.console’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘quantile’
initialize,sdcTargetMatrixClass: no visible global function definition
  for ‘flush.console’
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
File ‘SDDE/libs/SDDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘result.txt’
prepare_Rd: sdd.Rd:46-47: Dropping empty section \seealso
prepare_Rd: sddpack-package.Rd:31-32: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:29-30: Dropping empty section \references
prepare_Rd: sddsolve.Rd:38-39: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:40-41: Dropping empty section \examples
.ACF.compute: no visible global function definition for ‘pnorm’
.ACF.compute: no visible global function definition for ‘qnorm’
.ACF.compute: no visible global function definition for ‘pchisq’
.ACF.plot: no visible global function definition for ‘abline’
.ADF.compute: no visible global function definition for ‘qnorm’
.ADF.compute: no visible global function definition for ‘chisq.test’
.ADF.compute: no visible global function definition for ‘qchisq’
.ADF.compute: no visible global function definition for ‘pchisq’
.ADF.plot: no visible global function definition for ‘abline’
.CADF.plot: no visible global function definition for ‘points’
.DeltaADF.plot: no visible global function definition for ‘abline’
.RPADF.compute: no visible global function definition for ‘pchisq’
.RPADF.compute: no visible global function definition for ‘qchisq’
.RPADF.plot: no visible global function definition for ‘abline’
.RPADF.plot: no visible global function definition for ‘rect’
.fmin: no visible global function definition for ‘optimize’
.fobj: no visible global function definition for ‘pchisq’
.gen.plot: no visible global function definition for ‘axis’
.gen.plot: no visible global function definition for ‘box’
.gen.plot: no visible global function definition for ‘abline’
.lcv: no visible global function definition for ‘bw.nrd0’
.lcv: no visible global function definition for ‘nlm’
ADF: no visible binding for global variable ‘p.adjust.methods’
ADF: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  abline axis box bw.nrd0 chisq.test nlm optimize p.adjust
  p.adjust.methods pchisq pnorm points qchisq qnorm rect
Consider adding
  importFrom("graphics", "abline", "axis", "box", "points", "rect")
  importFrom("stats", "bw.nrd0", "chisq.test", "nlm", "optimize",
             "p.adjust", "p.adjust.methods", "pchisq", "pnorm", "qchisq",
             "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
File ‘sde/libs/sde.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Undeclared package ‘randomNames’ in Rd xrefs
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Undeclared package ‘rJava’ in Rd xrefs
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
dimplot: no visible global function definition for ‘par’
dimplot: no visible global function definition for ‘barplot’
dimplot: no visible global function definition for ‘axis’
find.traj: no visible global function definition for ‘flush.console’
nullprob: no visible global function definition for ‘pbinom’
pbox: no visible global function definition for ‘rect’
pbox: no visible global function definition for ‘par’
prim.traj: no visible global function definition for ‘flush.console’
prim.trajauto: no visible global function definition for
  ‘flush.console’
resampstats: no visible binding for global variable ‘sd’
scatterbox: no visible binding for global variable ‘box’
sd.start: no visible global function definition for ‘read.csv’
sd.start: no visible global function definition for ‘par’
sd.start: no visible global function definition for ‘graphics.off’
sd.start: no visible global function definition for ‘hist’
sd.start: no visible global function definition for ‘plot.ecdf’
sd.start: no visible global function definition for ‘write.csv’
sd.start: no visible global function definition for ‘flush.console’
trajplot: no visible global function definition for ‘points’
trajplot: no visible global function definition for ‘flush.console’
trajplot: no visible global function definition for ‘lm’
trajplot: no visible global function definition for ‘predict.lm’
trajplot: no visible global function definition for ‘identify’
Undefined global functions or variables:
  axis barplot box flush.console graphics.off hist identify lm par
  pbinom plot.ecdf points predict.lm read.csv rect sd write.csv
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "axis", "barplot", "box", "hist", "identify",
             "par", "points", "rect")
  importFrom("stats", "lm", "pbinom", "plot.ecdf", "predict.lm", "sd")
  importFrom("utils", "flush.console", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘demofile.txt’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
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.
Rd file 'createTree.Rd':
  \usage lines wider than 90 characters:
     createTree(data, treeType = "quad", dataType = "point", columns = if (dataType=="point") 1:2 else 1:4, ...)

These lines will be truncated in the PDF manual.
File ‘SearchTrees/libs/SearchTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
adx: no visible global function definition for ‘abline’
adx: no visible global function definition for ‘legend’
dx: no visible global function definition for ‘abline’
dx: no visible global function definition for ‘legend’
maxd: no visible global function definition for ‘abline’
maxd: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘rainbow’
pc: no visible global function definition for ‘abline’
pc: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘points’
pcu: no visible global function definition for ‘rainbow’
pcu: no visible global function definition for ‘abline’
pcu: no visible global function definition for ‘legend’
pcu: no visible global function definition for ‘points’
rmsd: no visible global function definition for ‘abline’
rmsd: no visible global function definition for ‘legend’
rsd: no visible global function definition for ‘abline’
rsd: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "points")
to your NAMESPACE file.
Undeclared package ‘shiny’ in Rd xrefs
Note: found 3 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘NADA’ ‘lubridate’ ‘survival’
  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:
  ‘examplePlots0404104041.pdf’ ‘myfit104035.pdf’ ‘myfit104037.pdf’
  ‘myfit104041.pdf’ ‘myfit1_survregCall.txt’ ‘myfit304041.pdf’
  ‘myfit3_survregCall.txt’
Package in Depends field not imported from: ‘JM’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for ‘rect’
SEchart: no visible global function definition for ‘par’
SEchart: no visible global function definition for ‘grid’
SEchart: no visible global function definition for ‘axis’
SEchart: no visible global function definition for ‘text’
SEchart: no visible global function definition for ‘lines’
SEchart: no visible global function definition for ‘heat.colors’
SEchart: no visible global function definition for ‘topo.colors’
SEchart: no visible global function definition for ‘cm.colors’
SEchart: no visible global function definition for ‘terrain.colors’
SEchart: no visible global function definition for ‘gray.colors’
SEchart: no visible global function definition for ‘rainbow’
SEchart: no visible global function definition for ‘points’
SEchart: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par points
  rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "points", "rect", "text")
to your NAMESPACE file.
Undeclared package ‘Hmisc’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
fdc2s: no visible global function definition for ‘lm’
fdc3s: no visible global function definition for ‘lm’
fds2s: no visible global function definition for ‘lm’
fds3s: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  17.6Mb
GNU make is a SystemRequirements.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Package suggested but not available for checking: ‘rsbml’
Malformed Description field: should contain one or more complete sentences.
.read.SeerStatTXT: no visible global function definition for
  ‘read.table’
.write.SeerStatTXT: 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.
prepare_Rd: SEER2RTestdata.Rd:77-78: Dropping empty section \source
Rd file 'SEER2R-package.Rd':
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

Rd file 'read.SeerStat.Rd':
  \usage lines wider than 90 characters:
     read.SeerStat(DICfileName, TXTfileName = NULL, UseVarLabelsInData = FALSE,ReadHeaderOnly=FALSE,...)
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

Rd file 'write.SeerStat.Rd':
  \usage lines wider than 90 characters:
     write.SeerStat(myData, DICfileName, TXTfileName = NULL, UseVarLabelsInTxtFile = TRUE, LabVarsNames = NULL,...)
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘testrun1.dic’ ‘testrun1.txt’ ‘testrun2.dic’ ‘testrun2.txt’
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
get.infectiousness: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘selac’
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
get_statistics_from_file: no visible global function definition for
  ‘read.csv’
glm_anova: no visible global function definition for ‘aov’
glm_anova: no visible global function definition for ‘glm’
glm_anova: no visible global function definition for ‘gaussian’
glm_anova: no visible global function definition for ‘anova’
glm_anova: no visible global function definition for ‘quasipoisson’
glm_anova: no visible global function definition for ‘sd’
glm_anova: no visible global function definition for ‘p.adjust’
ttest_cohens_d: no visible global function definition for ‘t.test’
ttest_cohens_d: no visible global function definition for ‘sd’
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘expression.csv’ ‘group.csv’
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta predict runif splinefun uniroot
Consider adding
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package in Depends field not imported from: ‘sem’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'semdiag.Rd':
  \usage lines wider than 90 characters:
     semdiag(x,  EQSmodel, varphi=0.1, EQSdata='data.txt', D='E', delete=integer(0), max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial= ... [TRUNCATED]

Rd file 'semdiag.robfit.Rd':
  \usage lines wider than 90 characters:
     semdiag.robfit(lisrel0, x, q, varphi, EQSmodel, EQSdata, max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial=1234)
     semdiag.robfit1(lisrel0, x, q, varphi, EQSmodel, EQSdata, max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial=1234)

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Found the following files/directories:
  ‘Rprof.out’
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.
ChiSquaredLRTest: no visible global function definition for ‘na.omit’
ChiSquaredLRTest: no visible global function definition for ‘cov’
ChiSquaredLRTest: no visible global function definition for ‘dmvnorm’
ChiSquaredLRTest: no visible global function definition for ‘pchisq’
NormalTheoryLRTest: no visible global function definition for ‘na.omit’
NormalTheoryLRTest: no visible global function definition for ‘cov’
NormalTheoryLRTest: no visible global function definition for ‘dmvnorm’
NormalTheoryLRTest: no visible global function definition for ‘sd’
NormalTheoryLRTest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
Undeclared package ‘SemNetCleaner’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.
Undeclared package ‘SemNetCleaner’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘XML’ ‘boot’ ‘sem’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’
  ‘resempls’ ‘residuals.sempls’
Namespaces in Imports field not imported from:
  ‘expm’ ‘matrixStats’ ‘matrixcalc’
  All declared Imports should be used.
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Undeclared package ‘stringr’ in Rd xrefs
.plot_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
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 ‘rtiff’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'addDefault.Rd':
  \examples lines wider than 100 characters:
     plot.calls = c("boxplot(count ~ spray, data = InsectSprays, col = 'lightgray')", "plot(1:3,1:3, col='blue', xlab='', ylab=''); points(1 ... [TRUNCATED]
     plt.extras=list(figure1= "rect(xleft=c(3,1), ytop=c(25,5),xright=c(4,2),  ybottom=c(20,0));title(main='A', cex=3)", figure2="polygon(x= ... [TRUNCATED]
     Splot = addDefault(Splot, data=c("This is default", "data2"), data.labels=c("label", "d2"), links=c("http://www.buffalo.edu, http://www ... [TRUNCATED]

Rd file 'sendplot.Rd':
  \examples lines wider than 100 characters:
     plot.calls = c("plot(x,y,col='green', pch=3)","plot(0,0, col='purple',pch=22,bg='purple')","plot(1:3,1:3, type='b',pch=21,bg='red',col= ... [TRUNCATED]
         "plot(0,0, col='purple',pch=22,bg='purple')","plot(1:3,1:3, type='b',pch=21,bg='red',col='red')","curve(x^3-3*x,-2,2, col='blue')")

These lines will be truncated in the PDF manual.
gconv: no visible global function definition for ‘convolve’
sens.analysis.aberrant.rank: no visible global function definition for
  ‘pnorm’
sens.analysis.mh: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for ‘quantile’
senmwCI : funcCI: no visible global function definition for ‘qnorm’
senmwCI : funcCI2: no visible global function definition for ‘qnorm’
separable1k: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for ‘gray’
sensitivitySGD: no visible global function definition for ‘tail’
sensitivitySGL: no visible global function definition for ‘tail’
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘sensitivityPStrat/libs/sensitivityPStrat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  nested.cpp:25:55: warning: 'bind1st<std::__1::divides<int>, int>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/sensitivity.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   3.3Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs    18.3Mb
    models   1.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.3Mb
Undeclared packages ‘MCS’, ‘stopwords’, ‘lexicon’ in Rd xrefs
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  16.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: ‘muscle’
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘seqMeta’
File ‘seqMeta/libs/seqMeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
GNU make is a SystemRequirements.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   1.1Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
plotenz : addmark: no visible global function definition for ‘par’
plotenz : addmark: no visible global function definition for ‘text’
plotenz : addmark: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘layout’
plotenz: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new layout par segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "segments", "text")
to your NAMESPACE file.
Rd file 'plotenz.Rd':
  \usage lines wider than 90 characters:
     plotenz(sequences, enznames, enzdata, side = TRUE, type = c("RFLP", "TRFLP"), Terminal = c("T5", "T3"))

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘total’
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘kinship2’ in Rd xrefs
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Undeclared package ‘Hmisc’ in Rd xrefs
Malformed Title field: should not end in a period.
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Found the following files/directories:
  ‘RSession.Rda’
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
setpath: no visible global function definition for ‘cov’
setpath: no visible global function definition for ‘median’
setpath: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for ‘runif’
random.number.test: no visible global function definition for ‘rnorm’
setRNG: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'loomR', 'SDMTools', 'MAST', 'monocle'

Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   7.7Mb
Package unavailable to check Rd xrefs: ‘loomR’
Unknown package ‘SDMTools’ in Rd xrefs
'library' or 'require' call to ‘graphics’ which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for ‘qnorm’
severity: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for ‘pnorm’
L_hNV: no visible global function definition for ‘pnorm’
L_trunc: no visible global function definition for ‘pnorm’
L_trunc_mufest: no visible global function definition for ‘pnorm’
dgp: no visible global function definition for ‘runif’
dgp: no visible global function definition for ‘rnorm’
eff.sfa: no visible global function definition for ‘predict’
fitted.sfa: no visible global function definition for ‘predict’
predict.sfa: no visible global function definition for ‘coef’
print.sfa: no visible global function definition for ‘coef’
residuals.sfa: no visible global function definition for ‘fitted’
sfa: no visible global function definition for ‘model.frame’
sfa: no visible global function definition for ‘model.response’
sfa.fit: no visible global function definition for ‘lm’
sfa.fit: no visible global function definition for ‘resid’
sfa.fit: no visible global function definition for ‘var’
sfa.fit: no visible global function definition for ‘optim’
summary.sfa: no visible global function definition for ‘logLik’
summary.sfa: no visible global function definition for ‘pchisq’
te.eff.sfa: no visible global function definition for ‘residuals’
te.eff.sfa: no visible global function definition for ‘pnorm’
u.sfa: no visible global function definition for ‘residuals’
u.sfa: no visible global function definition for ‘dnorm’
u.sfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    doc     11.9Mb
    libs    10.3Mb
    sqlite   1.5Mb
Undeclared packages ‘e1071’, ‘Hmisc’, ‘gmp’, ‘pastecs’, ‘polynom’, ‘robustbase’ in Rd xrefs
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Undeclared package ‘tripack’ in Rd xrefs
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
Malformed Description field: should contain one or more complete sentences.
.computePStar: no visible global function definition for ‘uniroot’
plotBoundary: no visible global function definition for
  ‘scale_y_continuous’
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.4Mb
amse: no visible global function definition for ‘na.omit’
arb: no visible global function definition for ‘na.omit’
rdatagen: no visible global function definition for ‘qnorm’
rdatagen: no visible global function definition for ‘pbinom’
rdatagen: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
File ‘sharpData/libs/sharpData.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘hydromad’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘brms’
  All declared Imports should be used.
popify: no visible global function definition for ‘runif’
tipify: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘VGAM’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’
  ‘latticeExtra’ ‘msm’ ‘plotly’ ‘shinyBS’ ‘shinydashboard’ ‘xtable’
  All declared Imports should be used.
Undeclared package ‘WrightMap’ in Rd xrefs
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinyjs)
  
  Attaching package: 'shinyjs'
  
  The following objects are masked from 'package:methods':
  
      removeClass, show
  
  > 
  > test_check("shinyjs")
  free(): double free detected in tcache 2
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘R6’ ‘getPass’ ‘svglite’ ‘websocket’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.3Mb
Namespaces in Imports field not imported from:
  ‘CARE1’ ‘LCMCR’ ‘coda’ ‘conting’ ‘dga’ ‘future’ ‘ggplot2’ ‘ipc’
  ‘promises’ ‘reshape’ ‘shinycssloaders’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’ ‘plotly’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    www   8.0Mb
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
Undeclared package ‘brms’ in Rd xrefs
shrink.estim: no visible global function definition for ‘cov’
shrink.estim: no visible global function definition for ‘cor’
shrink.estim: no visible global function definition for ‘cov2cor’
targetCor: no visible global function definition for ‘cor.test’
targetCor: no visible global function definition for ‘cor’
targetCor: no visible global function definition for ‘sd’
targetCor: no visible global function definition for ‘cov’
targetD: no visible binding for global variable ‘var’
targetF: no visible global function definition for ‘cov’
targetF: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘sd’
targetG: no visible global function definition for ‘cov’
targetGpos: no visible global function definition for ‘cor’
targetGpos: no visible global function definition for ‘sd’
targetGpos: no visible global function definition for ‘cov’
targetGstar: no visible global function definition for ‘cor’
targetGstar: no visible global function definition for ‘sd’
targetGstar: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Depends: includes the non-default packages:
  'hdrcde', 'coda', 'MASS', 'bayesm', 'mnormt', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘coda’ ‘hdrcde’ ‘mnormt’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'siarmcmcdirichletv4.Rd':
  \usage lines wider than 90 characters:
     siarmcmcdirichletv4(data, sources, corrections = 0, concdep = 0, iterations=200000, burnin=50000, howmany=10000, thinby=15, prior = rep ... [TRUNCATED]

Rd file 'siarplotdata.Rd':
  \usage lines wider than 90 characters:
     siarplotdata(siardata, siarversion = 0, grp=1:siardata$numgroups,panel=NULL,isos=c(0,0),leg=1)

Rd file 'siarproportionbygroupplot.Rd':
  \usage lines wider than 90 characters:
     siarproportionbygroupplot(siardata, siarversion=0,probs=c(95,75,50),xlabels=NULL, grp=NULL, type="boxes",clr=gray((9:1)/10),scl=1,xspc= ... [TRUNCATED]

Rd file 'siarproportionbysourceplot.Rd':
  \usage lines wider than 90 characters:
     siarproportionbysourceplot(siardata, siarversion=0,probs=c(95,75,50),xlabels=NULL, grp=NULL, type="boxes",clr=gray((9:1)/10),scl=1,xspc ... [TRUNCATED]

Rd file 'siarsolomcmcv4.Rd':
  \usage lines wider than 90 characters:
     siarsolomcmcv4(data, sources, corrections = 0, concdep = 0, iterations=200000, burnin=50000, howmany=10000, thinby=15, prior = rep(1, n ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘siar/libs/siar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘ade4’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  ‘princomp’
filter.mRMR.default: no visible global function definition for
  ‘discretize’
gaussian.default: no visible global function definition for ‘cov’
gaussian.default: no visible global function definition for
  ‘cov.shrink’
plot.verify.cv: no visible global function definition for ‘points’
plot.verify.ho: no visible global function definition for ‘points’
plot.verify.loo: no visible global function definition for ‘points’
predict.dpa1: no visible global function definition for ‘cor’
predict.filter.PCA: no visible global function definition for ‘predict’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘is.struct’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘var’
simulator.Simple1: no visible global function definition for ‘rnorm’
verify.ho.default: no visible global function definition for ‘predict’
verify.loo.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct points predict princomp rnorm
  var
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
Rd file 'plot.verify.ho.Rd':
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[129:256,],Yval=key[129:256],nbreV ... [TRUNCATED]

Rd file 'sideChannelAttack-package.Rd':
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[129:256,],Yval=key[129:256],nbreV ... [TRUNCATED]

Rd file 'verify.ho.Rd':
  \usage lines wider than 90 characters:
     verify.ho(model, filter, Xlearn, Ylearn, Xval, Yval, nbreVarX, param.model=list(), param.fs=list(), ...)
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[128:256,],Yval=key[128:256],nbreV ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘3_FindHaplo_Example2_modified.txt’
  ‘4_Example3_HapPerPop_Weighted.txt’
  ‘4_Example3_IndelDistanceMatrixMullerMod.txt’
  ‘4_FindHaplo_Example2_modified.txt’ ‘FindHaplo.txt’
  ‘Haplotypes_DefaultNames.txt’ ‘Haplotypes_sequentialNames.txt’
  ‘Interaction.txt’ ‘Modules_summary.txt’
  ‘NINA.ThresholdEstimation.txt’ ‘NINA_Network.pdf’ ‘Network.pdf’
  ‘PercThr Estimation.pdf’ ‘PercThresholdEstimation.txt’
  ‘PercolatedNetwork.pdf’ ‘PopulationDistances.r.txt’ ‘Weighted.txt’
  ‘ex1.fas’ ‘ex2.2.fas’ ‘ex2.fas’ ‘ex2_unique.fas’ ‘ex3.fas’
  ‘simulated_sequences_rep1.fas’ ‘simulated_sequences_rep2.fas’
  ‘simulated_sequences_tips_rep1.fas’
  ‘simulated_sequences_tips_rep2.fas’
dSepAdji: no visible global function definition for ‘as’
dag2cpdagAdj: no visible global function definition for ‘as’
randomDAG: no visible global function definition for ‘rbinom’
structIntervDist: no visible global function definition for ‘as’
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
.cluster: no visible global function definition for ‘kmeans’
.plot.sigclust: no visible global function definition for ‘par’
.plot.sigclust: no visible global function definition for ‘density’
.plot.sigclust: no visible global function definition for ‘runif’
.plot.sigclust: no visible global function definition for ‘dnorm’
.plot.sigclust: no visible global function definition for ‘lines’
.plot.sigclust: no visible global function definition for ‘points’
.plot.sigclust: no visible global function definition for ‘title’
.plot.sigclust: no visible global function definition for ‘text’
.plot.sigclust: no visible global function definition for ‘qnorm’
.plot.sigclust: no visible global function definition for ‘abline’
.plot.sigclust: no visible global function definition for ‘quantile’
.plot.sigclust: no visible global function definition for ‘legend’
.simnull: no visible global function definition for ‘rnorm’
.vareigen: no visible global function definition for ‘mad’
.vareigen: no visible global function definition for ‘cov’
sigclust: no visible global function definition for ‘sd’
sigclust: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Sight.Est: no visible global function definition for ‘glm’
Sight.Est: no visible global function definition for ‘binomial’
Sight.Est: no visible global function definition for ‘coef’
Sight.Est: no visible global function definition for ‘terms’
Sight.Est: no visible binding for global variable ‘binomial’
covtheta: no visible global function definition for ‘cov’
print.sightest: no visible global function definition for ‘qnorm’
summary.sightest: no visible global function definition for ‘qnorm’
vardiff: no visible global function definition for ‘vcov’
vardiff: no visible global function definition for ‘coef’
vardiff: no visible global function definition for ‘terms’
varlog.lam: no visible global function definition for ‘vcov’
varlog.lam: no visible global function definition for ‘coef’
varlog.lam: no visible global function definition for ‘terms’
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'
Packages unavailable to check Rd xrefs: ‘TFBSTools’, ‘motifmatchr’, ‘chromVAR’
Undeclared package ‘matlab’ in Rd xrefs
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
signmedian.test: no visible global function definition for ‘median’
signmedian.test: no visible global function definition for ‘binom.test’
signmedian.test: no visible global function definition for ‘pbinom’
signmedian.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Found the following files/directories:
  ‘ExportFigtree1.tre’
'library' or 'require' calls in package code:
  ‘gdata’ ‘splines’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for ‘lines’
plot.SII: no visible global function definition for ‘abline’
plot.SII: no visible global function definition for ‘legend’
sii : approx.l: no visible global function definition for ‘approx’
sii.excel: no visible global function definition for ‘predict’
sii.excel : approx.l: no visible global function definition for
  ‘approx’
Undefined global functions or variables:
  abline approx legend lines predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
Undeclared packages ‘ade4’, ‘labdsv’, ‘sp’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
Undeclared packages ‘GenOrd’, ‘PoisNor’ in Rd xrefs
Undeclared packages ‘sde’, ‘fptdApprox’, ‘DiffusionRgqd’, ‘ks’, ‘yuima’ in Rd xrefs
getFormula: no visible global function definition for ‘as.formula’
internalSimXyplot : f: no visible global function definition for
  ‘median’
runSimulation: no visible global function definition for ‘runif’
setup: no visible global function definition for ‘runif’
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable ‘cnam’
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable ‘cnam’
initialize,DCARContControl: no visible binding for global variable
  ‘rnorm’
initialize,DataControl: no visible binding for global variable ‘rnorm’
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
GNU make is a SystemRequirements.
File ‘simFrame/libs/simFrame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Namespaces in Imports field not imported from:
  ‘future’ ‘magrittr’ ‘purrr’ ‘rlang’ ‘utils’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  12.8Mb
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
cumallcausehr: no visible global function definition for ‘integrate’
plotbe: no visible global function definition for ‘lines’
plotbe: no visible global function definition for ‘legend’
plotcph: no visible global function definition for ‘confint’
plotcph: no visible global function definition for ‘abline’
plotcph: no visible global function definition for ‘axis’
plotcph: no visible global function definition for ‘polygon’
plotcph: no visible global function definition for ‘lines’
simCR: no visible global function definition for ‘rnorm’
simEBMT: no visible global function definition for ‘model.matrix’
simexit: no visible global function definition for ‘runif’
simexitinner: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix polygon rnorm
  runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
Undeclared packages ‘BinNonNor’, ‘PoisNor’, ‘PoisBinOrdNor’, ‘PoisBinOrdNonNor’ in Rd xrefs
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.txt’
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘readr’ ‘rmarkdown’ ‘shinycssloaders’
  All declared Imports should be used.
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Undeclared package ‘sampling’ in Rd xrefs
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Package in Depends field not imported from: ‘mclust’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for ‘Mclust’
Simpsons: no visible global function definition for ‘lm’
Simpsons: no visible global function definition for ‘abline’
Simpsons: no visible global function definition for ‘par’
Simpsons: no visible global function definition for ‘legend’
Simpsons: no visible global function definition for ‘txtProgressBar’
Simpsons: no visible global function definition for ‘setTxtProgressBar’
Simpsons: no visible global function definition for ‘quantile’
plot.Simpson: no visible global function definition for ‘lm’
plot.Simpson: no visible global function definition for ‘abline’
plot.Simpson: no visible global function definition for ‘par’
plot.Simpson: no visible global function definition for ‘legend’
Undefined global functions or variables:
  Mclust abline legend lm par quantile setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
File ‘SimReg/libs/SimReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following files/directories:
  ‘crop_device.pdf’
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘abind’ ‘svUnit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for ‘abind’
simSummary_unitTests: no visible global function definition for
  ‘clearLog’
simSummary_unitTests: no visible global function definition for
  ‘runTest’
simSummary_unitTests: no visible global function definition for
  ‘svSuite’
simSummary_unitTests: no visible global function definition for ‘Log’
simSummary_unitTests: no visible global function definition for ‘stats’
simSummary_unitTests: no visible global function definition for
  ‘metadata’
simSummary_unitTests: no visible global function definition for
  ‘errorLog’
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  23.6Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
plotBGpvalues: no visible global function definition for ‘par’
plotBGpvalues: no visible global function definition for ‘title’
plotBGpvalues: no visible global function definition for ‘axis’
plotBGpvalues: no visible binding for global variable ‘abline’
plotBGpvalues: no visible global function definition for ‘box’
plotCGpvalues: no visible global function definition for ‘par’
plotCGpvalues: no visible global function definition for ‘title’
plotCGpvalues: no visible global function definition for ‘axis’
plotCGpvalues: no visible binding for global variable ‘abline’
plotCGpvalues: no visible global function definition for ‘box’
plotDAGpvalues: no visible global function definition for ‘par’
plotDAGpvalues: no visible global function definition for ‘title’
plotDAGpvalues: no visible global function definition for ‘axis’
plotDAGpvalues: no visible binding for global variable ‘abline’
plotDAGpvalues: no visible global function definition for ‘box’
plotUGpvalues: no visible global function definition for ‘par’
plotUGpvalues: no visible global function definition for ‘title’
plotUGpvalues: no visible global function definition for ‘axis’
plotUGpvalues: no visible binding for global variable ‘abline’
plotUGpvalues: no visible global function definition for ‘box’
simpvalueVec: no visible binding for global variable ‘pnorm’
sinBG: no visible global function definition for ‘cov2cor’
sinCG : sinAMP: no visible global function definition for ‘cov2cor’
sinCG : sinLWF: no visible global function definition for ‘cov2cor’
sinDAG: no visible global function definition for ‘cov2cor’
sinUG: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  abline axis box cov2cor par pnorm title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "title")
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘pagedown’ ‘rosr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
Running examples in ‘SIRItoGTFS-Ex.R’ failed
The error most likely occurred in:

> ### Name: STG
> ### Title: Wrapper function for the SIRItoGTFS library
> ### Aliases: STG
> ### Keywords: package spatial
> 
> ### ** Examples
> 
> require(SIRItoGTFS)
> require(data.table)
Loading required package: data.table
> # use the sample SIRI data included with the package
> data("sirisample")
> SIRIsample$Longitude = as.numeric(SIRIsample$Longitude)
> SIRIsample$Latitude = as.numeric(SIRIsample$Latitude)
> # load your own GTFS data with `readGTFS()`
> # or use the subset of GTFS data conformable to the SIRI sample, also included in the package
> data("GTFSstops")
> data("GTFSstop_times")
> data("GTFScalendar")
> data("GTFStrips")
> data("GTFSagency")
> data("GTFSroutes")
> busesDF = STG(SIRIsample,
+              GTFSstops. = GTFSstops,
+              GTFSagency. = GTFSagency,
+              GTFScalendar. = GTFScalendar,
+              GTFSroutes. = GTFSroutes,
+              GTFSstop_times. = GTFSstop_times,
+              GTFStrips. = GTFStrips,
+              linerefs = unique(SIRIsample$LineRef[1]))
[1] "Strating"
Error: $ operator is invalid for atomic vectors
Execution halted
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   8.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Running examples in ‘sistec-Ex.R’ failed
The error most likely occurred in:

> ### Name: compare_sistec
> ### Title: Comparison between Sistec and a student registration dataset
> ### Aliases: compare_sistec
> 
> ### ** Examples
> 
> # these datasets are not real. It is just for test purpose.
> qacademico <- read_qacademico(system.file("extdata/examples/qacademico",
+                                           package = "sistec"))
> sistec <- read_sistec(system.file("extdata/examples/sistec",
+                                   package = "sistec"))
>                                   
> compare_sistec(sistec, qacademico)                                   
Error: Input must be a vector, not a `data.frame/sistec_data_frame` object.
Backtrace:
     █
  1. ├─sistec::compare_sistec(sistec, qacademico)
  2. ├─sistec:::compare_sistec.qacademico_data_frame(sistec, qacademico)
  3. │ └─sistec:::compare_sistec_qacademico(sistec, student_registration)
  4. │   └─sistec:::filter_cpf_sistec(sistec)
  5. │     ├─dplyr::filter(x, !!sym("NU_CPF") == "")
  6. │     └─dplyr:::filter.data.frame(x, !!sym("NU_CPF") == "")
  7. │       ├─dplyr::dplyr_row_slice(.data, loc, preserve = .preserve)
  8. │       └─dplyr:::dplyr_row_slice.data.frame(.data, loc, preserve = .preserve)
  9. │         ├─dplyr::dplyr_reconstruct(vec_slice(data, i), data)
 10. │         │ └─dplyr:::dplyr_new_data_frame(data)
 11. │         │   ├─row.names %||% .row_names_info(x, type = 0L)
 12. │         │   └─base::.row_names_info(x, type = 0L)
 13. │         └─vctrs::vec_slice(data, i)
 14. └─vctrs::
Execution halted
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘helicopter.pdf’
Undeclared package ‘tidyselect’ in Rd xrefs
Undeclared packages ‘stringr’, ‘pillar’ in Rd xrefs
Undeclared packages ‘tidyselect’, ‘RColorBrewer’, ‘modelr’, ‘snakecase’ in Rd xrefs
Undeclared packages ‘tidyselect’, ‘tibble’ in Rd xrefs
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.
cvskda: no visible global function definition for ‘detectCores’
cvskda: no visible global function definition for ‘makeCluster’
cvskda: no visible global function definition for ‘clusterApplyLB’
cvskda: no visible global function definition for ‘mclapply’
cvskda: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘het.test’ ‘lmtest’ ‘lubridate’ ‘magrittr’ ‘tibble’ ‘tseries’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
dskt: no visible global function definition for ‘dt’
pskt: no visible global function definition for ‘pt’
qskt: no visible global function definition for ‘qt’
rskt: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘vctrs’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.9Mb
GNU make is a SystemRequirements.
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
slcestimates: no visible global function definition for ‘par’
slcestimates: no visible global function definition for ‘abline’
slcestimates: no visible global function definition for ‘lines’
slcestimates: no visible global function definition for ‘axis’
slcestimates: no visible global function definition for ‘points’
slcestimates: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis lines par points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "points",
             "title")
to your NAMESPACE file.
Undeclared package ‘RcmdrPlugin.SLC’ in Rd xrefs
File ‘sld/libs/sld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘shiny’ in Rd xrefs
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Note: found 2 marked Latin-1 strings
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
GNU make is a SystemRequirements.
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘Boruta’ ‘DMwR’ ‘MVN’ ‘NoiseFiltersR’ ‘VIM’ ‘adaptiveGPCA’
  ‘class’ ‘clusterSim’ ‘denoiseR’ ‘discretization’ ‘imbalance’ ‘lle’
  ‘missForest’ ‘missMDA’ ‘outliers’ ‘unbalanced’
  All declared Imports should be used.
Undeclared packages ‘InformationValue’, ‘ggthemes’, ‘DataExplorer’ in Rd xrefs
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 1122 marked UTF-8 strings
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   1.3Mb
File ‘smco/R/smco.R’:
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

smco: no visible global function definition for ‘runif’
smco: no visible global function definition for ‘rnorm’
smco: no visible global function definition for ‘qnorm’
smco: no visible global function definition for ‘pnorm’
smco: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "optim", "pnorm", "qnorm", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘etc’
File ‘SMC/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

See section ‘Good practice’ in '?.onAttach'.

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for ‘runif’
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for ‘runif’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘rnorm’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘runif’
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘runif’
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
File ‘SMC/libs/SMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
em: no visible global function definition for ‘coxph’
em: no visible global function definition for ‘optim’
plotpredictsmcure: no visible global function definition for ‘matplot’
plotpredictsmcure: no visible global function definition for ‘lines’
smcure: no visible binding for global variable ‘na.omit’
smcure: no visible global function definition for ‘model.frame’
smcure: no visible global function definition for ‘model.extract’
smcure: no visible global function definition for ‘model.matrix’
smcure: no visible global function definition for ‘coxph’
smcure: no visible global function definition for ‘survreg’
smcure: no visible binding for global variable ‘var’
smcure: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
Grad.sph: no visible global function definition for ‘dist’
IMDS: no visible global function definition for ‘cmdscale’
IMDS: no visible global function definition for ‘as.dist’
IMDS: no visible global function definition for ‘runif’
IMDS: no visible global function definition for ‘optim’
idistSph: no visible global function definition for ‘dist’
obj.sph: no visible global function definition for ‘dist’
plot.imds: no visible binding for global variable ‘lines’
plot.imds: no visible global function definition for ‘text’
plot.imds: no visible global function definition for ‘rect’
Undefined global functions or variables:
  as.dist cmdscale dist lines optim rect runif text
Consider adding
  importFrom("graphics", "lines", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
File ‘smds/libs/smds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines points
Consider adding
  importFrom("graphics", "lines", "points")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘rPython’
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Fourier2d: no visible global function definition for ‘fft’
kernel2dsmooth: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  11.6Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Found the following files/directories:
  ‘my_new_social_media_plot.png’
Malformed Description field: should contain one or more complete sentences.
dNMR: no visible global function definition for ‘pnorm’
dNMR: no visible global function definition for ‘dnorm’
pNMR: no visible global function definition for ‘pnorm’
pNMR: no visible global function definition for ‘dnorm’
rMR: no visible global function definition for ‘rnorm’
rMR: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SMVar.paired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.paired: no visible global function definition for ‘var’
SMVar.paired: no visible global function definition for ‘pt’
SMVar.paired: no visible global function definition for ‘p.adjust’
SMVar.paired: no visible global function definition for ‘write.table’
SMVar.unpaired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.unpaired: no visible global function definition for ‘var’
SMVar.unpaired: no visible global function definition for ‘pt’
SMVar.unpaired: no visible global function definition for ‘p.adjust’
SMVar.unpaired: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'SMVar.paired.Rd':
  \usage lines wider than 90 characters:
     SMVar.paired(geneNumbers, logratio, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

Rd file 'SMVar.unpaired.Rd':
  \usage lines wider than 90 characters:
     SMVar.unpaired(geneNumbers, listcond, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
File ‘snipEM/libs/snipEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘snnR/libs/snnR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KS.test: no visible global function definition for ‘quantile’
KS.test : Fgaus: no visible global function definition for ‘pnorm’
KS.test: no visible global function definition for ‘setNames’
cs.test: no visible global function definition for ‘pbinom’
cs.test: no visible global function definition for ‘pnorm’
cs.test: no visible global function definition for ‘setNames’
kde: no visible global function definition for ‘quantile’
kde : Fgaus: no visible global function definition for ‘pnorm’
kde: no visible global function definition for ‘par’
kre: no visible global function definition for ‘quantile’
kre: no visible global function definition for ‘lines’
ns.test: no visible global function definition for ‘complete.cases’
ns.test: no visible global function definition for ‘qnorm’
ns.test: no visible global function definition for ‘pnorm’
ns.test: no visible global function definition for ‘pchisq’
ns.test: no visible global function definition for ‘setNames’
ns.test: no visible global function definition for ‘qt’
quant.test: no visible global function definition for ‘complete.cases’
quant.test: no visible global function definition for ‘pbinom’
quant.test: no visible global function definition for ‘pnorm’
quant.test: no visible global function definition for ‘setNames’
quant.test: no visible global function definition for ‘quantile’
quant.test: no visible global function definition for ‘phyper’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘setNames’
runs.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      3.0Mb
Found the following files/directories:
  ‘geneSet.set’ ‘snplistdb.sqlite’
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘combinat’
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for ‘chisq.test’
maxsel: no visible global function definition for ‘complete.cases’
maxsel.asymp.test: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
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.
Packages in Depends field not imported from:
  ‘colorspace’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for ‘is’
write.sbams: no visible global function definition for ‘as’
write.sbams: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘.R_Test’
Namespaces in Imports field not imported from:
  ‘devtools’ ‘raster’ ‘rlang’ ‘sp’ ‘usethis’
  All declared Imports should be used.
Note: found 833 marked UTF-8 strings
Found the following significant warnings:
  pcnt_loop.cpp:45:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SocEpi.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
calculate.areas: no visible global function definition for ‘runif’
calculate.gradedareas: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Warning: no function found corresponding to methods exports from ‘SoDA’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the 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.
Missing or unexported object: ‘base::WHAT’
Call with DUP:
   .Fortran("GEODISTV", as.double(lat1), as.double(lon1), as.double(lat2), 
       as.double(lon2), dist = double(nok), as.integer(nok), DUP = DUP, 
       PACKAGE = "SoDA")
DUP is no longer supported and will be ignored.
File ‘SoDA/libs/SoDA.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
‘configure’: /bin/bash is not portable
Malformed Description field: should contain one or more complete sentences.
Ssimpute.als: no visible global function definition for ‘rnorm’
Ssvd.als: no visible global function definition for ‘rnorm’
cs.default: no visible binding for global variable ‘weighted.mean’
simpute.als: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
File ‘softImpute/libs/softImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
compileDatabase: no visible global function definition for ‘use_data’
Undefined global functions or variables:
  use_data
Note: found 145 marked UTF-8 strings
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AGread’ ‘caret’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Running examples in ‘solitude-Ex.R’ failed
The error most likely occurred in:

> ### Name: isolationForest
> ### Title: Fit an Isolation Forest
> ### Aliases: isolationForest
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data("attrition", package = "rsample")
Warning in data("attrition", package = "rsample") :
  data set ‘attrition’ not found
> set.seed(1)
> index = sample(ceiling(nrow(attrition) * 0.2))
Error in nrow(attrition) : object 'attrition' not found
Calls: sample -> nrow
Execution halted
Malformed Description field: should contain one or more complete sentences.
Undeclared package ‘XML’ in Rd xrefs
soma: 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.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for ‘pbinom’
kfweOrd: no visible global function definition for ‘qnbinom’
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘someMTP’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the 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.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   6.7Mb
'library' or 'require' call to ‘hexbin’ which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for ‘quantile’
hexbinpie: no visible global function definition for ‘polygon’
hexbinpie: no visible global function definition for ‘text’
makehexbinplot: no visible global function definition for ‘rainbow’
makehexbinplot: no visible global function definition for ‘col2rgb’
makehexbinplot: no visible global function definition for ‘edit’
makehexbinplot: no visible global function definition for ‘dev.new’
makehexbinplot: no visible global function definition for ‘plot.new’
makehexbinplot: no visible global function definition for ‘plot.window’
makehexbinplot: no visible global function definition for ‘box’
makehexbinplot: no visible global function definition for ‘axis’
makehexbinplot: no visible global function definition for ‘legend’
som.plot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
Malformed Title field: should not end in a period.
License components which are templates and need '+ file LICENSE':
  MIT
Non-standard files/directories found at top level:
  ‘README.markdown’ ‘build_package.sh’ ‘upload.sh’
Found the following files/directories:
  ‘asc.gif’ ‘bg.gif’ ‘desc.gif’ ‘jquery-1.4.2.js’
  ‘jquery.tablesorter.js’ ‘sample.html’ ‘style.css’
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Undeclared package ‘units’ in Rd xrefs
Found the following files/directories:
  ‘splineSearch.xls’
Note: found 1349 marked UTF-8 strings
Package suggested but not available for checking: ‘SciencesPo’
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Package suggested but not available for checking: ‘DropletUtils’
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   9.8Mb
    doc    1.1Mb
License components which are templates and need '+ file LICENSE':
  MIT
Package suggested but not available for checking: ‘r2cytoscape’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
exploreSP23Design: no visible global function definition for
  ‘txtProgressBar’
exploreSP23Design: no visible global function definition for
  ‘setTxtProgressBar’
generateClinicalTrialData : <anonymous>: no visible global function
  definition for ‘runif’
generateClinicalTrialData: no visible global function definition for
  ‘rbinom’
generateClinicalTrialData: no visible global function definition for
  ‘rexp’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘pnorm’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.b: no visible global function definition for ‘qnorm’
mHP.b: no visible global function definition for ‘uniroot’
mHP.c : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.c: no visible global function definition for ‘uniroot’
mHP.c: no visible global function definition for ‘qnorm’
performInterimLook: no visible global function definition for ‘optim’
performInterimLook: no visible global function definition for
  ‘constrOptim’
performInterimLook: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  Miwa constrOptim optim pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'space.joint.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

Rd file 'space.neighbor.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

These lines will be truncated in the PDF manual.
File ‘space/libs/space.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘colorSpec’ in Rd xrefs
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Undeclared package ‘rebus.base’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Undeclared package ‘sp’ in Rd xrefs
Undeclared package ‘moments’ in Rd xrefs
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  35.1Mb
Undeclared package ‘magic’ in Rd xrefs
hausman: no visible global function definition for ‘pchisq’
span.formula: no visible global function definition for ‘model.frame’
span.formula: no visible global function definition for ‘model.matrix’
span.formula: no visible global function definition for
  ‘model.response’
spbe: no visible global function definition for ‘cor’
spbe: no visible global function definition for ‘pt’
spfe: no visible global function definition for ‘cor’
spfe: no visible global function definition for ‘pt’
sprandom: no visible global function definition for ‘cor’
sprandom: no visible global function definition for ‘pt’
summary.span: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  ‘URLencode’
SPARQL: no visible binding for global variable ‘getURL’
SPARQL: no visible global function definition for ‘URLencode’
SPARQL: no visible binding for global variable ‘xmlParse’
SPARQL: no visible global function definition for ‘getNodeSet’
SPARQL: no visible global function definition for ‘xpathApply’
SPARQL: no visible binding for global variable ‘postForm’
get_attr: no visible global function definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xpathSApply’
get_value: no visible binding for global variable ‘xmlValue’
get_value: no visible global function definition for ‘xpathApply’
get_value: no visible binding for global variable ‘xmlGetAttr’
readCSVstring: no visible global function definition for ‘read.csv’
readTSVstring: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
f.I2.cont: no visible global function definition for ‘combn’
f.I2.dich: no visible global function definition for ‘combn’
f.pstar.cont: no visible global function definition for ‘combn’
f.pstar.dich: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Undeclared packages ‘splancs’, ‘spatstat.data’ in Rd xrefs
Package suggested but not available for checking: ‘RCy3’
Undeclared package ‘sparsebn’ in Rd xrefs
Package unavailable to check Rd xrefs: ‘RCy3’
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Found the following sources/headers with CR or CRLF line endings:
  inst/include/MatrixAddons.h
  inst/include/sparseLTSEigen.h
Some Unix compilers require LF line endings.
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparsereg/libs/sparsereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
File ‘sparseSEM/libs/sparseSEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseTSCGM/libs/SparseTSCGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
File ‘spate/libs/spate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
Checking should be performed on sources prepared by ‘R CMD build’.
Found the following sources/headers not terminated with a newline:
  src/calc.c
Some compilers warn on such files.
File ‘spatialfil/libs/spatialfil.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   1.2Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 25 marked Latin-1 strings
  Note: found 335 marked UTF-8 strings
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  31.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following sources/headers not terminated with a newline:
  inst/include/STCXEM.h
  inst/include/STCXEMnonspatial.h
  inst/include/STCXEMspatial.h
  inst/include/STCdata.h
  inst/include/STCmodel.h
  inst/include/STCparam.h
  inst/include/STCtune.h
Some compilers warn on such files.
File ‘SpaTimeClus/libs/SpaTimeClus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    6.1Mb
    help   5.3Mb
    libs   2.2Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs  11.7Mb
GenerateCliquesCovariance: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data     2.2Mb
    shapes   3.2Mb
Note: found 56 marked UTF-8 strings
Malformed Title field: should not end in a period.
bartlett: no visible global function definition for ‘pchisq’
local.rbfdot: no visible binding for global variable ‘sd’
local.rbfdot: no visible global function definition for ‘dist’
local.rbfdot : <anonymous>: no visible global function definition for
  ‘median’
speccalt: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for ‘qnorm’
ChaoLee1992: no visible global function definition for ‘qnorm’
Pmix: no visible global function definition for ‘dpois’
PmixSCon: no visible global function definition for ‘dbeta’
bootPCG: no visible global function definition for ‘flush.console’
bootPCG: no visible global function definition for ‘quantile’
bootPnpmle: no visible global function definition for ‘flush.console’
bootPnpmle: no visible global function definition for ‘quantile’
bootUnpmle: no visible global function definition for ‘flush.console’
bootUnpmle: no visible global function definition for ‘quantile’
chao1984: no visible global function definition for ‘qnorm’
jackknife: no visible global function definition for ‘dbinom’
jackknife: no visible global function definition for ‘qnorm’
pcg: no visible global function definition for ‘flush.console’
unpmle: no visible global function definition for ‘flush.console’
untrunPmix: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.9Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘usethis’
  All declared Imports should be used.
Note: found 5 marked Latin-1 strings
Namespace in Imports field not imported from: ‘pdftools’
  All declared Imports should be used.
Undeclared package ‘biglm’ in Rd xrefs
'library' or 'require' call to ‘leaps’ which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for ‘glm’
modSearch: no visible binding for global variable ‘binomial’
modSearch: no visible global function definition for ‘na.omit’
modSearch: no visible global function definition for ‘as.formula’
speff: no visible binding for global variable ‘na.pass’
speff: no visible global function definition for ‘model.matrix’
speff: no visible global function definition for ‘terms’
speff: no visible global function definition for ‘model.response’
speff: no visible global function definition for ‘as.formula’
speff: no visible global function definition for ‘predict’
speff: no visible global function definition for ‘na.omit’
speff: no visible global function definition for ‘glm’
speff: no visible binding for global variable ‘na.omit’
speffSurv: no visible global function definition for ‘model.matrix’
speffSurv: no visible global function definition for ‘terms’
speffSurv: no visible global function definition for ‘model.response’
speffSurv: no visible global function definition for ‘as.formula’
speffSurv: no visible global function definition for ‘uniroot’
summary.speff: no visible global function definition for ‘qnorm’
summary.speff: no visible global function definition for ‘pnorm’
summary.speffSurv: no visible global function definition for ‘qnorm’
summary.speffSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  ‘.neig’
Malformed Description field: should contain one or more complete sentences.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spe/libs/spe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘spGARCH’
Package in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for ‘runif’
rgl.sphMW: no visible global function definition for ‘plot3d’
rgl.sphcirc: no visible global function definition for ‘rotate3d’
rgl.sphcirc: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘open3d’
rgl.sphgrid: no visible global function definition for ‘plot3d’
rgl.sphgrid: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘text3d’
rgl.sphpoints: no visible global function definition for ‘points3d’
rgl.sphsun: no visible global function definition for ‘plot3d’
rgl.sphtext: no visible global function definition for ‘text3d’
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
Packages in Depends field not imported from:
  ‘lars’ ‘parallel’ ‘randomForest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GGally’ ‘tibble’ ‘webshot’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘spinifex_vignette.Rmd’ using rmarkdown
Using width 2.38
New names:
* X1 -> X1...1
* X2 -> X2...2
* X3 -> X3...3
* X1 -> X1...4
* X2 -> X2...5
* ...
Quitting from lines 129-139 (spinifex_vignette.Rmd) 
Error: processing vignette 'spinifex_vignette.Rmd' failed with diagnostics:
Can't subset columns that don't exist.
✖ Column `X3` doesn't exist.
--- failed re-building ‘spinifex_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘spinifex_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘quadprog’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for ‘density’
SPIn: no visible global function definition for ‘quantile’
SPIn: no visible global function definition for ‘solve.QP’
bootSPIn: no visible global function definition for ‘runif’
plot.SPIn: no visible global function definition for ‘hist’
plot.SPIn: no visible global function definition for ‘lines’
plot.SPIn: no visible global function definition for ‘text’
plot.SPIn: no visible global function definition for ‘quantile’
plot.SPIn: no visible global function definition for ‘legend’
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
spi: no visible global function definition for ‘read.table’
spi: no visible global function definition for ‘ecdf’
spi: no visible global function definition for ‘qnorm’
spi: no visible global function definition for ‘colorRampPalette’
spi: no visible global function definition for ‘filled.contour’
spi: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
prepare_Rd: spi.Rd:117-119: Dropping empty section \note
prepare_Rd: spi.Rd:123-125: Dropping empty section \seealso
Rd file 'spi.Rd':
  \examples lines wider than 100 characters:
     spi(7,"spi.txt",1963,2010,"Standardized Precipitation Index - Rio Grande do Norte State",1,"years","months")

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘spi.txt’
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
Undeclared packages ‘reshape2’, ‘sampling’, ‘dplyr’ in Rd xrefs
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Malformed Description field: should contain one or more complete sentences.
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Ell.Theta: no visible global function definition for ‘ell.theta’
confid.int.theta: no visible global function definition for ‘qchisq’
confid.int.theta : sim.c: no visible global function definition for
  ‘runif’
confid.int.theta: no visible global function definition for ‘quantile’
dd.est: no visible global function definition for ‘ecdf’
ks.sporm : Simul: no visible global function definition for ‘runif’
ks.stat: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘ecdf’
test.theta: no visible global function definition for ‘ecdf’
test.theta : sim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ecdf ell.theta qchisq quantile runif
Consider adding
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
Note: found 7587 marked UTF-8 strings
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.
fetch_NBAPlayerStatistics: 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.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs  10.4Mb
Undeclared package ‘RcppArmadillo’ in Rd xrefs
Note: found 17 marked UTF-8 strings
Found the following sources/headers with CR or CRLF line endings:
  inst/include/sppmix.h
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Rd file 'SlrArd.Rd':
  \usage lines wider than 90 characters:
     SlrArd(T, X, bias = TRUE, method = c("VB", "VBMacKay", "PX-VB"), control = list(), check.lb=TRUE, a0 = 0, b0 = 0, mu0 = 0, xi0 = 1)

These lines will be truncated in the PDF manual.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘abline’
print.SPRT: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline head par
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("utils", "head")
to your NAMESPACE file.
installed size is 58.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  56.4Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
sGda : <anonymous>: no visible global function definition for ‘cov’
sortgene: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for ‘read.csv’
cacheQuery: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable ‘median’
SQN: no visible global function definition for ‘quantile’
SQN.demo.data: no visible global function definition for ‘rnorm’
mix.qn: no visible global function definition for ‘ecdf’
mix.qn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Undeclared packages ‘RColorBrewer’, ‘colorspace’ in Rd xrefs
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
File ‘sROC/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

See section ‘Good practice’ in '?.onAttach'.

AUC : TrapezInt: no visible global function definition for ‘approx’
AUC : SimpsonInt: no visible global function definition for ‘approx’
CI.CDF: no visible global function definition for ‘qnorm’
bw.CDF: no visible global function definition for ‘sd’
bw.CDF: no visible global function definition for ‘IQR’
bw.CDF.pi: no visible global function definition for ‘sd’
bw.CDF.pi: no visible global function definition for ‘bw.nrd0’
bw.CDF.pi: no visible global function definition for ‘bw.nrd’
bw.CDF.pi: no visible global function definition for ‘bw.ucv’
bw.CDF.pi: no visible global function definition for ‘bw.bcv’
bw.CDF.pi: no visible global function definition for ‘bw.SJ’
bw.CDF.pi: no visible global function definition for ‘IQR’
plot.CDF: no visible global function definition for ‘plot.default’
plot.CDF: no visible global function definition for ‘lines’
plot.CDF: no visible global function definition for ‘polygon’
plot.ROC: no visible global function definition for ‘plot.default’
plot.ROC: no visible global function definition for ‘abline’
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'CI.CDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kCDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kROC.Rd':
  \usage lines wider than 90 characters:
     kROC(x, y, bw.x="pi_ucv", bw.y="pi_ucv", adjust=1, kernel=c("normal", "epanechnikov"), xgrid, 

These lines will be truncated in the PDF manual.
File ‘sROC/libs/sROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Undeclared package ‘plyr’ in Rd xrefs
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
ssd : correction_method_D: no visible global function definition for
  ‘rnorm’
ssd : generate_bootstrap: no visible global function definition for
  ‘rmultinom’
ssd : bootstrap_method: no visible global function definition for
  ‘median’
ssd : bootstrap_method: no visible global function definition for
  ‘quantile’
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for ‘rmultinom’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘median’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘quantile’
ssd: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for ‘pnorm’
L_hNV_rho: no visible global function definition for ‘pnorm’
eff.ssfa: no visible global function definition for ‘pnorm’
plot_fitted: no visible global function definition for ‘lines’
plot_moran: no visible global function definition for ‘residuals’
print.summary.ssfa: no visible global function definition for
  ‘printCoefmat’
ssfa: no visible global function definition for ‘model.frame’
ssfa: no visible global function definition for ‘model.response’
ssfa.fit: no visible global function definition for ‘lm’
ssfa.fit: no visible global function definition for ‘var’
ssfa.fit: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pnorm’
summary.ssfa: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pchisq’
summary.ssfa: no visible binding for global variable ‘df’
u.ssfa: no visible global function definition for ‘dnorm’
u.ssfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survey’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for ‘hadamard’
Undefined global functions or variables:
  hadamard
Namespace in Imports field not imported from: ‘sessioninfo’
  All declared Imports should be used.
possible bashism in configure line 19 ('command' with option other than -p):
  if [ $(command -v pkg-config) ]; then
  possible bashism in configure line 33 ($(OS|MACH)TYPE):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (alternative test command ([[ foo ]] should be [ foo ])):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (should be 'b = a'):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 34 ('command' with option other than -p):
    if [ $(command -v brew) ]; then
  possible bashism in configure line 38 (should be '.', not 'source'):
      source autobrew
Malformed Title field: should not end in a period.
mem.usage: 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.
installed size is 94.6Mb
  sub-directories of 1Mb or more:
    libs  94.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Undeclared package ‘XML’ in Rd xrefs
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
error.est : <anonymous>: no visible global function definition for
  ‘median’
holm.robust: no visible global function definition for ‘pnorm’
holm.robust: no visible global function definition for ‘median’
holm.robust: no visible global function definition for ‘mad’
huberize: no visible global function definition for ‘quantile’
ssvd.initial: no visible global function definition for ‘mad’
ssvd.iter.thresh: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
Note: found 123 marked UTF-8 strings
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
Undeclared packages ‘pryr’, ‘functional’, ‘dplyr’, ‘ks’, ‘purrr’, ‘data.table’ in Rd xrefs
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par")
to your NAMESPACE file.
Found the following files/directories:
  ‘Rplot001.pdf’
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Rd file 'stkde.sig.rd':
  \examples lines wider than 100 characters:
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=1))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=2))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken

These lines will be truncated in the PDF manual.
find.names: no visible global function definition for ‘na.omit’
generate.names: no visible global function definition for ‘na.omit’
standardize.countrynames: no visible global function definition for
  ‘data’
standardize.names: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Rd file 'standardize.countrynames.Rd':
  \usage lines wider than 90 characters:
     standardize.countrynames(input, input.column = NULL, standard = "default", standard.column = NULL, only.names = FALSE, na.rm = FALSE, s ... [TRUNCATED]

Rd file 'standardize.text.Rd':
  \usage lines wider than 90 characters:
     standardize.text(input, input.column = NULL, standard, standard.column = NULL, regex = NULL, codes = NULL, match = FALSE, only.names =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    include  10.7Mb
    lib       2.9Mb
Package which this enhances but not available for checking: ‘Zelig’
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'library' or 'require' call to ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘starsdata’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   1.9Mb
    nc    4.5Mb
Unexported objects imported by ':::' calls:
  ‘s2dverification:::.KnownLatNames’ ‘s2dverification:::.KnownLonNames’
  See the note in ?`:::` about the use of this operator.
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘maxLik’ ‘nloptr’ ‘stats4’ ‘vars’
  All declared Imports should be used.
Undeclared package ‘rgr’ in Rd xrefs
Found the following files/directories:
  ‘testmat.sdml’ ‘testmat2.sdml’
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Undeclared package ‘distrEx’ in Rd xrefs
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
Note: found 47 marked UTF-8 strings
inspect: no visible global function definition for ‘par’
inspect: no visible global function definition for ‘abline’
inspect: no visible global function definition for ‘lines’
inspect: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘dev.off’
plotfit: no visible global function definition for ‘par’
plotfit: no visible global function definition for ‘lines’
plotfit: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘legend’
plothill: no visible global function definition for ‘par’
plothill: no visible global function definition for ‘abline’
plothill: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘par’
plotmultifit: no visible global function definition for ‘lines’
plotmultifit: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘pexp’
plotmultifit: no visible global function definition for ‘plnorm’
plotmultifit: no visible global function definition for ‘ppois’
plotmultifit: no visible global function definition for ‘legend’
plotols: no visible global function definition for ‘dev.off’
plotols: no visible global function definition for ‘lm’
plotols: no visible global function definition for ‘par’
plotols: no visible global function definition for ‘abline’
plotols: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘fortunes’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
Undeclared package ‘metaBMA’ in Rd xrefs
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘STB’
File ‘STB/libs/STB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.9Mb
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘rlist’ ‘tm’ ‘zoo’
  All declared Imports should be used.
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘axis’
plot.steeptest: no visible global function definition for ‘box’
plot.steeptest: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘abline’
plot.steeptest: no visible global function definition for ‘legend’
plot.steeptest: no visible global function definition for
  ‘as.graphicsAnnot’
steeptest: no visible global function definition for ‘lm’
summary.steeptest: no visible global function definition for ‘var’
summary.steeptest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Stem.Bootstrap: no visible global function definition for ‘runif’
filtering: no visible global function definition for ‘is.ts’
filtering: no visible global function definition for ‘ts’
filtering: no visible global function definition for ‘start’
filtering: no visible global function definition for ‘end’
filtering: no visible global function definition for ‘frequency’
kalman: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘is.ts’
smoothing: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘start’
smoothing: no visible global function definition for ‘end’
smoothing: no visible global function definition for ‘frequency’
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Found the following files/directories:
  ‘corrviz.html’
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.2Mb
Rd file 'calc.stoich.coef.Rd':
  \usage lines wider than 90 characters:
     calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)

These lines will be truncated in the PDF manual.
Note: found 15980 marked UTF-8 strings
Malformed Title field: should not end in a period.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
Note: found 327 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.7Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BSgenome’ ‘BiocManager’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘dplyr-support.Rmd’ using rmarkdown

Attaching package: 'strapgod'

The following object is masked from 'package:stats':

    filter


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 127-137 (dplyr-support.Rmd) 
Error: processing vignette 'dplyr-support.Rmd' failed with diagnostics:
The returned data frame cannot contain the original grouping variables: .bootstrap.
--- failed re-building ‘dplyr-support.Rmd’

--- re-building ‘virtual-bootstraps.Rmd’ using rmarkdown

Attaching package: 'strapgod'

The following object is masked from 'package:stats':

    filter


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘virtual-bootstraps.Rmd’

SUMMARY: processing the following file failed:
  ‘dplyr-support.Rmd’

Error: Vignette re-building failed.
Execution halted
StratPhyloCongruence: no visible global function definition for ‘runif’
StratPhyloCongruence: no visible global function definition for
  ‘txtProgressBar’
StratPhyloCongruence: no visible global function definition for
  ‘setTxtProgressBar’
StratPhyloCongruence: no visible global function definition for ‘pnorm’
StratPhyloCongruence: no visible global function definition for ‘sd’
geoscalePhylo: no visible global function definition for ‘data’
geoscalePhylo: no visible global function definition for ‘par’
geoscalePhylo: no visible global function definition for ‘text’
geoscalePhylo: no visible global function definition for ‘segments’
geoscalePhylo: no visible global function definition for ‘rect’
geoscalePhylo: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘RColorBrewer’ ‘Rcpp’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Found the following files/directories:
  ‘myNewStrat.R’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
Undeclared package ‘HDoutliers’ in Rd xrefs
Missing or unexported object: ‘limma::ebayes’
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  12.2Mb
Namespace in Imports field not imported from: ‘dbscan’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Note: found 3 marked UTF-8 strings
Package suggested but not available for checking: ‘STRaitRazoR’
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
Warning: no function found corresponding to methods exports from ‘stsm.class’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for ‘is.ts’
stsm.model: no visible global function definition for ‘var’
stsm.model: no visible global function definition for ‘frequency’
stsm.model: no visible global function definition for ‘na.omit’
stsm.model: no visible global function definition for ‘fft’
stsm.model: no visible global function definition for ‘new’
stsm.sgf: no visible global function definition for ‘frequency’
char2numeric,stsm: no visible global function definition for
  ‘frequency’
set.cpar,stsm: no visible global function definition for ‘validObject’
set.nopars,stsm: no visible global function definition for
  ‘validObject’
set.pars,stsm: no visible global function definition for ‘validObject’
transPars,stsm: no visible global function definition for ‘var’
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
Found the following files/directories:
  ‘EmiStatR_output’ ‘ExamplePlot-event.pdf’ ‘ExamplePlot-season.pdf’
  ‘Output1_MC-uncertainty_360min-event.pdf’
  ‘Output1_MC-uncertainty_360min-season.pdf’ ‘gof.RData’ ‘gof.csv’
  ‘gofGoF_results.RData’ ‘gofGoF_results.csv’ ‘mc.RData’ ‘sim1.RData’
  ‘summ.RData’ ‘variance.RData’
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper read.table symbols
Consider adding
  importFrom("graphics", "par", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘DT’ ‘V8’ ‘bsplus’ ‘colourpicker’ ‘dplyr’ ‘grDevices’ ‘graphics’
  ‘jsonlite’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
ELF: no visible global function definition for ‘pt’
ELF: no visible global function definition for ‘qnorm’
ELF: no visible global function definition for ‘lm’
ELF: no visible global function definition for ‘lowess’
ELF: no visible global function definition for ‘dnorm’
ELF: no visible global function definition for ‘approx’
subtype: no visible global function definition for ‘runif’
subtype: no visible global function definition for ‘hclust’
subtype: no visible global function definition for ‘dist’
subtype: no visible global function definition for ‘cutree’
subtype: no visible global function definition for ‘pt’
subtype: no visible global function definition for ‘heatmap’
test_subtype_only: no visible global function definition for ‘pt’
test_subtype_only: no visible global function definition for ‘survdiff’
test_subtype_only: no visible global function definition for ‘survfit’
test_subtype_only: no visible global function definition for ‘title’
ufun: no visible global function definition for ‘dnorm’
ufun: no visible global function definition for ‘lowess’
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
Rd file 'subtype.Rd':
  \usage lines wider than 90 characters:
     subtype(GEset, outcomeLabels, treatment=NULL, Npermutes=10, Nchunks = 25, minClusterSizeB = 20, NclustersASet = 100, FDRpermutation = T ... [TRUNCATED]
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

Rd file 'summary.Rd':
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for
  ‘segments’
playSudoku : replot: no visible global function definition for ‘text’
playSudoku: no visible global function definition for ‘tktoplevel’
playSudoku: no visible global function definition for ‘tkwm.title’
playSudoku: no visible global function definition for ‘tkrplot’
playSudoku: no visible global function definition for ‘tktext’
playSudoku: no visible global function definition for ‘tkscrollbar’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkyview’
playSudoku: no visible global function definition for ‘tkconfigure’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkset’
playSudoku: no visible global function definition for ‘tkpack’
playSudoku: no visible global function definition for ‘tcl’
playSudoku: no visible global function definition for ‘tkcget’
playSudoku : showz: no visible global function definition for
  ‘tkrreplot’
playSudoku : type: no visible global function definition for ‘tkinsert’
playSudoku : type: no visible global function definition for ‘tksee’
playSudoku : kb: no visible global function definition for ‘tkdestroy’
playSudoku: no visible global function definition for
  ‘getGraphicsEvent’
playSudoku: no visible global function definition for ‘tkbind’
playSudoku: no visible global function definition for ‘tkwait.window’
Undefined global functions or variables:
  getGraphicsEvent par segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "segments", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SUE.fitted.values: no visible global function definition for
  ‘model.frame’
SUE.lm: no visible global function definition for ‘model.frame’
SUE.lm: no visible global function definition for ‘lm’
SUE.lm: no visible global function definition for ‘anova’
SUE.residuals: no visible global function definition for ‘model.frame’
parameters : para2: no visible global function definition for ‘uniroot’
parameters: no visible global function definition for ‘optimize’
parameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  anova lm model.frame optimize uniroot
Consider adding
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Found the following files/directories:
  ‘CFH.scores.full.vcf’
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 78 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.4Mb
Malformed Description field: should contain one or more complete sentences.
MCMCCV: no visible global function definition for ‘rnorm’
MLCVGauss: no visible global function definition for ‘runif’
MLCVGauss: no visible global function definition for ‘optim’
SimSunderData: no visible global function definition for ‘runif’
SimSunderData: no visible global function definition for ‘dist’
SimSunderData: no visible global function definition for ‘rnorm’
SimSunderData: no visible global function definition for ‘qgamma’
SimSunderData: no visible global function definition for ‘pnorm’
SimSunderData: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Malformed Description field: should contain one or more complete sentences.
sunter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  ‘rgamma’
supcluster : itgamma: no visible global function definition for
  ‘dgamma’
supcluster : itgamma: no visible global function definition for ‘runif’
supcluster : itbeta: no visible global function definition for ‘rnorm’
supcluster : itbeta: no visible global function definition for ‘runif’
supcluster : itj: no visible global function definition for ‘dmultinom’
supcluster: no visible global function definition for ‘kmeans’
tab1: no visible global function definition for ‘image’
tab1: no visible global function definition for ‘gray’
tab1: no visible global function definition for ‘var’
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Call with DUP:
   .C(R_clusterer, E = as.double(E), X = as.double(X), W = as.double(W), 
       P = as.double(P), y = as.double(y), prob = as.double(prob), 
       theta = as.double(theta), lambda = as.double(lambda * n), 
       n = as.integer(n), g = as.integer(g), m = as.integer(m), 
       p = as.integer(p), critflag = as.integer(critflag), penflag = as.integer(penflag), 
       blockflag = as.integer(blockflag), valiflag = as.integer(valiflag), 
       traceflag = as.integer(trace), genliste = integer(lSize), 
       kriterium = double(lSize), DUP = FALSE)
DUP is no longer supported and will be ignored.
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to
  'digits'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to
  'width'
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol'
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of 'nr' to 'nrow'
aggtrees: no visible global function definition for ‘predict’
coef.pelora: no visible global function definition for ‘fitted’
dlda: no visible binding for global variable ‘var’
logreg: no visible global function definition for ‘glm’
logreg: no visible binding for global variable ‘binomial’
logreg: no visible global function definition for ‘predict’
plot.pelora: no visible global function definition for ‘text’
plot.wilma: no visible global function definition for ‘fitted’
plot.wilma: no visible global function definition for ‘text’
predict.pelora: no visible global function definition for ‘fitted’
predict.pelora: no visible global function definition for ‘coef’
predict.wilma: no visible global function definition for ‘fitted’
print.wilma: no visible global function definition for ‘fitted’
ridge.coef: no visible binding for global variable ‘var’
sign.change: no visible binding for global variable ‘cov’
standardize.genes: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  binomial coef cov fitted glm predict sd text var
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "binomial", "coef", "cov", "fitted", "glm",
             "predict", "sd", "var")
to your NAMESPACE file.
File ‘supclust/libs/supclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
HCLtree: no visible global function definition for ‘hclust’
HCLtree: no visible global function definition for ‘as.dist’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matplot’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matlines’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘axis’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matplot’
plotProfilesWithinBicluster: no visible global function definition for
  ‘title’
plotProfilesWithinBicluster: no visible global function definition for
  ‘axis’
plotProfilesWithinBicluster: no visible global function definition for
  ‘par’
plotProfilesWithinBicluster: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matlines’
plotProfilesWithinBicluster: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘boa’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for ‘as.mcmc.list’
superdiag: no visible global function definition for ‘as.mcmc’
superdiag: no visible global function definition for ‘runif’
superdiag: no visible global function definition for ‘geweke.diag’
superdiag: no visible global function definition for ‘heidel.diag’
superdiag: no visible global function definition for ‘raftery.diag’
superdiag: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'library' or 'require' call to ‘gam’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  All declared Imports should be used.
'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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
Undeclared packages ‘mlogit’, ‘gmnl’, ‘apollo’ in Rd xrefs
Undeclared package ‘mded’ in Rd xrefs
Undeclared package ‘truncdist’ in Rd xrefs
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
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.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘lines’
plot.survErr: no visible global function definition for ‘lines’
schemper: no visible global function definition for ‘predict’
schemper: no visible global function definition for ‘survfit’
schemper: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx lines predict survfit
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Est.PH: no visible global function definition for ‘coxph’
Inf.Cval: no visible global function definition for ‘rexp’
Inf.Cval: no visible global function definition for ‘var’
Inf.Cval.Delta: no visible global function definition for ‘rexp’
Inf.Cval.Delta: no visible global function definition for ‘var’
cvC: no visible global function definition for ‘coxph’
cvC: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
File ‘survC1/libs/survC1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘points’
survcorr: no visible global function definition for ‘model.frame’
survcorr: no visible global function definition for ‘qnorm’
survcorr: no visible global function definition for ‘runif’
survcorr: no visible global function definition for ‘pnorm’
survcorr: no visible global function definition for ‘var’
survcorr: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cor model.frame par pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   2.0Mb
Undeclared packages ‘RColorBrewer’, ‘scoringRules’, ‘coin’, ‘gtable’ in Rd xrefs
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.
AER: no visible binding for global variable ‘survexp.fr’
AER: no visible global function definition for ‘na.omit’
AER: no visible global function definition for ‘survexp’
AER: no visible global function definition for ‘poisson’
AER: no visible global function definition for ‘glm’
AER: no visible global function definition for ‘qnorm’
LR: no visible binding for global variable ‘survexp.fr’
LR: no visible global function definition for ‘na.omit’
LR: no visible global function definition for ‘survexp’
LR: no visible global function definition for ‘pchisq’
SMR: no visible binding for global variable ‘survexp.fr’
SMR: no visible global function definition for ‘na.omit’
SMR: no visible global function definition for ‘survexp’
SMR: no visible global function definition for ‘qnorm’
SMR: no visible global function definition for ‘pchisq’
SMR: no visible global function definition for ‘glm’
SMR: no visible binding for global variable ‘poisson’
survexp_plot: no visible binding for global variable ‘survexp.fr’
survexp_plot: no visible global function definition for ‘na.omit’
survexp_plot: no visible global function definition for ‘par’
survexp_plot: no visible global function definition for ‘survfit’
survexp_plot: no visible global function definition for ‘survexp’
survexp_plot: no visible global function definition for ‘lines’
survexp_plot: no visible global function definition for ‘legend’
survexp_plot: no visible global function definition for ‘curve’
survexp_plot: no visible global function definition for ‘arrows’
survexp_plot: no visible global function definition for ‘points’
Undefined global functions or variables:
  arrows curve glm legend lines na.omit par pchisq points poisson qnorm
  survexp survexp.fr survfit
Consider adding
  importFrom("graphics", "arrows", "curve", "legend", "lines", "par",
             "points")
  importFrom("stats", "glm", "na.omit", "pchisq", "poisson", "qnorm")
to your NAMESPACE file.
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
installed size is 176.5Mb
  sub-directories of 1Mb or more:
    libs  175.0Mb
GNU make is a SystemRequirements.
Packages in Depends field not imported from:
  ‘survC1’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for ‘coxph’
Est.HR.FUN: no visible global function definition for ‘basehaz’
Est.HR.FUN: no visible global function definition for ‘approx’
Ghat.FUN: no visible global function definition for ‘survfit’
IDI.INF: no visible global function definition for ‘kmcens’
IDI.INF: no visible global function definition for ‘quantile’
IDI.INF.GRAPH: no visible global function definition for ‘lines’
IDI.INF.GRAPH: no visible global function definition for ‘abline’
IDI.INF.GRAPH: no visible global function definition for ‘points’
IDI.INF.GRAPH: no visible global function definition for ‘title’
PTB.IDI.FUN: no visible global function definition for ‘rexp’
shade: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines points polygon quantile rexp
  survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "points", "polygon", "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
Rd file 'IDI.INF.GRAPH.Rd':
  \usage lines wider than 90 characters:
     IDI.INF.GRAPH(x, main = NULL, xlab = NULL, ylab = NULL, cex.main = NULL, cex.lab = NULL, ...)

Rd file 'IDI.INF.Rd':
  \usage lines wider than 90 characters:
     IDI.INF(indata, covs0, covs1, t0, npert = 300, npert.rand = NULL, seed1 = NULL, alpha = 0.05)

These lines will be truncated in the PDF manual.
File ‘survIDINRI/libs/survIDINRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.2Mb
    doc    3.4Mb
Malformed Description field: should contain one or more complete sentences.
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Undeclared package ‘survJamda’ in Rd xrefs
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.1Mb
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘DALEX’ in Rd xrefs
Malformed Title field: should not end in a period.
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘svapls’
fitModel: no visible global function definition for ‘var’
fitModel: no visible global function definition for ‘cov’
svpls: no visible global function definition for ‘pt’
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   7.3Mb
Calls with DUP:
   .C("myInversion", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, DUP = FALSE, PACKAGE = "svcm")
   .C("myTrace", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, BBenv$diag, BBenv$env, BBenv$xenv, BBenv$N, 
       BBenv$Nenv, BBenv$Nplus1, ED = ED, DUP = FALSE, PACKAGE = "svcm")
   .C("dsC2env", N, A@x, as.integer(A@i), as.integer(A@p), diagvec = diagvec, 
       env = env, xenv = as.integer(xenv), DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
Malformed Description field: should contain one or more complete sentences.
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
.onAttach : svBrowser: no visible global function definition for
  ‘browseURL’
.onAttach: no visible global function definition for ‘loadhistory’
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File ‘SVMMatch/libs/SVMMatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘svHttp’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
svycox.calibrate: no visible global function definition for ‘quantile’
svycox.calibrate: no visible binding for global variable ‘median’
svycox.calibrate: no visible global function definition for
  ‘as.formula’
svycox.calibrate: no visible global function definition for ‘arrows’
svycox.calibrate: no visible global function definition for ‘abline’
svycox.nomogram: no visible global function definition for ‘predict’
svycox.nomogram: no visible global function definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘formula’
Undefined global functions or variables:
  abline arrows as.formula formula median predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for ‘aggregate’
additional_compPV : <anonymous>: no visible global function definition
  for ‘aggregate’
cor.aux.func : <anonymous>: no visible global function definition for
  ‘cov.wt’
eta.func : <anonymous>: no visible global function definition for ‘lm’
eta.func : <anonymous>: no visible global function definition for
  ‘anova’
glm.dummy.no.std: no visible global function definition for
  ‘as.formula’
pv_by: no visible binding for global variable ‘var’
pv_perc: no visible binding for global variable ‘var’
pv_quantile: no visible binding for global variable ‘var’
svyPVcor: no visible global function definition for ‘update’
svyPVcor: no visible global function definition for ‘var’
svyPVeta: no visible global function definition for ‘update’
svyPVeta: no visible global function definition for ‘var’
svyPVglm: no visible global function definition for ‘gaussian’
svyPVglm: no visible binding for global variable ‘as.formula’
svyPVglm: no visible binding for global variable ‘var’
svyPVglm: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘as.formula’
svyPVttest: no visible global function definition for ‘var’
svyPVttest: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘var’
t.test.aux: no visible global function definition for ‘as.formula’
t.test.aux: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘swephRdata’
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘scales’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘MASS’ ‘fda’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for ‘getbasismatrix’
fj_pl: no visible global function definition for ‘create.bspline.basis’
fj_pl: no visible global function definition for ‘getbasispenalty’
forward_backward.quantities : <anonymous>: no visible global function
  definition for ‘dnorm’
function_cases1AND2: no visible global function definition for ‘dnorm’
function_cases3AND4: no visible global function definition for ‘dnorm’
pij_iid: no visible global function definition for ‘dnorm’
pilj: no visible global function definition for ‘dnorm’
updateLambda: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cplexAPI’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘cplexAPI’
Package suggested but not available for checking: ‘cplexAPI’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
symbol: no visible global function definition for ‘plot.new’
symbol: no visible global function definition for ‘plot.window’
symbol: no visible global function definition for ‘axis’
symbol: no visible global function definition for ‘box’
symbol: no visible global function definition for ‘title’
symbol: no visible global function definition for ‘rainbow’
symbol: no visible global function definition for ‘hsv’
symbol: no visible global function definition for ‘rect’
symbol: no visible global function definition for ‘polygon’
symbol: no visible global function definition for ‘lines’
symbol: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
Rd file 'symbol.Rd':
  \usage lines wider than 90 characters:
     symbol(df, type="star", colin=NULL, colout=NULL, colin2=NA, colout2=1, ssize=NULL, labels=0, labelsize=0.6,
            scheme=1, sortby=0, descending=FALSE, coorx=NULL, coory=NULL, lty=1, main=NULL, sub=NULL, xlab=NULL, ylab=NULL,
            add=FALSE, xlim=NULL, ylim=NULL, facew=0.5, faceh=0.5, eyes=0.5, eyed=0.5, mouthw=0.5, mouthc=0.5, brows=0.5,
            browp=0.5, nosel=0.5, nosew=0.5, ears=0.5, pupils=0.5, body=0.5, limb1=0.5, limb2=0.5, limb3=0.5, limb4=0.5, defcol=NA)

These lines will be truncated in the PDF manual.
Requires orphaned package: ‘bit’
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
possible bashism in configure line 12 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 22 (echo -n):
  echo -n "  checking for OS..."
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘doc’
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

Rd file 'gridinfer.rd':
  \examples lines wider than 100 characters:
       #are nested inside it. In a network analysis this kind of element will behave as intermediary node.  

Rd file 'reweight.rd':
  \examples lines wider than 100 characters:
       plot(unlist(ej),unlist(reweight(ej)), xlab = "Input matrix", ylab = "Reweighted matrix", main = "First reweighting")

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘lines’
mainNetFunction: no visible global function definition for ‘legend’
mainNetFunction: no visible global function definition for ‘dev.off’
plotROC: no visible global function definition for ‘lines’
simulatedData: no visible global function definition for ‘rpois’
simulatedData : <anonymous>: no visible global function definition for
  ‘rpois’
simulatedData : rlognormpois: no visible global function definition for
  ‘rnorm’
simulatedData : rlognormpois: no visible global function definition for
  ‘rpois’
Undefined global functions or variables:
  dev.off legend lines png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following files/directories:
  ‘test.csv’
Undeclared package ‘Ecdat’ in Rd xrefs
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
.checkDimAndTest: no visible global function definition for
  ‘chisq.test’
.checkDimAndTest: no visible global function definition for
  ‘fisher.test’
plotTable1Heatmap: no visible global function definition for ‘par’
plotTable1Heatmap: no visible global function definition for ‘image’
plotTable1Heatmap: no visible global function definition for ‘abline’
plotTable1Heatmap: no visible global function definition for ‘axis’
plotTable1Heatmap: no visible global function definition for ‘text’
plotTable1Heatmap: no visible global function definition for ‘legend’
plotTable1Heatmap: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
Found the following files/directories:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Found the following files/directories:
  ‘myhtmlcode.html’
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘perturb’ 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: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for ‘grid.rect’
cellgram: no visible global function definition for ‘gpar’
cellgram: no visible global function definition for ‘grid.segments’
cellgram: no visible global function definition for ‘grid.circle’
cellgram: no visible global function definition for ‘grid.polygon’
cellgram: no visible global function definition for ‘grid.text’
cellgram: no visible global function definition for ‘unit’
compare: no visible global function definition for ‘sd’
tableplot.colldiag: no visible global function definition for
  ‘colldiag’
tableplot.colldiag: no visible global function definition for ‘xtabs’
tableplot.default: no visible global function definition for
  ‘grid.newpage’
tableplot.default: no visible global function definition for
  ‘grid.layout’
tableplot.default: no visible global function definition for ‘unit’
tableplot.default: no visible global function definition for
  ‘pushViewport’
tableplot.default: no visible global function definition for ‘viewport’
tableplot.default: no visible global function definition for
  ‘grid.text’
tableplot.default: no visible global function definition for
  ‘upViewport’
tableplot.default: no visible global function definition for ‘gpar’
tableplot.default: no visible global function definition for
  ‘grid.rect’
tableplot.default: no visible global function definition for
  ‘popViewport’
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
Rd file 'Linehan.Rd':
  \examples lines wider than 100 characters:
             cell.specs=list(list(0,"grey50",1,1,"red",1,"white","grey90",2,.7,"black",FALSE,"black",99)),
             cell.specs=list(list(0,c("black","blue"),1,1,c("black","blue"),1,"white","grey80",2,.7,"black",FALSE,"black",99))

Rd file 'cellgram.Rd':
  \usage lines wider than 90 characters:
     cellgram(cell, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape.lty.neg = 1, cell.fill = "whi ... [TRUNCATED]

Rd file 'congruence.array.Rd':
  \usage lines wider than 90 characters:
     congruence.array(X, FUN = congruence.coef, stat.name = "phi", round = FALSE, scale = 1, ref = "last")

Rd file 'make.specs0.Rd':
  \usage lines wider than 90 characters:
     make.specs0(n = NULL, as.data.frame = FALSE, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape ... [TRUNCATED]
     cell.fill = "white", back.fill = "white", label = 0, label.size = 0.7, label.col = "black", ref.lines = FALSE, ref.col = "gray80",  sca ... [TRUNCATED]

Rd file 'tableplot.Rd':
  \usage lines wider than 90 characters:
             v.parts = 0, h.parts = 0, gap = 2, text.m = 0, empty.text.size = 0.8, empty.text.col = "grey30", 
             title = NULL, table.label = TRUE, label.size = 0.8, side.rot = 0, left.space = 10, top.space = 10+10*(!is.null(title)), ...)
  \examples lines wider than 100 characters:
             cell.specs = list(list(0,"grey50",1,0,"red",1,"white","grey80",1,0.7,"black",FALSE,"black",93)),

These lines will be truncated in the PDF manual.
Undeclared package ‘gplots’ in Rd xrefs
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
Undeclared package ‘parsedate’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘gee’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gibble’ ‘rlang’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
Note: found 3 marked UTF-8 strings
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pmatch’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.6Mb
Undeclared package ‘mirt’ in Rd xrefs
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘spruce.taper.pars.rdata’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
Undeclared package ‘GEOmap’ in Rd xrefs
Packages suggested but not available for checking: 'MonetDBLite', 'duckdb'
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
Undeclared package ‘ape’ in Rd xrefs
Note: found 137 marked UTF-8 strings
Found the following files/directories:
  ‘nameNode.sqlite’
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
License components which are templates and need '+ file LICENSE':
  MIT
BootTree: no visible global function definition for ‘hclust’
BootTree: no visible global function definition for ‘dist’
BootTree: no visible global function definition for ‘as.dist’
BootTree: no visible global function definition for ‘cor’
BootTree: no visible binding for global variable ‘var’
Pgpd: no visible global function definition for ‘optim’
Pgpd : <anonymous>: no visible global function definition for ‘optim’
Pgpd: no visible global function definition for ‘var’
Pgpd: no visible global function definition for ‘rnorm’
Pgpd: no visible global function definition for ‘quantile’
Pvalue: no visible global function definition for ‘rnorm’
SigTree: no visible global function definition for ‘data’
TreeStat: no visible global function definition for ‘hclust’
TreeStat: no visible global function definition for ‘as.dist’
TreeStat: no visible global function definition for ‘dist’
TreeStat: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘hclust’
plot.best: no visible global function definition for ‘as.dist’
plot.best: no visible global function definition for ‘dist’
plot.best: no visible global function definition for ‘cor’
treetext: no visible global function definition for ‘par’
treetext: no visible global function definition for ‘text’
Undefined global functions or variables:
  as.dist cor data dist hclust optim par quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘glmnet’ ‘quadprog’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.8Mb
    libs   1.2Mb
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘RSEIS’ ‘pracma’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CalcCorners: no visible global function definition for ‘abline’
ConvDiffCoef: no visible global function definition for ‘pascal’
ConvolveTrace: no visible global function definition for ‘filter’
DeconTrace: no visible global function definition for ‘as.Zpg’
DeconTrace: no visible global function definition for ‘butter’
DeconTrace: no visible global function definition for ‘filter’
GetDPZ: no visible global function definition for ‘data’
MakeDPZ: no visible global function definition for ‘bilinear’
MakeDPZ: no visible global function definition for ‘fft’
MakeDPZ: no visible global function definition for ‘lines’
MakeDPZ: no visible global function definition for ‘legend’
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  ‘fft’
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  ‘filter’
MatchCoefDPZ : generate: no visible global function definition for
  ‘runif’
MatchCoefDPZ : generate: no visible global function definition for
  ‘rnorm’
MatchCoefDPZ: no visible global function definition for ‘fft’
MatchCoefDPZ: no visible global function definition for ‘filter’
MatchCoefDPZ: no visible global function definition for ‘Zpg’
MatchCoefDPZ: no visible global function definition for ‘lines’
MatchCoefDPZ: no visible global function definition for ‘abline’
Metropolis: no visible global function definition for ‘runif’
PZ2Coef: no visible global function definition for ‘Poly’
PlotResp: no visible global function definition for ‘fft’
PlotResp: no visible global function definition for ‘filter’
PlotResp: no visible global function definition for ‘lines’
Undefined global functions or variables:
  Poly Zpg abline as.Zpg bilinear butter data fft filter legend lines
  pascal rnorm runif
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "fft", "filter", "rnorm", "runif")
  importFrom("utils", "data")
to your NAMESPACE file.
Undeclared package ‘survivalROC’ in Rd xrefs
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    apps   3.2Mb
    libs  11.1Mb
Package suggested but not available for checking: ‘R2wd’
Undeclared package ‘scales’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  17.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Calls with DUP:
   .C(tensoraCmulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.complex(X[xtidx]), as.complex(Y[ytidx]), 
       erg = complex(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
   .C(tensoramulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.numeric(X[xtidx]), as.numeric(Y[ytidx]), 
       erg = numeric(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
DUP is no longer supported and will be ignored.
S3 methods shown with full name in documentation object 'mean.tensor':
  ‘mean.tensor’

S3 methods shown with full name in documentation object 'solve.tensor':
  ‘solve.tensor’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘tensorA/libs/tensorA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘fICA’ in Rd xrefs
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  32.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(raster)
  Loading required package: sp
  > library(terra)
  This is terra version 0.6.9 (alpha-release)
  > 
  > test_check("terra")
  ERROR 6: Too many command options '=`'
  Warning 1: The output raster dataset has a SRS, but the input vector layer SRS is unknown.
  Ensure input vector has the same SRS, otherwise results might be incorrect.
  ── 1. Failure: rasterize (@test-raster-vector.R#22)  ───────────────────────────
  values(rv) not equivalent to values(rvx).
  75/200 mismatches (average diff: 253)
  [43] 255 - 1 == 254
  [44] 255 - 1 == 254
  [49] 255 - 3 == 252
  [50] 255 - 3 == 252
  [51] 255 - 3 == 252
  [57] 255 - 2 == 253
  [58] 255 - 2 == 253
  [62] 255 - 1 == 254
  [63] 255 - 1 == 254
  ...
  
  ── 2. Failure: crop (@test-raster-vector.R#30)  ────────────────────────────────
  values(rc) not equivalent to values(rcx).
  75/114 mismatches (average diff: 253)
  [3]  255 - 1 == 254
  [4]  255 - 1 == 254
  [9]  255 - 3 == 252
  [10] 255 - 3 == 252
  [11] 255 - 3 == 252
  [17] 255 - 2 == 253
  [18] 255 - 2 == 253
  [21] 255 - 1 == 254
  [22] 255 - 1 == 254
  ...
  
  ERROR 6: Too many command options '}+'
  Warning 1: The output raster dataset has a SRS, but the input vector layer SRS is unknown.
  Ensure input vector has the same SRS, otherwise results might be incorrect.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: rasterize (@test-raster-vector.R#22) 
  2. Failure: crop (@test-raster-vector.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 42 (should be '.', not 'source'):
      source autobrew
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘ExtinctionRateChanges.txt’ ‘ExtinctionRates.txt’
  ‘MassExtinctionTimes.txt’ ‘SpeciationRateChanges.txt’
  ‘SpeciationRates.txt’ ‘SurvivalProbabilities.txt’ ‘analysis_conifer’
  ‘input_tree.tre’ ‘run_1’ ‘run_2’ ‘samples_numCategories.txt’
Found the following files/directories:
  ‘par-7269706c6579’
Package suggested but not available for checking: ‘gurobi’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.1Mb
Namespaces in Imports field not imported from:
  ‘stringi’ ‘utils’
  All declared Imports should be used.
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘details’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'glmmADMB', 'Zelig'
Unknown package ‘Zelig’ in Rd xrefs
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   5.1Mb
Undeclared package ‘NLP’ in Rd xrefs
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Undeclared package ‘gsubfn’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Undeclared package ‘tm’ in Rd xrefs
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘points’
progression: no visible global function definition for ‘legend’
progression: no visible global function definition for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘dhyper’
specificities.distribution.plot: no visible global function definition
  for ‘Axis’
specificities.distribution.plot: no visible global function definition
  for ‘arrows’
specificities.distribution.plot: no visible global function definition
  for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘title’
specificities.probabilities.vector: no visible global function
  definition for ‘phyper’
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "points", "text",
             "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
Undeclared package ‘tm’ in Rd xrefs
Undeclared package ‘tm’ in Rd xrefs
Undeclared packages ‘tm’, ‘textreadr’ in Rd xrefs
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Undeclared package ‘NMOF’ in Rd xrefs
transfer: no visible global function definition for ‘rgamma’
transfer: no visible global function definition for ‘rnorm’
transfer: no visible global function definition for ‘rnbinom’
transfer: no visible global function definition for ‘rpois’
transfer: no visible global function definition for ‘rbinom’
transfer: no visible global function definition for ‘runif’
plot,transfer: no visible global function definition for ‘barplot’
plot,transfer: no visible global function definition for ‘axis’
plot,transfer: no visible global function definition for ‘par’
plot,transfer: no visible global function definition for ‘hist’
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘tmp.test.data.csv’
ParseTrueFX: no visible global function definition for ‘read.csv’
TrueFXRef: no visible global function definition for ‘download.file’
TrueFXRef: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
Undeclared package ‘akima’ in Rd xrefs
File ‘tgp/libs/tgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    7.1Mb
Namespace in Imports field not imported from: ‘proxy’
  All declared Imports should be used.
Undeclared package ‘glmnet’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
Thinknum: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
installed size is 38.6Mb
  sub-directories of 1Mb or more:
    libs  38.2Mb
GNU make is a SystemRequirements.
.LoadTickDataHK: no visible global function definition for ‘read.csv’
.LoadTickDataSHSZ: no visible global function definition for ‘read.csv’
DrawDown: no visible global function definition for ‘na.omit’
PerformanceReport: no visible global function definition for
  ‘aggregate’
PerformanceReport: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
newTiddler: no visible global function definition for ‘new’
twImage: no visible global function definition for ‘new’
twLink: no visible global function definition for ‘new’
twList: no visible global function definition for ‘new’
twTable: 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').
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Undeclared packages ‘dplyr’, ‘fastDummies’ in Rd xrefs
Undeclared packages ‘tidyfst’, ‘tidyr’, ‘fastDummies’ in Rd xrefs
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Evomorph’ ‘cowplot’ ‘factoextra’ ‘gridExtra’ ‘lme4’ ‘lsr’ ‘plotly’
  ‘png’ ‘shapes’
  All declared Imports should be used.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Note: found 24 marked UTF-8 strings
Note: found 113 marked UTF-8 strings
Note: found 229801 marked UTF-8 strings
Running examples in ‘tidystopwords-Ex.R’ failed
The error most likely occurred in:

> ### Name: generate_stoplist
> ### Title: Listing of stop words with control over language and part of
> ###   speech.
> ### Aliases: generate_stoplist
> 
> ### ** Examples
> 
>     # standard usage (might return some non-ASCII characters):
>     generate_stoplist(lang_name = "English")
Error: Can't combine `..1$language_id` <logical> and `..2$language_id` <character>.
Backtrace:
    █
 1. ├─tidystopwords::generate_stoplist(lang_name = "English")
 2. │ └─dplyr::bind_rows(stoplist_db, ling_filter_db)
 3. │   └─vctrs::vec_rbind(!!!dots, .names_to = .id)
 4. └─vctrs::vec_default_ptype2(...)
 5.   └─vctrs::stop_incompatible_type(...)
 6.     └─vctrs:::stop_incompatible(...)
 7.       └─vctrs:::stop_vctrs(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘tidystopwords.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

tidystopwords version: 0.9.0
Quitting from lines 127-129 (tidystopwords.Rmd) 
Error: processing vignette 'tidystopwords.Rmd' failed with diagnostics:
Can't combine `..1$language_id` <logical> and `..2$language_id` <character>.
--- failed re-building ‘tidystopwords.Rmd’

SUMMARY: processing the following file failed:
  ‘tidystopwords.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
Note: found 62 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘keyring’ ‘nlme’ ‘rgdal’ ‘stringi’ ‘usethis’
  All declared Imports should be used.
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.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.
File ‘tiff/libs/tiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'library' or 'require' call to ‘shiny’ 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: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for ‘ggplot’
timeline: no visible global function definition for ‘geom_segment’
timeline: no visible global function definition for ‘aes_string’
timeline: no visible global function definition for ‘geom_rect’
timeline: no visible global function definition for ‘geom_text’
timeline: no visible global function definition for ‘theme’
timeline: no visible global function definition for ‘element_blank’
timeline: no visible global function definition for ‘xlab’
timeline: no visible global function definition for ‘ylab’
timeline: no visible global function definition for ‘xlim’
timeline: no visible global function definition for
  ‘scale_y_continuous’
timeline: no visible global function definition for ‘geom_point’
timeline: no visible global function definition for ‘scale_color_grey’
timeline: no visible global function definition for ‘geom_hline’
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for ‘isWeekday’
plotCalendarHeatmap: no visible global function definition for ‘ddply’
plotCalendarHeatmap: no visible global function definition for ‘.’
plotCalendarHeatmap: no visible binding for global variable ‘year’
plotCalendarHeatmap: no visible binding for global variable ‘month’
plotCalendarHeatmap: no visible binding for global variable ‘week’
plotCalendarHeatmap: no visible global function definition for ‘ggplot’
plotCalendarHeatmap: no visible global function definition for ‘aes’
plotCalendarHeatmap: no visible binding for global variable ‘monthweek’
plotCalendarHeatmap: no visible binding for global variable ‘weekday’
plotCalendarHeatmap: no visible global function definition for
  ‘geom_tile’
plotCalendarHeatmap: no visible global function definition for
  ‘facet_grid’
plotCalendarHeatmap: no visible global function definition for
  ‘scale_fill_gradientn’
projectDate: no visible global function definition for ‘holidayNYSE’
projectDate: no visible global function definition for
  ‘sparse.model.matrix’
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘boot’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot_autocov: no visible global function definition for ‘is.ts’
boot_autocov: no visible global function definition for ‘tsboot’
boot_autocov: no visible global function definition for ‘quantile’
boot_autocov: no visible global function definition for ‘par’
boot_autocov: no visible global function definition for ‘frequency’
boot_autocov: no visible global function definition for ‘polygon’
boot_autocov: no visible global function definition for ‘lines’
boot_autocov: no visible global function definition for ‘abline’
boot_autocov: no visible global function definition for ‘acf’
boot_spec: no visible global function definition for ‘is.ts’
boot_spec: no visible global function definition for ‘tsboot’
boot_spec: no visible global function definition for ‘spec.pgram’
boot_spec: no visible global function definition for ‘quantile’
boot_spec: no visible global function definition for ‘polygon’
boot_spec: no visible global function definition for ‘lines’
redraw: no visible global function definition for ‘spec.pgram’
statistic: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Note: found 2750 marked UTF-8 strings
author.search: no visible binding for global variable ‘na.omit’
reference.list: 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.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf segments text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘timma/libs/timma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘_paramEst.txt’
‘cleanup’: /bin/bash is not portable
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
Non-standard file/directory found at top level:
  ‘CONTENTS’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
ls.tree: no visible global function definition for ‘lm’
ls.tree: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
File ‘TKF/libs/TKF.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
File ‘tkrplot/libs/tkrplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FLXmclust.Density: no visible global function definition for ‘dmvnorm’
FLXmclust.Estimate: no visible global function definition for ‘flexmix’
FLXmclust.Estimate: no visible global function definition for
  ‘FLXmclust’
coefmclust: no visible global function definition for ‘parameters’
flexmix.Density: no visible global function definition for
  ‘model.matrix’
flexmix.Density: no visible global function definition for
  ‘model.response’
flexmix.Density: no visible global function definition for
  ‘model.frame’
flexmix.Density: no visible global function definition for ‘dnorm’
flexmix.Density: no visible global function definition for ‘dpois’
flexmix.Density: no visible global function definition for ‘dbinom’
flexmix.Estimate: no visible global function definition for ‘flexmix’
flexmix.Estimate: no visible global function definition for ‘FLXglm’
tleplot,TLE-data.frame: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
Undeclared package ‘modeltools’ in Rd xrefs
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
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.
EMN: no visible global function definition for ‘dmvnorm’
EMN: no visible global function definition for ‘pmvnorm’
EMT: no visible global function definition for ‘GenzBretz’
EMT: no visible global function definition for ‘dmvt’
EMT: no visible global function definition for ‘pmvt’
MomemNT: no visible global function definition for ‘pnorm’
MomemNT: no visible global function definition for ‘dnorm’
MomemNT: no visible global function definition for ‘pmvnorm’
MomemNT: no visible global function definition for ‘dmvnorm’
TT.moment: no visible global function definition for ‘GenzBretz’
TT.moment: no visible global function definition for ‘pmvt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dmvt’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
inits: no visible global function definition for ‘lm’
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
Rd file 'UTIdata.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]

These lines will be truncated in the PDF manual.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Undeclared packages ‘raster’, ‘sp’ in Rd xrefs
Namespace in Imports field not imported from: ‘KernSmooth’
  All declared Imports should be used.
Undeclared package ‘sp’ in Rd xrefs
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    examples  15.0Mb
    include    3.0Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
Note: found 134043 marked UTF-8 strings
File ‘tmg/libs/tmg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
extractContentDOM: no visible global function definition for
  ‘capture.output’
extractHTMLStrip: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
Undeclared packages ‘tm.plugin.dc’, ‘readtext’, ‘graph’, ‘tau’, ‘tokenizers’ in Rd xrefs
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Requires orphaned package: ‘bit’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
Undeclared package ‘stm’ in Rd xrefs
Package suggested but not available for checking: ‘corpus.JSS.papers’
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Note: found 1946 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Tosls.formula: no visible global function definition for ‘model.matrix’
Tosls.formula: no visible global function definition for
  ‘model.response’
summary: no visible global function definition for ‘coef’
summary: 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.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Note: found 64 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Package suggested but not available for checking: ‘CollessLike’
Unknown package ‘CollessLike’ in Rd xrefs
Undeclared package ‘vcd’ in Rd xrefs
Found the following files/directories:
  ‘test-001.png’ ‘test-002.png’ ‘test-003.png’ ‘test-004.png’
  ‘test-005.png’ ‘test-006.png’ ‘test-007.png’ ‘test-008.png’
  ‘test-009.png’ ‘test-010.png’ ‘test-011.png’ ‘test-012.png’
  ‘test-013.png’ ‘test-014.png’ ‘test-015.png’ ‘test-016.png’
  ‘test-017.png’ ‘test-018.png’ ‘test-019.png’ ‘test-020.png’
  ‘test-021.png’ ‘test-022.png’ ‘test-023.png’ ‘test-024.png’
  ‘test-025.png’ ‘test-026.png’ ‘test-027.png’ ‘test-028.png’
  ‘test-029.png’ ‘test-030.png’ ‘test-031.png’ ‘test-032.png’
  ‘test-033.png’ ‘test-034.png’ ‘test-035.png’ ‘test-036.png’
  ‘test-037.png’ ‘test-038.png’ ‘test-039.png’ ‘test-040.png’
  ‘test-041.png’ ‘test-042.png’ ‘test-043.png’ ‘test-044.png’
  ‘test-045.png’ ‘test-046.png’ ‘test-047.png’ ‘test-048.png’
  ‘test-049.png’ ‘test-050.png’ ‘test.pdf’
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘01_spontaneous lethality.txt’ ‘02.sample size.txt’
  ‘03.dosestrategy.txt’ ‘doseD4.txt’ ‘setD.txt’ ‘spoDa.txt’ ‘spoDb.txt’
License components which are templates and need '+ file LICENSE':
  MIT
align1d : obj: no visible global function definition for ‘dist’
align2d : obj: no visible global function definition for ‘dist’
align2d : pen: no visible global function definition for ‘dist’
align2d: no visible global function definition for ‘dist’
sumt: no visible global function definition for ‘optim’
tpe1d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘cmdscale’
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

These lines will be truncated in the PDF manual.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Undeclared package ‘rlang’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Undeclared packages ‘g.data’, ‘filehash’ in Rd xrefs
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
Package suggested but not available for checking: ‘taxidata’
Undeclared package ‘TraMineRextras’ in Rd xrefs
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
Malformed Description field: should contain one or more complete sentences.
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘trapezoid/libs/trapezoid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘forcats’ in Rd xrefs
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(data.table)
  > library(rpart)
  > library(rpart.plot)
  > library(rpart.utils)
  
  Attaching package: 'rpart.utils'
  
  The following object is masked from 'package:rpart.plot':
  
      rpart.rules
  
  > library(tree.bins)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:data.table':
  
      between, first, last
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("tree.bins")
  ── 1. Error: Test to see if lookup tables and joins are performed correctly (@te
  Items of 'old' not found in column names: [Categories]. Consider skip_absent=TRUE.
  Backtrace:
   1. test.df.adj.Nei[, !(names(test.df.adj.Nei) %in% "Neighborhood")]
   1. data.table::as.data.table(.)
   9. data.table::setnames(., "Categories", "Neighborhood")
  
  ── 2. Error: Testing for 2 predictors,
            both will recategorize the vari
  Items of 'old' not found in column names: [Categories]. Consider skip_absent=TRUE.
  Backtrace:
   1. test.df.adj.Nei[, !(names(test.df.adj.Nei) %in% "Neighborhood")]
   1. data.table::as.data.table(.)
   9. data.table::setnames(., "Categories", "Neighborhood")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 11 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: Test to see if lookup tables and joins are performed correctly (@test-bin.oth.R#63) 
  2. Error: Testing for 2 predictors,
            both will recategorize the variable.
            Recategorized variable will contain multiple leaves. (@test-tree.bins.R#169) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Undeclared package ‘dplR’ in Rd xrefs
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Build_JTree: no visible global function definition for ‘flush.console’
Run_JTree: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs     12.5Mb
Running examples in ‘TreeLS-Ex.R’ failed
The error most likely occurred in:

> ### Name: gpsTimeFilter
> ### Title: Filter points based on gpstime
> ### Aliases: gpsTimeFilter
> 
> ### ** Examples
> 
> file = system.file("extdata", "model_boles.laz", package="TreeLS")
> tls = readTLS(file)
Error: Invalid data: gpstime contains some NAs
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for ‘hist’
plot.treeperm: no visible global function definition for ‘points’
plot.treeperm: no visible global function definition for ‘text’
treeperm.formula: no visible global function definition for
  ‘model.frame’
treeperm.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Undeclared packages ‘strucchange’, ‘Kendall’, ‘psych’ in Rd xrefs
installed size is 141.1Mb
  sub-directories of 1Mb or more:
    doc     3.8Mb
    libs  136.3Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par qtnorm quantile rug
  title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Undeclared package ‘akima’ in Rd xrefs
Running ‘spelling.R’
  Running ‘testthat.R’ [38s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trip)
  > 
  > test_check("trip")
  ── 1. Failure: speedfilter and sdafilter works (@test-algos.R#23)  ─────────────
  `sda(tr, smax = 1000, pre = filt1)` produced warnings.
  
  ── 2. Failure: print and show (@test-methods.R#16)  ────────────────────────────
  `{ ... }` produced warnings.
  
  
  Longitudes contain values greater than 180, assuming proj.4 +over
  
  
  
  
   Data fully validated: returning object of class  trip 
  ── 3. Failure: trip works (@test-trip.R#40)  ───────────────────────────────────
  `sp::spTransform(walrus818[1:100, ], "+proj=laea +datum=WGS84")` produced warnings.
  
  ── 4. Failure: plot works (@test-trip.R#52)  ───────────────────────────────────
  `{ ... }` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 125 | SKIPPED: 0 | WARNINGS: 113 | FAILED: 4 ]
  1. Failure: speedfilter and sdafilter works (@test-algos.R#23) 
  2. Failure: print and show (@test-methods.R#16) 
  3. Failure: trip works (@test-trip.R#40) 
  4. Failure: plot works (@test-trip.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Undeclared package ‘SIBER’ in Rd xrefs
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
DrawMargin: no visible global function definition for ‘qnorm’
DrawProbability: no visible global function definition for ‘pnorm’
Factor: no visible global function definition for ‘new’
Gaussian: no visible global function definition for ‘new’
LikelihoodFactor: no visible global function definition for ‘new’
Parameters: no visible global function definition for ‘new’
Player: no visible global function definition for ‘new’
PriorFactor: no visible global function definition for ‘new’
SumFactor: no visible global function definition for ‘new’
TruncateFactor: no visible global function definition for ‘new’
Variable: no visible global function definition for ‘new’
Vdraw: no visible global function definition for ‘dnorm’
Vdraw: no visible global function definition for ‘pnorm’
Vwin: no visible global function definition for ‘dnorm’
Vwin: no visible global function definition for ‘pnorm’
Wdraw: no visible global function definition for ‘dnorm’
Wdraw: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Undeclared package ‘carData’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
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.
cdens: no visible global function definition for ‘head’
dplot: no visible global function definition for ‘knots’
dplot: no visible global function definition for ‘median’
dplot: no visible global function definition for ‘par’
dplot: no visible global function definition for ‘plot.stepfun’
dplot: no visible global function definition for ‘abline’
edf: no visible global function definition for ‘approxfun’
mctest : rdist: no visible global function definition for ‘runif’
mctest : S: no visible global function definition for ‘optim’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Undeclared packages ‘MTS’, ‘tsbox’, ‘dr’ in Rd xrefs
tfDetails: no visible global function definition for ‘start’
tfDetails: no visible global function definition for ‘end’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘TSSQLite’, ‘TSMySQL’, ‘TSPostgreSQL’ in Rd xrefs
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.7Mb
Undeclared package ‘STPGA’ in Rd xrefs
Undeclared package ‘rugarch’ in Rd xrefs
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
vintageMap: no visible global function definition for ‘read.table’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘frequency’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘frequency’
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for ‘cov’
FAfitStats.TSFmodel: no visible global function definition for ‘cov’
FAfitStats.default: no visible global function definition for ‘cor’
FAfitStats.default: no visible global function definition for
  ‘factanal’
FAfitStats.default: no visible global function definition for ‘pchisq’
FAmodelFitStats: no visible global function definition for ‘pchisq’
checkResiduals.TSFmodel: no visible global function definition for
  ‘cov’
distribution.factorsEstEval: no visible global function definition for
  ‘par’
distribution.factorsEstEval: no visible binding for global variable
  ‘par’
distribution.factorsEstEval: no visible global function definition for
  ‘density’
distribution.factorsEstEval: no visible global function definition for
  ‘matplot’
distribution.factorsEstEval: no visible global function definition for
  ‘title’
summary.TSFmodel: no visible global function definition for ‘start’
summary.TSFmodel: no visible global function definition for ‘end’
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
Func.SAX: no visible global function definition for ‘sd’
Func.SAX: no visible global function definition for ‘qnorm’
Func.matrix: no visible global function definition for ‘qnorm’
Func.motif: no visible global function definition for ‘sd’
Func.motif: no visible global function definition for ‘na.omit’
Func.motif: no visible global function definition for ‘combn’
Func.motif.multivariate: no visible global function definition for
  ‘txtProgressBar’
Func.motif.multivariate: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
dLag : dlag.f: no visible global function definition for
  ‘complete.cases’
distmat: no visible global function definition for ‘dist’
fitCity: no visible global function definition for ‘glm.control’
fitCity: no visible global function definition for ‘terms’
ldmvnorm: no visible global function definition for ‘mahalanobis’
lspline: no visible global function definition for ‘quantile’
plot.tsdecomp: no visible global function definition for ‘par’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.8Mb
GNU make is a SystemRequirements.
Undeclared package ‘tseries’ in Rd xrefs
Malformed Title field: should not end in a period.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘gimms’ in Rd xrefs
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Found the following files/directories:
  ‘XMIwords.txt’
Undeclared package ‘glmnet’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
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'.
TT.GS : TT.GS.sp: no visible global function definition for ‘qt’
TT.GS : TT.GS.sp: no visible global function definition for ‘runif’
TT.GS : TT.GS.sp: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
.saveDevice: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
ttwa: no visible global function definition for ‘aggregate’
ttwa: no visible global function definition for ‘txtProgressBar’
ttwa: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘multcomp’, ‘agricolae’ in Rd xrefs
Undeclared package ‘randomForest’ in Rd xrefs
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Note: found 34 marked Latin-1 strings
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘TwoCop/libs/TwoCop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoPhaseInd/libs/TwoPhaseInd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘debug.txt’
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette rbinom setTxtProgressBar
  txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
GNU make is a SystemRequirements.
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘plotly’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘shinythemes’ ‘zip’
  All declared Imports should be used.
Note: found 162 marked UTF-8 strings
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       23.7Mb
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
Undeclared packages ‘userfriendlyscience’, ‘behaviorchange’, ‘car’ in Rd xrefs
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    libs      3.2Mb
Running ‘testthat.R’ [49s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("UKgrid")
  Loading required package: UKgrid
  ── 1. Failure: Using arguments - tsibble with monthly aggregation, pulling two v
  all(class(x$TIMESTAMP) %in% c("yearmonth", "Date")) not equal to TRUE.
  1 element mismatch
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 13 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: Using arguments - tsibble with monthly aggregation, pulling two variables (@test-obj_class.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    help   3.9Mb
Undeclared package ‘sem’ in Rd xrefs
ubRacing : predCandidate: no visible global function definition for
  ‘predict’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘pchisq’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘qt’
ubRacing : aux.friedman.edit: no visible global function definition for
  ‘wilcox.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘t.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘p.adjust’
ubRacing : idFolds: no visible global function definition for
  ‘quantile’
ubRacing: no visible binding for global variable ‘sd’
ubSmoteExs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for ‘quantile’
uh: no visible global function definition for ‘mad’
uh.bu: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
dudewicz.unif.test: no visible global function definition for ‘runif’
frosini.unif.test: no visible global function definition for ‘runif’
hegazy.unif.test: no visible global function definition for ‘runif’
kolmogorov.unif.test: no visible global function definition for ‘runif’
kuiper.unif.test: no visible global function definition for ‘runif’
neyman.unif.test: no visible global function definition for ‘runif’
quesenberry.unif.test: no visible global function definition for
  ‘runif’
sarkadi.unif.test: no visible global function definition for ‘runif’
sherman.unif.test: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Note: found 548 marked UTF-8 strings
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Undeclared package ‘mirt’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs  13.4Mb
GNU make is a SystemRequirements.
Note: found 4494 marked UTF-8 strings
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Undeclared package ‘tibble’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Undeclared package ‘sampling’ in Rd xrefs
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘httr’ in Rd xrefs
Note: found 488 marked UTF-8 strings
Undeclared package ‘rje’ in Rd xrefs
Package suggested but not available for checking: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
Undeclared package ‘sp’ in Rd xrefs
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000tract/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000tract\").\n")
    cat("Type help(package=\"UScensus2000tract\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MSA.Rd':
  \usage lines wider than 90 characters:
     MSA(msafips = NULL, msaname = NULL, state=NULL , statefips=FALSE, level = c("tract", "blk", "blkgrp"), proj = NULL)

Rd file 'areaPoly.Rd':
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"den00",color = list(fun = "rainbow", attr = list(4)),main="2010 US Counties \n Oregon",type="plot",border=" ... [TRUNCATED]

Rd file 'choropleth.Rd':
  \usage lines wider than 90 characters:
     choropleth(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0.6, 0 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"P0010001",color = list(fun = "rainbow", attr = list(4)),main="2010 Counties \n Oregon",type="plot",border=" ... [TRUNCATED]
     choropleth(oregon.county10,"P0010001",main="2010 Counties \n Oregon",border="transparent",type="spplot")

Rd file 'choropleth.plot.Rd':
  \usage lines wider than 90 characters:
     choropleth.plot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0 ... [TRUNCATED]

Rd file 'choropleth.spplot.Rd':
  \usage lines wider than 90 characters:
     choropleth.spplot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, ... [TRUNCATED]

Rd file 'county.Rd':
  \usage lines wider than 90 characters:
     county(fips = NULL, name = NULL, state, level = c("tract", "blk", "blkgrp"), statefips = FALSE, sp.object=NULL, proj=NULL)

These lines will be truncated in the PDF manual.
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘devtools’ in Rd xrefs
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
Note: found 1 marked UTF-8 string
Malformed Title field: should not end in a period.
Undeclared package ‘dplyr’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
uwham.boot: no visible binding for global variable ‘var’
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/V8.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespaces in Imports field not imported from:
  ‘rstudioapi’ ‘testthat’
  All declared Imports should be used.
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Undeclared package ‘candisc’ in Rd xrefs
Found the following files/directories:
  ‘Output.txt’ ‘Overlap.csv’ ‘Polar coordinates.csv’
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Found the following sources/headers not terminated with a newline:
  inst/include/Algorithm.h
  inst/include/AlgorithmCategorical.h
  inst/include/AlgorithmContinuous.h
  inst/include/AlgorithmInteger.h
  inst/include/AlgorithmMixed.h
  inst/include/Data.h
  inst/include/DataCategorical.h
  inst/include/DataContinuous.h
  inst/include/DataInteger.h
  inst/include/DataMixed.h
  inst/include/Param.h
  inst/include/ParamCategorical.h
  inst/include/ParamContinuous.h
  inst/include/ParamInteger.h
  inst/include/ParamMixed.h
  inst/include/XEM.h
  inst/include/XEMCategorical.h
  inst/include/XEMContinuous.h
  inst/include/XEMInteger.h
  inst/include/XEMMixed.h
  inst/include/XEMPen.h
Some compilers warn on such files.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘matrixcalc’ ‘saemix’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Undeclared package ‘vars’ in Rd xrefs
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘VCA’
Undeclared packages ‘coin’, ‘alr3’, ‘Hmisc’ in Rd xrefs
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘freetypeharfbuzz’
  All declared Imports should be used.
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
DrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Undeclared packages ‘ade4’, ‘cclust’, ‘bipartite’, ‘labdsv’, ‘ellipse’, ‘vegan3d’, ‘coda’, ‘maptools’, ‘ape’, ‘picante’ in Rd xrefs
Undeclared packages ‘mclust’, ‘e1071’ in Rd xrefs
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of 'arg' to
  'args'
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
prepare_Rd: H.Rd:41-42: Dropping empty section \note
prepare_Rd: M.homog.Rd:19-21: Dropping empty section \details
prepare_Rd: M.homog.Rd:35-36: Dropping empty section \note
prepare_Rd: Rel.homog.Rd:24-25: Dropping empty section \note
prepare_Rd: bootstrap.Rd:34: Dropping empty section \note
prepare_Rd: d.Rd:35-36: Dropping empty section \note
prepare_Rd: normalize.rows.Rd:26-27: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:23-24: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:26: Dropping empty section \examples
prepare_Rd: sim.groups.Rd:27-28: Dropping empty section \note
prepare_Rd: sim.table.Rd:25-26: Dropping empty section \note
prepare_Rd: similarity.Rd:25-26: Dropping empty section \note
prepare_Rd: turnover.Rd:17-18: Dropping empty section \details
prepare_Rd: turnover.Rd:29-30: Dropping empty section \note
Undeclared package ‘stringdist’ in Rd xrefs
Note: found 128 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Found the following files/directories:
  ‘Fig3-1_triple_labels_sub_and_superscripts.tiff’
  ‘Fig3-2_Euler_3set_simple_with_subscripts.tiff’
  ‘Pairwise_Venn_diagram.tiff’ ‘Quad_Venn_diagram.tiff’
  ‘Quintuple_Venn_diagram.tiff’ ‘Single_Venn_diagram.tiff’
  ‘Triple_Venn_diagram.tiff’ ‘Venn_2set_complex.tiff’
  ‘Venn_4set_pretty.tiff’ ‘Venn_5set_pretty.tiff’
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by ‘R CMD build’.
Non-standard file/directory found at top level:
  ‘src-java’
plot.VennDiagram : <anonymous>: no visible global function definition
  for ‘hcl’
plot.VennDiagram: no visible global function definition for ‘plot.new’
plot.VennDiagram: no visible global function definition for
  ‘plot.window’
plot.VennDiagram: no visible global function definition for ‘col2rgb’
plot.VennDiagram: no visible global function definition for ‘rgb’
plot.VennDiagram: no visible global function definition for ‘polygon’
plot.VennDiagram: no visible global function definition for ‘text’
plot.VennDiagram: no visible global function definition for ‘title’
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘VFP’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    doc    1.2Mb
    help   2.9Mb
Undeclared packages ‘car’, ‘gam’, ‘lmtest’ in Rd xrefs
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Note: found 60 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘sp’ ‘viridis’
  All declared Imports should be used.
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

These lines will be truncated in the PDF manual.
hyperpara: no visible binding for global variable ‘var’
hyperpara: no visible global function definition for ‘hist’
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
File ‘VIGoR/libs/VIGoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Undeclared packages ‘mvoutlier’, ‘mi’ in Rd xrefs
Note: found 2754 marked UTF-8 strings
Undeclared packages ‘foreach’, ‘copula’ in Rd xrefs
installed size is 50.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.2Mb
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
prepare_Rd: panel.meansdplot.Rd:42-45: Dropping empty section \value
prepare_Rd: panel.meansdplot.Rd:49-51: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:40-42: Dropping empty section \details
prepare_Rd: panel.violinm.Rd:43-49: Dropping empty section \value
prepare_Rd: panel.violinm.Rd:53-55: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:50-52: Dropping empty section \author
prepare_Rd: violinmplot.Rd:34-36: Dropping empty section \details
prepare_Rd: violinmplot.Rd:48-50: Dropping empty section \note
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
viopoints.default: no visible global function definition for ‘par’
viopoints.default: no visible global function definition for ‘plot.new’
viopoints.default: no visible global function definition for
  ‘plot.window’
viopoints.default: no visible global function definition for ‘axis’
viopoints.default: no visible global function definition for ‘arrows’
viopoints.default: no visible global function definition for
  ‘getFromNamespace’
viopoints.default: no visible global function definition for ‘title’
viopoints.default: no visible global function definition for ‘box’
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
Undeclared packages ‘vioplot’, ‘beanplot’, ‘beeswarm’, ‘parviol’ in Rd xrefs
Undeclared package ‘foreach’ in Rd xrefs
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘plyr’ ‘reshape’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘diptest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.0Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ingredients’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glue’ ‘tidyr’
  All declared Imports should be used.
Missing or unexported object: ‘jsonlite::rbind.pages’
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines")
to your NAMESPACE file.
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Found the following significant warnings:
  commonlib.c:857:3: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/volesti.Rcheck/00install.out’ for details.
installed size is 86.9Mb
  sub-directories of 1Mb or more:
    libs  86.6Mb
Note: found 4954 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.