Non-standard file/directory found at top level:
  ‘src-java’
Found the following apparent S3 methods exported but not registered:
  scagnostics.data.frame scagnostics.default scagnostics.list
  scagnostics.matrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
Packages in Depends field not imported from:
  ‘MASS’ ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  predict.scalreg print.scalreg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
lse: no visible global function definition for ‘lm’
predict.scalreg: no visible global function definition for ‘fitted’
slassoEst: no visible global function definition for ‘qnorm’
slassoEst: no visible global function definition for ‘lars’
slassoEst: no visible global function definition for ‘predict.lars’
Undefined global functions or variables:
  fitted lars lm predict.lars qnorm
Consider adding
  importFrom("stats", "fitted", "lm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  ./BGPscan.h:114:5: warning: field 'm_beta_alt' will be initialized after field 'm_inc_idx' [-Wreorder]
  ./USTscan.h:66:5: warning: field 'm_counts' will be initialized after field 'm_num_locs' [-Wreorder]
  ./USTscan.h:71:5: warning: field 'm_zone_lengths' will be initialized after field 'm_store_everything' [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/scanstatistics.Rcheck/00install.out’ for details.
plot.scair: no visible global function definition for ‘par’
plot.scair: no visible global function definition for ‘plot’
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 ‘plot’
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 plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
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.
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.
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.
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’.
futuresplot: no visible global function definition for ‘rainbow’
plot.schwartz2f.fit: no visible global function definition for
  ‘colorRampPalette’
plot.schwartz2f.fit: no visible global function definition for
  ‘rainbow’
plot,schwartz2f.fit-missing: no visible global function definition for
  ‘colorRampPalette’
plot,schwartz2f.fit-missing: no visible global function definition for
  ‘rainbow’
Undefined global functions or variables:
  colorRampPalette rainbow
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
to your NAMESPACE file.
File ‘SciencesPo/libs/SciencesPo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘QUIC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
scio.cv: no visible global function definition for ‘cov’
scio.refit: no visible global function definition for ‘QUIC’
Undefined global functions or variables:
  QUIC cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
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.
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.
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
File ‘scorer/libs/scorer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  calcscore.default calcscore.formula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
bdecomp : <anonymous>: no visible global function definition for ‘var’
betafam: no visible global function definition for ‘integrate’
calcscore.formula: no visible global function definition for
  ‘model.response’
plotscore: no visible binding for global variable ‘plot’
plotscore: no visible global function definition for ‘lines’
Undefined global functions or variables:
  integrate lines model.response plot var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "model.response", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  SK.aov SK.aovlist SK.default SK.nest SK.nest.aov SK.nest.aov
  SK.nest.aovlist SK.nest.aovlist SK.nest.default SK.nest.default
  plot.SK summary.SK summary.SK.nest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.SK: no visible global function definition for ‘plot’
plot.SK: no visible global function definition for ‘segments’
plot.SK: no visible global function definition for ‘axis’
plot.SK: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext plot segments
Consider adding
  importFrom("graphics", "axis", "mtext", "plot", "segments")
to your NAMESPACE file.
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.
Found the following apparent S3 methods exported but not registered:
  WW.default print.WW
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Newsboy: no visible global function definition for ‘qnorm’
Newsboy: no visible global function definition for ‘dnorm’
Newsboy: no visible global function definition for ‘pnorm’
SCperf: no visible global function definition for ‘ARMAtoMA’
SCperf: no visible global function definition for ‘qnorm’
SSL: no visible global function definition for ‘qnorm’
SSL: no visible global function definition for ‘ARMAtoMA’
Undefined global functions or variables:
  ARMAtoMA dnorm pnorm qnorm
Consider adding
  importFrom("stats", "ARMAtoMA", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file.
Rd file 'WW.Rd':
  \examples lines wider than 100 characters:
     #  couple of months, when the winter season will be under way. However, this would necessitate holding

These lines will be truncated in the PDF manual.
License components which are templates and need '+ file LICENSE':
  MIT License
'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.
'library' or 'require' calls in package code:
  ‘MASS’ ‘oligoClasses’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following calls to attach():
File ‘scriptests/R/source.pkg.R’:
  attach(NULL, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
  attach(envir, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
See section ‘Good practice’ in ‘?attach’.
Files which contain pragma(s) suppressing diagnostics:
  ‘src/scrm/macros.h’ ‘src/scrm/model.h’
File ‘scrypt/libs/scrypt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘scs/libs/scs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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
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.
Error in re-building vignettes:
  ...
Loading required package: sp
sdm 1.0-41 (2017-07-26)
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-6 
Loading required package: dismo
Loading required package: mgcv
Quitting from lines 45-52 (quick_sdm.Rmd) 
Error: processing vignette ‘quick_sdm.Rmd’ failed with diagnostics:
fitFunction cannot be identified!
Execution halted
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SDMTools.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘raster’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘SDMTools/libs/SDMTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘sdnet/libs/sdnet.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.
File ‘sdprisk/libs/sdprisk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘sdwd/libs/sdwd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
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 ‘plot’
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 ‘plot’
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 plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  image.seas.sum plot.interarrival plot.seas.norm plot.seas.sum
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘seas/libs/seas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘NADA’ ‘lubridate’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ‘plot’
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 plot
  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",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
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.
.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.
File ‘seewave/libs/seewave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Segmentor3IsBack.Rcheck/00install.out’ for details.
File ‘Segmentor3IsBack/libs/Segmentor3IsBack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 in package code:
  ‘rgdal’ ‘spdep’ ‘spgrass6’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.use.spgrass6: no visible global function definition for ‘listw2mat’
.use.spgrass6: no visible global function definition for ‘sn2listw’
conprof: no visible global function definition for ‘axis’
conprof: no visible global function definition for ‘lines’
isp: no visible global function definition for ‘combn’
points.SegLocal: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis combn lines listw2mat points sn2listw
Consider adding
  importFrom("graphics", "axis", "lines", "points")
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘seg/libs/seg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
File ‘seismicRoll/libs/seismicRoll.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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_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.
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’
plot.SEL: no visible global function definition for ‘plot’
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 plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  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.
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.
Found the following apparent S3 methods exported but not registered:
  chisqNull.objectiveML print.summaryGOF
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  fitted.spm lines.spm plot.spm predict.spm print.spm residuals.spm
  summary.spm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘datautils’ ‘irlba’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  add.linkinfo check.linkinfo del.linkinfo length.linkinfo
  transform.linkinfo
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
computeKernel: no visible binding for global variable ‘sd’
computeKernel: no visible global function definition for ‘dist’
computeKernel: no visible global function definition for ‘quantile’
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for ‘irlba’
distortions: no visible binding for global variable ‘sd’
distortions: no visible global function definition for ‘dist’
Undefined global functions or variables:
  dist irlba quantile sd
Consider adding
  importFrom("stats", "dist", "quantile", "sd")
to your NAMESPACE file.
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.
'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’
efficiencies.semsfa: no visible global function definition for ‘dnorm’
efficiencies.semsfa: no visible global function definition for ‘pnorm’
fan: no visible global function definition for ‘pnorm’
plot.semsfa: no visible global function definition for ‘hist’
plot.semsfa: no visible global function definition for ‘plot’
plot.semsfa: no visible global function definition for ‘density’
semsfa: no visible global function definition for ‘residuals’
semsfa: no visible global function definition for ‘loess’
semsfa: no visible global function definition for ‘optimize’
semsfa: no visible global function definition for ‘pnorm’
semsfa: no visible binding for global variable ‘sd’
summary.semsfa: no visible global function definition for ‘pt’
summary.semsfa: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  density dnorm hist loess optimize plot pnorm printCoefmat pt
  residuals sd
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "density", "dnorm", "loess", "optimize", "pnorm",
             "printCoefmat", "pt", "residuals", "sd")
to your NAMESPACE file.
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.
.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.
'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.
S3 methods shown with full name in documentation object 'cbind.Simulations':
  ‘cbind.Simulations’

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.
separationplot: no visible global function definition for ‘dev.new’
separationplot: no visible global function definition for ‘pdf’
separationplot: no visible global function definition for ‘par’
separationplot: no visible global function definition for ‘plot’
separationplot: no visible global function definition for ‘title’
separationplot: no visible global function definition for ‘segments’
separationplot: no visible global function definition for ‘rect’
separationplot: no visible global function definition for ‘points’
separationplot: no visible global function definition for ‘lines’
separationplot: no visible global function definition for
  ‘colorRampPalette’
separationplot: no visible global function definition for ‘layout’
separationplot: no visible global function definition for ‘plot.new’
separationplot: no visible global function definition for ‘legend’
separationplot: no visible global function definition for ‘dev.off’
separationplot: no visible global function definition for ‘locator’
sp.categorical: no visible global function definition for ‘dev.new’
sp.categorical: no visible global function definition for ‘pdf’
sp.categorical: no visible global function definition for ‘par’
sp.categorical: no visible global function definition for ‘layout’
sp.categorical: no visible global function definition for ‘plot’
sp.categorical: no visible global function definition for ‘text’
sp.categorical: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  colorRampPalette dev.new dev.off layout legend lines locator par pdf
  plot plot.new points rect segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "pdf")
  importFrom("graphics", "layout", "legend", "lines", "locator", "par",
             "plot", "plot.new", "points", "rect", "segments", "text",
             "title")
to your NAMESPACE file.
Rd file 'sp.categorical.Rd':
  \examples lines wider than 100 characters:
       read.dta("http://www2.lse.ac.uk/dataFiles/geographyAndEnvironment/Replication/Article%20for%20JCR%20(Human%20Rights).dta")

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GammaDist: no visible binding for global variable ‘rgamma’
VEpowerPP: no visible global function definition for ‘qnorm’
applyStopRules: no visible global function definition for ‘qnorm’
finalLogRankTest: no visible global function definition for ‘qnorm’
finalLogRankTest: no visible global function definition for ‘pchisq’
generateDropout: no visible global function definition for ‘rexp’
generateEnrollment: no visible global function definition for ‘rpois’
generateEnrollment: no visible global function definition for ‘runif’
generateInfection: no visible global function definition for ‘rexp’
generateInfection : <anonymous>: no visible global function definition
  for ‘rexp’
getAlphaPerTest: no visible global function definition for ‘uniroot’
getHarmBound: no visible global function definition for ‘dbinom’
getHarmBound: no visible global function definition for ‘write.csv’
getTreatmentAssignment : <anonymous>: no visible global function
  definition for ‘runif’
getTreatmentAssignment: no visible global function definition for
  ‘runif’
simTrial: no visible global function definition for ‘runif’
sumTrialOneTrtArm: no visible global function definition for ‘quantile’
testVE: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  dbinom pchisq qnorm quantile rexp rgamma rpois runif uniroot
  write.csv
Consider adding
  importFrom("stats", "dbinom", "pchisq", "qnorm", "quantile", "rexp",
             "rgamma", "rpois", "runif", "uniroot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
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.
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/seqminer.Rcheck/00install.out’ for details.
plotenz : addmark: no visible global function definition for ‘par’
plotenz : addmark: no visible global function definition for ‘plot’
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 plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "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.
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.
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 calls to attach():
File ‘session/R/session.R’:
  attach(sub("file:", "", i))
See section ‘Good practice’ in ‘?attach’.
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.
'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.
Found the following apparent S3 methods exported but not registered:
  print.extmod print.simpextmod
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
Found the following calls to attach():
File ‘sfsmisc/R/sourceAttach.R’:
  attach(ENV, pos = pos, name = name, warn.conflicts = warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/interprocess/mapped_region.hpp:351:63: warning: result of comparison 'boost::uintmax_t' (aka 'unsigned long') > 18446744073709551615 is always false [-Wtautological-constant-compare]
  ./data/data_set.h:24:31: warning: field 'xpMat_' will be initialized after field 'Y' [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:19:5: warning: field 'scale_' will be initialized after field 'gamma_' [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:26:34: warning: field 'eta_' will be initialized after field 'a_' [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sgd.Rcheck/00install.out’ for details.
File ‘sgd/libs/sgd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
File ‘sglasso/libs/sglasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registration problems:
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$block_dim, 
       args$groupWeights, args$parameterWeights, args$alpha, lambda, 
       idx, algorithm.config)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$block_dim, 
       args$groupWeights, args$parameterWeights, args$alpha, d, 
       lambda.min, lambda.min.rel, algorithm.config)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, data, beta)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$test_data, 
       args$block_dim, args$groupWeights, args$parameterWeights, 
       args$alpha, lambda.list[[task]], algorithm.config)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$test_data, 
       args$block_dim, args$groupWeights, args$parameterWeights, 
       args$alpha, lambda.list[[task]], algorithm.config)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$block_dim, 
       args$groupWeights, args$parameterWeights, algorithm.config)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
coxCrossVal: no visible binding for global variable ‘sd’
error.bars: no visible global function definition for ‘segments’
linCrossVal: no visible binding for global variable ‘sd’
logitCrossVal: no visible binding for global variable ‘sd’
plot.cv.SGL: no visible global function definition for ‘points’
Undefined global functions or variables:
  points sd segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
Rd file 'SGL.Rd':
  \usage lines wider than 90 characters:
     SGL(data, index, type = "linear", maxit = 1000, thresh = 0.001, min.frac = 0.1, nlam = 20, gamma = 0.8, standardize = TRUE, verbose = F ... [TRUNCATED]

Rd file 'cvSGL.Rd':
  \usage lines wider than 90 characters:
     cvSGL(data, index, type = "linear", maxit = 1000, thresh = 0.001, min.frac = 0.05, nlam = 20, gamma = 0.8, nfold = 10, standardize = TR ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.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.
Malformed Description field: should contain one or more complete sentences.
Deprecated license: BSD
Packages in Depends field not imported from:
  ‘Matrix’ ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distLaplacian: no visible global function definition for ‘sparseMatrix’
gmdDeflation: no visible global function definition for ‘rnorm’
laplacian: no visible global function definition for ‘sparseMatrix’
Undefined global functions or variables:
  rnorm sparseMatrix
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
File ‘sGPCA/libs/sGPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
UQnormalize.count: no visible binding for global variable ‘quantile’
plotNScores: no visible global function definition for ‘par’
plotNScores: no visible global function definition for ‘hist’
plotNScores: no visible global function definition for ‘title’
plotScores: no visible global function definition for ‘par’
plotScores: no visible global function definition for ‘hist’
plotScores: no visible global function definition for ‘title’
sgRSEA: no visible binding for global variable ‘sd’
sgRSEA: no visible global function definition for ‘p.adjust’
sgRSEA.mean: no visible binding for global variable ‘sd’
sgRSEA.mean: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
File ‘sharpeRratio/libs/sharpeRratio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
get_selected_names: no visible global function definition for ‘tail’
get_selected_names: no visible global function definition for ‘head’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
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.
.params: no visible binding for global variable ‘URLencode’
.params: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: sysfonts
Loading required package: showtextdb
Quitting from lines 42-58 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'curl'
Execution halted
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.
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.
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 ‘plot’
plot.verify.cv: no visible global function definition for ‘points’
plot.verify.ho: no visible global function definition for ‘plot’
plot.verify.ho: no visible global function definition for ‘points’
plot.verify.loo: no visible global function definition for ‘plot’
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 plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "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.
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 apparent S3 methods exported but not registered:
  [.std c.std plot.std summary.std
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.std: no visible global function definition for ‘rainbow’
plot.std: no visible global function definition for ‘legend’
read.std: no visible global function definition for ‘read.table’
std: no visible global function definition for ‘na.exclude’
Undefined global functions or variables:
  legend na.exclude rainbow read.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend")
  importFrom("stats", "na.exclude")
  importFrom("utils", "read.table")
to your NAMESPACE file.
.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.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.intersect as.data.frame.receiver
  as.data.frame.transmitter plot.intersect plot.receiver
  plot.transmitter print.intersect print.receiver print.transmitter
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.intersect: no visible global function definition for ‘points’
plot.intersect: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘points’
plot.receiver: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘segments’
plot.transmitter: no visible global function definition for ‘points’
plot.transmitter: no visible global function definition for ‘plot’
plot.transmitter: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot points segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
to your NAMESPACE file.
File ‘signalHsmm/libs/signalHsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
'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 ‘plot’
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 plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.simexaft summary.simexaft
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
linearextrapolation: no visible global function definition for ‘coef’
linearextrapolation: no visible global function definition for ‘lm’
plotsimexaft: no visible global function definition for ‘plot’
plotsimexaft: no visible global function definition for ‘lm’
plotsimexaft: no visible global function definition for ‘predict’
plotsimexaft: no visible global function definition for ‘lines’
plotsimexaft: no visible global function definition for ‘points’
plotsimexaft: no visible global function definition for ‘legend’
print.simexaft: no visible global function definition for ‘coef’
quadraticextrapolation: no visible global function definition for
  ‘coef’
quadraticextrapolation: no visible global function definition for ‘lm’
simexaft: no visible global function definition for ‘terms’
simexaft: no visible global function definition for ‘rnorm’
simexaft: no visible binding for global variable ‘var’
simexaft: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef legend lines lm plot pnorm points predict rnorm terms var
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "coef", "lm", "pnorm", "predict", "rnorm", "terms",
             "var")
to your NAMESPACE file.
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.
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.
File ‘simLife/libs/simLife.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.
cumallcausehr: no visible global function definition for ‘integrate’
plotbe: no visible global function definition for ‘plot’
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 ‘plot’
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’
plotnae: no visible global function definition for ‘plot’
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 plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
'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.
Found the following apparent S3 methods exported but not registered:
  pairs.boot
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘simpleboot/R/zzz.R’:
  .onLoad calls:
    require(boot)

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

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of ‘rep’ to ‘replace’
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of ‘rep’ to ‘replace’
S3 methods shown with full name in documentation object 'pairs.boot':
  ‘pairs.boot’

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.
randInitializeWeights: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
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.
Found the following significant warnings:
  expression.cpp:273:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:278:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:283:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:287:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:322:3: warning: field 'depexponent' will be initialized after field 'dependency' [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/simplr.Rcheck/00install.out’ for details.
File ‘simplr/libs/simplr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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 ‘plot’
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 ‘plot’
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 plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
simrel: no visible global function definition for ‘runif’
simrel: no visible global function definition for ‘rnorm’
simrelplot: no visible global function definition for ‘par’
simrelplot: no visible global function definition for ‘layout’
simrelplot: no visible global function definition for ‘devAskNewPage’
simrelplot: no visible global function definition for ‘dev.hold’
simrelplot: no visible global function definition for ‘plot’
simrelplot: no visible global function definition for ‘abline’
simrelplot: no visible global function definition for ‘dev.flush’
simrelplot: no visible global function definition for ‘points’
simrelplot: no visible global function definition for ‘axis’
simrelplot: no visible global function definition for ‘mtext’
simrelplot: no visible global function definition for ‘box’
simrelplot: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cov dev.flush dev.hold devAskNewPage layout mtext par
  plot points rnorm runif
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "box", "layout", "mtext",
             "par", "plot", "points")
  importFrom("stats", "cov", "rnorm", "runif")
to your NAMESPACE file.
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
evalGrids: no visible global function definition for ‘sessionInfo’
meanAndNormCI: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd sessionInfo
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.CorrAn plot.SimAn summary.CorrAn summary.SimAn
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.CorrAn : SAPplot: no visible global function definition for ‘plot’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘title’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.CorrAn: no visible global function definition for ‘dev.new’
plot.SimAn : SAPplot: no visible global function definition for ‘plot’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘title’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.SimAn: no visible global function definition for ‘dev.new’
plot.SimAn: no visible global function definition for ‘points’
plot.SimAn: no visible global function definition for ‘text’
plot.SimAn: no visible global function definition for ‘par’
plot.SimAn: no visible global function definition for ‘plot’
plot.SimAn: no visible global function definition for ‘title’
plot.SimAn: no visible global function definition for ‘axis’
plot.SimAn: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis dev.new mtext par plot points text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "arrows", "axis", "mtext", "par", "plot",
             "points", "text", "title")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.siRSM plot.siRSM.default plot.siRSM.default print.siRSM
  print.siRSM.default print.siRSM.default siRSM.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘sivipm/libs/sivipm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  logLik.PiecewiseLinear logLik.bent_cable
  plot.LocallyWeightedPolynomial plot.PiecewiseLinear plot.SiZer
  predict.PiecewiseLinear predict.bent_cable print.PiecewiseLinear
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
Found the following apparent S3 methods exported but not registered:
  print.summary.skewhypFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
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.
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.
Found the following apparent S3 methods exported but not registered:
  plot.sla print.sla print.summary.sla sla.default summary.sla
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.sla: no visible global function definition for ‘title’
plot.sla: no visible global function definition for ‘abline’
print.sla: no visible global function definition for ‘coef’
sla.default: no visible global function definition for ‘lm’
sla.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
slcestimates: no visible global function definition for ‘par’
slcestimates: no visible global function definition for ‘plot’
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 plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
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.
File ‘slfm/libs/slfm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
File ‘SLOPE/libs/SLOPE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
File ‘smaa/libs/smaa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cvsmac: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘smac/libs/smac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘smam/libs/smam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  fitted.sma
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SMCP.Rcheck/00install.out’ for details.
SMCP : fun: no visible global function definition for ‘cor’
manipulate : fun: no visible global function definition for ‘sd’
sp: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor sd
Consider adding
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
File ‘SMCP/libs/SMCP.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.
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.
em: no visible global function definition for ‘coxph’
em: no visible global function definition for ‘optim’
plotpredictsmcure: no visible global function definition for ‘plot’
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 plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
branching.resample: no visible global function definition for ‘rbinom’
cov.weights: no visible global function definition for ‘var’
inverse.cdf.weights: no visible global function definition for ‘runif’
multinomial.resample: no visible global function definition for ‘runif’
stratified.resample: no visible global function definition for ‘runif’
systematic.resample: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom runif var
Consider adding
  importFrom("stats", "rbinom", "runif", "var")
to your NAMESPACE file.
Rd file 'resampling.Rd':
  \usage lines wider than 90 characters:
     residual.resample(   weights, num.samples = length(weights), engine="R", rrf = "stratified")

These lines will be truncated in the PDF manual.
File ‘smcUtils/libs/smcUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘proxy’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘proxy’ ‘tm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
normalize: no visible binding for global variable ‘sd’
simDic: no visible global function definition for ‘simil’
simDoc: no visible global function definition for ‘simil’
Undefined global functions or variables:
  sd simil
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Rd file 'simDic.Rd':
  \usage lines wider than 90 characters:
     simDic(docMatrix1, docMatrix2, scoreDict, breaks = seq(-1, 1, length = 11), norm = FALSE, method = "cosine", scoreFunc = mean)

These lines will be truncated in the PDF manual.
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 ‘plot’
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 plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "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.
Found the following significant warnings:
  SME.c:70:21: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  SME.c:71:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  SME.c:477:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  SME.c:478:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sme.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘lattice’ ‘splines’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.sme sme.data.frame sme.default sme.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
getRoughnessMatrix: no visible global function definition for ‘ns’
plotSmeDiagnostic: no visible global function definition for ‘layout’
plotSmeDiagnostic: no visible global function definition for ‘plot’
plotSmeModel: no visible global function definition for ‘plot’
plotSmeModel: no visible global function definition for ‘lines’
plotSmeModel: no visible global function definition for ‘col2rgb’
plotSmeModel: no visible global function definition for ‘polygon’
plotSmeModel: no visible global function definition for ‘rgb’
plotSmeRaw: no visible global function definition for ‘xyplot’
plotSmeRaw : <anonymous>: no visible global function definition for
  ‘panel.xyplot’
plotSmeRaw : <anonymous>: no visible global function definition for
  ‘panel.lines’
sme.default: no visible global function definition for ‘ns’
sme.list: no visible binding for global variable ‘ns’
sme.list : <anonymous>: no visible global function definition for ‘ns’
vcov.sme: no visible global function definition for ‘ns’
Undefined global functions or variables:
  col2rgb layout lines ns panel.lines panel.xyplot plot polygon rgb
  xyplot
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "layout", "lines", "plot", "polygon")
to your NAMESPACE file.
File ‘sme/libs/sme.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
File ‘smfsb/libs/smfsb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 in package code:
  ‘MASS’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  disparity.glm disparity.lm summary.treg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
plot.SmithWilsonYieldCurve: no visible global function definition for
  ‘plot’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Warning: items ‘package:smotefamily’ were removed from the search path
Found the following apparent S3 methods exported but not registered:
  pairs.mod plot.glm.diag
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'plot.glm.diag.Rd':
  \usage lines wider than 90 characters:
     plot(x, glmdiag = glm.diag(x), subset = NULL, iden = FALSE, labels = NULL, ret = FALSE, ...)

Rd file 'poi.beta.laplace.Rd':
  \usage lines wider than 90 characters:
     poi.beta.laplace(data, alpha = get.alpha(data), phi = 1, nu = 0.1, beta = seq(from = 0, to = 7, length = 1000))

These lines will be truncated in the PDF manual.
'library' or 'require' calls in package code:
  ‘akima’ ‘misc3d’ ‘rgl’ ‘rpanel’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘sm/libs/sm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
Found the following significant warnings:
  /usr/include/python2.7/unicodeobject.h:534:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:553:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:575:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:593:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:173:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:174:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:175:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SnakeCharmR.Rcheck/00install.out’ for details.
File ‘sna/libs/sna.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
sclust: no visible global function definition for ‘var’
snipEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov quantile var
Consider adding
  importFrom("stats", "cov", "quantile", "var")
to your NAMESPACE file.
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.
File ‘SnowballC/libs/SnowballC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘snowboot/libs/snowboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  [.cluster
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
Error in re-building vignettes:
  ...
Quitting from lines 86-91 (snplist.Rnw) 
Error: processing vignette ‘snplist.Rnw’ failed with diagnostics:
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_91: DBI connect('database=ensembl_mart_91;host=hh-mysql-ens-grch37mart-web;port=4560','ensro',...) failed: Can't connect to MySQL server on 'hh-mysql-ens-grch37mart-web' (111) at /nfs/public/release/ensweb/latest/live/grch37-mart/www_91/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
Execution halted
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.
prepare_Rd: maxsel.rd:27-29: Dropping empty section \details
prepare_Rd: transf.inter.rd:23-25: Dropping empty section \details
MDSplot: no visible global function definition for ‘par’
MDSplot: no visible global function definition for ‘rainbow’
MDSplot: no visible global function definition for ‘plot’
MDSplot: no visible global function definition for ‘pairs’
classCenter : <anonymous>: no visible binding for global variable
  ‘median’
grow.snpRF: no visible global function definition for ‘update’
na.roughfix.data.frame : roughfix: no visible global function
  definition for ‘median’
na.roughfix.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘mad’
plot.margin: no visible global function definition for
  ‘installed.packages’
plot.margin: no visible global function definition for ‘rainbow’
plot.margin: no visible global function definition for ‘plot.default’
plot.snpRF: no visible global function definition for ‘matplot’
tuneSnpRF: no visible global function definition for ‘axis’
varImpPlot: no visible global function definition for ‘par’
varImpPlot: no visible global function definition for ‘dotchart’
varImpPlot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis dotchart installed.packages mad matplot median mtext pairs par
  plot plot.default rainbow update
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "dotchart", "matplot", "mtext", "pairs",
             "par", "plot", "plot.default")
  importFrom("stats", "mad", "median", "update")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
File ‘snpRF/libs/snpRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘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.
Packages in Depends field not imported from:
  ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘Rsamtools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
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.
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.
Packages in Depends field not imported from:
  ‘MASS’ ‘magic’ ‘ppls’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  ‘normalize.vector’
get.hnx.B.initialW: no visible global function definition for ‘adiag’
hclust.wrap: no visible global function definition for ‘hclust’
hclust.wrap: no visible global function definition for ‘dist’
hclust.wrap: no visible global function definition for ‘cutree’
my.normdata.gen: no visible global function definition for ‘mvrnorm’
my.normdata.gen: no visible global function definition for ‘rnorm’
odc.clust: no visible binding for global variable ‘kmeans’
odc.cv: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible global function definition for ‘tr’
odc.optimallambda2: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible binding for global variable ‘sd’
sodc.clust: no visible binding for global variable ‘kmeans’
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.sod_sq3
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
hsvScale: no visible global function definition for ‘hsv’
plotConcentric: no visible global function definition for ‘plot’
plotConcentric: no visible global function definition for ‘points’
plotConcentric: no visible global function definition for ‘legend’
plotPoints: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘polygon’
plotStress: no visible global function definition for ‘points’
Undefined global functions or variables:
  hsv legend plot points polygon
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "plot", "points", "polygon")
to your NAMESPACE file.
File ‘SOD/libs/SOD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
HardKMeansDemo: no visible global function definition for
  ‘graphics.off’
HardKMeansDemo: no visible global function definition for ‘plot’
HardKMeansDemo: no visible global function definition for ‘points’
initializeMeansMatrix: no visible global function definition for
  ‘runif’
initializeMeansMatrix: no visible global function definition for ‘dist’
normalizeMatrix: no visible global function definition for ‘sd’
plotRoughKMeans: no visible global function definition for
  ‘graphics.off’
plotRoughKMeans: no visible global function definition for ‘plot’
plotRoughKMeans: no visible global function definition for ‘points’
Undefined global functions or variables:
  dist graphics.off plot points runif sd
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "plot", "points")
  importFrom("stats", "dist", "runif", "sd")
to your NAMESPACE file.
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.
Packages in Depends field not imported from:
  ‘aqp’ ‘lattice’ ‘methods’ ‘munsell’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  head.profile.data.frame plot.profile.data.frame
  print.profile.data.frame summary.profile.data.frame
  tail.profile.data.frame
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls in package code:
  ‘chemometrics’ ‘spatstat’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.Spectra plot.ken.sto plot.trans predict.SpectraPoints
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘solidearthtide/libs/solidearthtide.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘solid.o’
File ‘solidearthtide/libs/solidearthtide.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.
plot.soma: no visible global function definition for ‘plot’
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
'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.
dfrag: no visible global function definition for ‘qgeom’
dfrag: no visible global function definition for ‘plogis’
dfrag: no visible global function definition for ‘dgeom’
estAbund: no visible global function definition for ‘xtabs’
mmN : <anonymous>: no visible global function definition for ‘uniroot’
pfrag: no visible global function definition for ‘qgeom’
phi.deriv.default: no visible global function definition for
  ‘model.matrix’
phi.deriv.default: no visible binding for global variable ‘sd’
phi.update.default: no visible global function definition for ‘glm’
phi.update.default: no visible binding for global variable
  ‘quasipoisson’
phi.update.default: no visible global function definition for ‘predict’
phi.update.lframe: no visible global function definition for ‘glm’
phi.update.lframe: no visible binding for global variable
  ‘quasipoisson’
phi.update.lframe: no visible global function definition for ‘predict’
pr.y.given.x : <anonymous>: no visible global function definition for
  ‘dpois’
pr.y.given.x : <anonymous> : <anonymous>: no visible global function
  definition for ‘dpois’
pr.y.given.x : <anonymous>: no visible global function definition for
  ‘convolve’
qfrag: no visible global function definition for ‘qgeom’
rfrag: no visible global function definition for ‘qgeom’
simSonic: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  convolve dgeom dpois glm model.matrix plogis predict qgeom
  quasipoisson rpois sd uniroot xtabs
Consider adding
  importFrom("stats", "convolve", "dgeom", "dpois", "glm",
             "model.matrix", "plogis", "predict", "qgeom",
             "quasipoisson", "rpois", "sd", "uniroot", "xtabs")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  ‘terrain.colors’
plot.soo_function: no visible binding for global variable ‘image’
plot.soo_function: no visible binding for global variable ‘contour’
plot3d: no visible global function definition for ‘persp3d’
plot3d: no visible global function definition for ‘terrain.colors’
random_parameters.soo_function: no visible global function definition
  for ‘runif’
random_rotation_matrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘soobench/libs/soobench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘README.markdown’ ‘build_package.sh’ ‘upload.sh’
simdata_contaminated : <anonymous>: no visible global function
  definition for ‘rbinom’
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for ‘runif’
which_min: no visible global function definition for ‘head’
which_min: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
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.
Non-standard files/directories found at top level:
  ‘sandbox’ ‘sos4R-Ex.R’
'library' or 'require' call to ‘rgdal’ 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.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.OmMeasurement as.data.frame.OmObservation
  as.list.OmObservationCollection length.OmObservationCollection
  names.OmMeasurement names.OmObservation names.OmObservationCollection
  plot.SOS plot.SensorML plot.SosObservationOffering
  print.summary.GmlTimePeriod print.summary.OmObservation
  print.summary.OmObservationCollection print.summary.OwsRange
  print.summary.SOS print.summary.SosObservationOffering
  summary.GmlTimePeriod summary.OmObservation
  summary.OmObservationCollection summary.OwsRange summary.SOS
  summary.SosObservationOffering
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
analyzeSP23Design: no visible global function definition for ‘plot’
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 plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
SPA: no visible global function definition for ‘var’
Score.Test.Interact: no visible global function definition for ‘pchisq’
Score.Test.Overall: no visible global function definition for ‘var’
Score.Test.Overall: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
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.
Packages in Depends field not imported from:
  ‘glasso’ ‘limSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for ‘cov’
glasso.miss: no visible global function definition for ‘glasso’
glasso.miss: no visible global function definition for ‘Solve’
space.miss: no visible global function definition for ‘Solve’
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Rd file 'glasso.miss.Rd':
  \examples lines wider than 100 characters:
     data(finStocksCn)  ##data of finance sector of Chinese Stock Market, from January 4th, 2011 to July 26th, 2011

Rd file 'space.miss.Rd':
  \examples lines wider than 100 characters:
     data(finStocksCn)  ##data of finance sector of Chinese Stock Market, from January 4th, 2011 to July 26th, 2011

These lines will be truncated in the PDF manual.
File ‘spaceExt/libs/spaceExt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘Matrix’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘igraph’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'SJ.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     #Fit conditional independence graph at one lambda , using the default basis functions (cubic polynomials).
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

Rd file 'generate.dag.data.Rd':
  \usage lines wider than 90 characters:
     generate.dag.data(g, n, basesd = 1, basemean = 0, bfuns = function(x){cbind(x, x^2, x^3)}, 
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)

Rd file 'spacejam-package.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GenPar: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘colorspace’ ‘picante’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'phy.dotplot.Rd':
  \usage lines wider than 90 characters:
     phy.dotplot(sp.plot, phy, edge.width = 0.2, lab.adj = c(0, 0), tips.adj = c(0.5, 3), tips.cex = 1.0, pch = 21, print.labs = FALSE, outf ... [TRUNCATED]

Rd file 'spacodi.by.nodes.Rd':
  \usage lines wider than 90 characters:
     spacodi.by.nodes(sp.plot, phy, sp.parm = "Bst", obs.only = FALSE, return.all = TRUE, n.rep = 10, method = "1s", parm = NULL, dmat = NUL ... [TRUNCATED]

Rd file 'spacodi.calc.Rd':
  \usage lines wider than 90 characters:
     spacodi.calc(sp.plot, phy = NULL, sp.traits = NULL, all.together = TRUE, prune = TRUE, pairwise = FALSE, ...)

Rd file 'spacodi.permutplot.Rd':
  \usage lines wider than 90 characters:
       spacodi.permutplot(spacodi.permutations, cex=list(pch=1.5, rand=0.1, node=0.5, legend=0.75), transp=0.8, col = list("black", "lightgr ... [TRUNCATED]
       bg = list("white", "lightgray", "black"), all.points = TRUE, add.id = TRUE, sig.plot = TRUE, cut.off = 0.05, envelope = FALSE, outfil ... [TRUNCATED]

Rd file 'spacodi.treeplot.Rd':
  \usage lines wider than 90 characters:
     spacodi.treeplot(spacodi.permutations, phy, cex=list(pch = 1.5, tip = 0.5, legend = 0.75), transp=0.8, sig.plot = TRUE, cut.off = 0.05, ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: sp
loading reproducible     0.1.3
loading quickPlot        0.1.2
loading SpaDES.core      0.1.0
loading SpaDES.tools     0.1.0
loading SpaDES.addins    0.1.0

Default paths for SpaDES directories set to:
  cachePath:  /tmp/RtmpfamZhQ/SpaDES/cache
  inputPath:  /tmp/RtmpfamZhQ/SpaDES/inputs
  modulePath: /tmp/RtmpfamZhQ/SpaDES/modules
  outputPath: /tmp/RtmpfamZhQ/SpaDES/outputs
These can be changed using 'setPaths()'. See '?setPaths'.
Quitting from lines 48-61 (iii-cache.Rmd) 
Error: processing vignette ‘iii-cache.Rmd’ failed with diagnostics:
Some packages required for the simulation are not installed:
    tkrplot
Execution halted
File ‘spaero/libs/spaero.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
plot.spa: no visible global function definition for ‘plot’
plot.spa: no visible global function definition for ‘lines’
plot.spa: no visible global function definition for ‘points’
plot.spa: no visible global function definition for ‘gray’
plot.spa: no visible global function definition for ‘box’
predict.spa: no visible global function definition for ‘fitted’
predict.spa: no visible global function definition for ‘coef’
spa.gcv: no visible global function definition for ‘density’
spa.gcv: no visible global function definition for ‘quantile’
spa.sim: no visible global function definition for ‘runif’
spa.sim: no visible global function definition for ‘rnorm’
spa.sim: no visible global function definition for ‘rbinom’
update.spa: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
Rd file 'predict.spa.Rd':
  \examples lines wider than 100 characters:
     title(switch(attr(dat,"type"),moon="Two Moon Simulated Data",supervised="Supervised Border Simulated set"))

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  plot.HierarchicalSparseCluster plot.HierarchicalSparseCluster.permute
  plot.KMeansSparseCluster plot.KMeansSparseCluster.permute
  print.HierarchicalSparseCluster
  print.HierarchicalSparseCluster.permute print.KMeansSparseCluster
  print.KMeansSparseCluster.permute
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'ColorDendrogram.Rd':
  \usage lines wider than 90 characters:
     ColorDendrogram(hc, y, main = "", branchlength = 0.7, labels = NULL, xlab = NULL, sub = NULL, ylab = "", cex.main = NULL)

Rd file 'HierarchicalSparseCluster.Rd':
  \usage lines wider than 90 characters:
     HierarchicalSparseCluster(x=NULL, dists=NULL,method=c("average","complete", "single","centroid"),
     wbound=NULL,niter=15,dissimilarity=c("squared.distance","absolute.value"), uorth=NULL,silent=FALSE,
  \examples lines wider than 100 characters:
       # faster than   sparsehc <- HierarchicalSparseCluster(x=x,wbound=perm.out$bestw, method="complete")
       sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete", dissimilarity="absolute.value")

Rd file 'HierarchicalSparseCluster.permute.Rd':
  \examples lines wider than 100 characters:
       sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete")

Rd file 'HierarchicalSparseCluster.wrapper.Rd':
  \usage lines wider than 90 characters:
     HierarchicalSparseCluster.wrapper(file,  method=c("average", "complete", "single", "centroid"),
     "single","centroid"),output.cluster.files=TRUE,outputfile.prefix=NULL,maxnumgenes=5000,standardize.arrays=TRUE)

These lines will be truncated in the PDF manual.
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.
File ‘sparc/libs/sparc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘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.
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.
image.matrixBC: no visible global function definition for ‘dev.new’
image.matrixBC: no visible global function definition for ‘image’
image.matrixBC: no visible global function definition for ‘heat.colors’
image.matrixBC: no visible global function definition for ‘axis’
image.matrixBC: no visible global function definition for ‘title’
image.sparseBC: no visible global function definition for ‘dev.new’
image.sparseBC: no visible global function definition for ‘image’
image.sparseBC: no visible global function definition for ‘heat.colors’
image.sparseBC: no visible global function definition for ‘axis’
image.sparseBC: no visible global function definition for ‘tail’
image.sparseBC: no visible global function definition for ‘title’
matrixBC: no visible global function definition for ‘kmeans’
sparseBC: no visible global function definition for ‘kmeans’
sparseBC.choosekr: no visible global function definition for ‘kmeans’
sparseBC.choosekr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  axis dev.new heat.colors image kmeans sd tail title
Consider adding
  importFrom("grDevices", "dev.new", "heat.colors")
  importFrom("graphics", "axis", "image", "title")
  importFrom("stats", "kmeans", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Unexported object imported by a ':::' call: ‘igraph:::as_graphnel’
  See the note in ?`:::` about the use of this operator.
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.
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.
Found the following apparent S3 methods exported but not registered:
  coef.cv.sparsenet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘sparsenet/libs/sparsenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
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 ‘sparsesvd/libs/sparsesvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘sparseSVM/libs/sparseSVM.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.
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.
Clarketest: no visible global function definition for ‘pbinom’
Clarketest: no visible global function definition for ‘qbinom’
DIC: no visible global function definition for ‘model.matrix’
LogLike: no visible global function definition for ‘model.matrix’
Vuongtest: no visible global function definition for ‘var’
Vuongtest: no visible global function definition for ‘qnorm’
Vuongtest: no visible global function definition for ‘pnorm’
est.sc: no visible global function definition for ‘model.matrix’
gpind: no visible global function definition for ‘rgamma’
nbind: no visible global function definition for ‘rgamma’
poiind: no visible global function definition for ‘rgamma’
zigpind: no visible global function definition for ‘rbinom’
zigpind: no visible global function definition for ‘rgamma’
zipind: no visible global function definition for ‘rbinom’
zipind: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  model.matrix pbinom pnorm qbinom qnorm rbinom rgamma var
Consider adding
  importFrom("stats", "model.matrix", "pbinom", "pnorm", "qbinom",
             "qnorm", "rbinom", "rgamma", "var")
to your NAMESPACE file.
Rd file 'est.sc.Rd':
  \examples lines wider than 100 characters:
     # gamma.true = vector of spatial effects according to the CAR model with mean 0, psi = 3 and sigma = 1
     nb <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="NB", sim.gmat, sim.nmat, totalit=10)
     gp <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="GP", sim.gmat, sim.nmat, totalit=10)
     zip <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="ZIP", sim.gmat, sim.nmat, totalit=10)
     zigp <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="ZIGP", sim.gmat, sim.nmat, totalit=10)
     Vuong.poi.nb <- Vuongtest(ll.poi, ll.nb, alpha = 0.05, p = DIC.poi$p.D, q = DIC.nb$p.D, correction = TRUE)
     Vuong.poi.gp <- Vuongtest(ll.poi, ll.gp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.gp$p.D, correction = TRUE)
     Vuong.poi.zip <- Vuongtest(ll.poi, ll.zip, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zip$p.D, correction = TRUE)
     Vuong.poi.zigp <- Vuongtest(ll.poi, ll.zigp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zigp$p.D, correction = TRUE)
     Clarke.poi.nb <- Clarketest(ll.poi, ll.nb, alpha = 0.05, p = DIC.poi$p.D, q = DIC.nb$p.D, correction = TRUE)
     Clarke.poi.gp <- Clarketest(ll.poi, ll.gp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.gp$p.D, correction = TRUE)
     Clarke.poi.zip <- Clarketest(ll.poi, ll.zip, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zip$p.D, correction = TRUE)
     Clarke.poi.zigp <- Clarketest(ll.poi, ll.zigp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zigp$p.D, correction = TRUE)

These lines will be truncated in the PDF manual.
File ‘spatcounts/libs/spatcounts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
File ‘SpatialEpi/libs/SpatialEpi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
gev.impute: no visible global function definition for ‘rnorm’
gev.init: no visible global function definition for ‘rbinom’
gev.init: no visible global function definition for ‘var’
gev.init: no visible global function definition for ‘optimize’
gev.logscore: no visible global function definition for ‘density’
gev.logscore: no visible global function definition for ‘splinefun’
gev.update.M: no visible global function definition for ‘runif’
gev.update.hyper: no visible global function definition for ‘rgamma’
gev.update.lambda: no visible global function definition for ‘rnorm’
gev.update.lambda: no visible global function definition for ‘dgamma’
gev.update.lambda: no visible global function definition for ‘dnorm’
gev.update.lambda: no visible global function definition for ‘runif’
gev.update.tau.kappa: no visible global function definition for ‘rnorm’
gev.update.tau.kappa: no visible global function definition for ‘dnorm’
gev.update.tau.kappa: no visible global function definition for ‘runif’
gev.update.tau.mu: no visible global function definition for ‘rnorm’
gev.update.tau.mu: no visible global function definition for ‘dnorm’
gev.update.tau.mu: no visible global function definition for ‘runif’
gev.update.tau.xi: no visible global function definition for ‘rnorm’
gev.update.tau.xi: no visible global function definition for ‘dnorm’
gev.update.tau.xi: no visible global function definition for ‘runif’
gev.update.theta: no visible global function definition for ‘rnorm’
gp.like.lambda: no visible global function definition for ‘dgamma’
Undefined global functions or variables:
  density dgamma dnorm optimize rbinom rgamma rnorm runif splinefun var
Consider adding
  importFrom("stats", "density", "dgamma", "dnorm", "optimize", "rbinom",
             "rgamma", "rnorm", "runif", "splinefun", "var")
to your NAMESPACE file.
codisp: no visible global function definition for ‘complete.cases’
cor.spatial: no visible global function definition for ‘complete.cases’
modified.ttest: no visible global function definition for
  ‘complete.cases’
modified.ttest: no visible global function definition for ‘cor’
plot.codisp: no visible global function definition for ‘plot’
plot.codisp: no visible global function definition for ‘title’
Undefined global functions or variables:
  complete.cases cor plot title
Consider adding
  importFrom("graphics", "plot", "title")
  importFrom("stats", "complete.cases", "cor")
to your NAMESPACE file.
I2BR: no visible global function definition for ‘pnorm’
I2SmD2: no visible global function definition for ‘pnorm’
IBR: no visible global function definition for ‘pnorm’
ISmD2: no visible global function definition for ‘pnorm’
MestimatorBR: no visible global function definition for ‘optim’
MestimatorSmith: no visible global function definition for ‘optim’
psidotBR: no visible global function definition for ‘dnorm’
psidotBR: no visible global function definition for ‘pnorm’
psidotSmD2: no visible global function definition for ‘dnorm’
psidotSmD2: no visible global function definition for ‘pnorm’
tailBRInt: no visible global function definition for ‘pnorm’
tailSmithInt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm optim pnorm
Consider adding
  importFrom("stats", "dnorm", "optim", "pnorm")
to your NAMESPACE file.
File ‘spatialTailDep/libs/spatialTailDep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bbox_to_SpatialPolygons: no visible global function definition for
  ‘CRS’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘Polygon’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘Polygons’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘SpatialPolygons’
list.raster.files: no visible global function definition for ‘CRS’
list.raster.files: no visible global function definition for
  ‘spTransform’
list.raster.files: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
list.raster.files: no visible global function definition for ‘spChFIDs’
predict_rasterEngine : predict.rasterEngine_function: no visible global
  function definition for ‘complete.cases’
projectRaster_rigorous : chunk_function: no visible global function
  definition for ‘spTransform’
projectRaster_rigorous : chunk_function: no visible global function
  definition for ‘CRS’
spatial_sync_raster: no visible global function definition for ‘bbox’
spatial_sync_vector: no visible global function definition for
  ‘spTransform’
spatial_sync_vector: no visible global function definition for ‘CRS’
Undefined global functions or variables:
  CRS Polygon Polygons SpatialPolygons SpatialPolygonsDataFrame bbox
  complete.cases spChFIDs spTransform
Consider adding
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
File ‘SpatialTools/libs/SpatialTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
Non-standard file/directory found at top level:
  ‘Rd_examples’
File ‘SpatioTemporal/libs/SpatioTemporal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  print.summary.specificity summary.specificity
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
randomCorrelations: no visible global function definition for ‘cor’
specGlm : <anonymous>: no visible global function definition for ‘coef’
specLm : <anonymous>: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
Missing or unexported objects:
  ‘ChemoSpec::readJDX’ ‘hyperSpec::spc.NA.linapprox’
Running examples in ‘specmine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: impute_nas_linapprox
> ### Title: Impute missing values with linear approximation
> ### Aliases: impute_nas_linapprox
> ### Keywords: missing values
> 
> ### ** Examples
> 
>   ## Example of NA imputation with linear approximation
>   data(propolis)
>   dataset = impute_nas_linapprox(propolis)
Error: 'spc.NA.linapprox' is not an exported object from 'namespace:hyperSpec'
Execution halted
File ‘spectral/libs/spectral.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
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.
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 apparent S3 methods exported but not registered:
  summary.sphet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘spikeSlabGAM/libs/spikeSlabGAM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘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.
'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.
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.
NoSep: no visible global function definition for ‘setNames’
Reshape: no visible global function definition for ‘setNames’
Reshape: no visible global function definition for ‘reshape’
read.concat: no visible global function definition for ‘count.fields’
read.concat: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  count.fields read.table reshape setNames
Consider adding
  importFrom("stats", "reshape", "setNames")
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  coef.sgpls coef.spls coef.splsda plot.spls predict.sgpls predict.spls
  predict.splsda print.sgpls print.spls print.splsda
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
Found the following apparent S3 methods exported but not registered:
  all.equal.list all.equal.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 49-57 (fmri_processing_spm12r.Rmd) 
Error: processing vignette ‘fmri_processing_spm12r.Rmd’ failed with diagnostics:
non-character argument
Execution halted
File ‘spMC/libs/spMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
plotor: no visible global function definition for ‘plot’
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 plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  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
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
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.
Found the following apparent S3 methods exported but not registered:
  coef.Lifedata.MLE coef.deglmx.MLE logLik.Lifedata.MLE plot.MICsplines
  print.Lifedata.MLE print.deglmx print.summary.Lifedata.MLE sqrt.mat
  summary.Lifedata.MLE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Registered S3 methods from standard package(s) overwritten by 'sprint':
  method            from   
  print.pam         cluster
  print.summary.pam cluster
  summary.pam       cluster
'library' or 'require' call to ‘RankProd’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
pRP: no visible global function definition for ‘plotRP’
pRPadvance: no visible global function definition for ‘plotRP’
pboot: no visible global function definition for ‘runif’
prandomForest.formula: no visible binding for global variable ‘na.fail’
prandomForest.formula: no visible global function definition for
  ‘model.response’
prandomForest.formula: no visible global function definition for
  ‘model.frame’
prandomForest.formula: no visible global function definition for
  ‘terms’
prandomForest.formula: no visible global function definition for
  ‘reformulate’
Undefined global functions or variables:
  model.frame model.response na.fail plotRP reformulate runif terms
Consider adding
  importFrom("stats", "model.frame", "model.response", "na.fail",
             "reformulate", "runif", "terms")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘sprint/libs/sprint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 '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 ‘plot’
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 plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
fssa20: no visible global function definition for ‘runif’
fssa2d: no visible global function definition for ‘runif’
fssa30: no visible global function definition for ‘runif’
fssa3d: no visible global function definition for ‘runif’
ssa20: no visible global function definition for ‘runif’
ssa2d: no visible global function definition for ‘runif’
ssa30: no visible global function definition for ‘runif’
ssa3d: no visible global function definition for ‘runif’
ssi20: no visible global function definition for ‘runif’
ssi2d: no visible global function definition for ‘runif’
ssi30: no visible global function definition for ‘runif’
ssi3d: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Rd file 'fssa30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssa3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,1)-neighborhood")

Rd file 'fssi30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssi3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,1)-neighborhood")

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
plotThin: no visible global function definition for ‘par’
plotThin: no visible global function definition for ‘dev.interactive’
plotThin: no visible global function definition for ‘plot’
plotThin: no visible global function definition for ‘hist’
thin: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  chaos.default chaos.spt chaos.st plot.spt plot.st print.spt print.st
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.GameSPT: no visible global function definition for ‘runif’
.GameSPT: no visible global function definition for ‘points’
.GameST: no visible global function definition for ‘runif’
.GameST: no visible global function definition for ‘points’
.arc: no visible global function definition for ‘lines’
.ptpedal: no visible global function definition for ‘polygon’
.sptpedal2: no visible global function definition for ‘segments’
.sptpedal3: no visible global function definition for ‘polygon’
.sptpedal4: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘plot’
chaos.spt: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘runif’
chaos.spt: no visible global function definition for ‘points’
chaos.st: no visible global function definition for ‘plot’
chaos.st: no visible global function definition for ‘polygon’
chaos.st: no visible global function definition for ‘runif’
chaos.st: no visible global function definition for ‘points’
plot.spt: no visible global function definition for ‘plot’
plot.spt: no visible global function definition for ‘polygon’
plot.st: no visible global function definition for ‘plot’
plot.st: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  lines plot points polygon runif segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon",
             "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  mean.transectHolder mean.trapTransect print.transectHolder
  print.trapTransect simulate.transectHolder
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
CMCSimulation: no visible global function definition for ‘rexp’
CMCSimulation: no visible global function definition for ‘plot’
CMCSimulation: no visible global function definition for ‘axis’
booking_clerkMC: no visible global function definition for ‘runif’
booking_clerkMC: no visible global function definition for ‘rexp’
fixedpoint_show: no visible global function definition for ‘plot’
fixedpoint_show: no visible global function definition for ‘lines’
mean.trapTransect: no visible global function definition for
  ‘weighted.mean’
newtonraphson_show: no visible global function definition for ‘plot’
newtonraphson_show: no visible global function definition for ‘lines’
print.transectHolder: no visible global function definition for ‘str’
print.trapTransect: no visible global function definition for ‘str’
sd.transectHolder: no visible global function definition for ‘sd’
simulate.transectHolder: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  axis lines plot rexp runif sd str weighted.mean
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "rexp", "runif", "sd", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
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.
'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.
plot.srafit: no visible global function definition for ‘layout’
plot.srafit: no visible global function definition for ‘par’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘dnorm’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘pnorm’
sraData : vartruncGauss: no visible global function definition for
  ‘uniroot’
sraPlotMean: no visible global function definition for ‘axis’
sraPlotMean: no visible global function definition for ‘points’
sraPlotMean: no visible global function definition for ‘lines’
sraPlotMeanResid: no visible global function definition for ‘axis’
sraPlotMeanResid: no visible global function definition for ‘abline’
sraPlotMeanResid: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘axis’
sraPlotVar: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘lines’
sraPlotVarResid: no visible global function definition for ‘axis’
sraPlotVarResid: no visible global function definition for ‘abline’
sraPlotVarResid: no visible global function definition for ‘points’
sraPlotlegend: no visible global function definition for ‘legend’
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for ‘rnorm’
sraStartingvalues: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
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 ‘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.
File ‘ssa/libs/ssa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Quitting from lines 37-40 (SSDM.Rmd) 
Error: processing vignette ‘SSDM.Rmd’ failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Execution halted
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
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.
sslCoTrain: no visible global function definition for ‘predict’
sslSelfTrain: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘SSL/libs/SSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  coef.heckit5rob coef.heckitrob fitted.heckit5rob fitted.heckitrob
  print.heckit5rob print.heckitrob print.summary.heckit5rob
  print.summary.heckitrob residuals.heckit5rob residuals.heckitrob
  summary.heckit5rob summary.heckitrob vcov.heckit5rob vcov.heckitrob
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘SSN-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: importSSN
> ### Title: Import an object of class SpatialStreamNetwork
> ### Aliases: importSSN
> 
> ### ** Examples
> 
> 
> library(SSN)
> # Create a SpatialStreamNetwork object that does not contain prediction points
> mf04 <- importSSN(system.file("lsndata/MiddleFork04.ssn", 
+ 	package = "SSN"), o.write = TRUE)
Error in createBinaryID(ssn, o.write = o.write) : object 'mm' not found
Calls: importSSN -> createBinaryID
Execution halted
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.
calcgroup : probtotrating: no visible global function definition for
  ‘convolve’
enterratdata: no visible global function definition for ‘edit’
gplot.SSrat: no visible global function definition for ‘par’
gplot.SSrat: no visible global function definition for ‘plot’
gplot.SSrat: no visible global function definition for ‘legend’
Undefined global functions or variables:
  convolve edit legend par plot
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "convolve")
  importFrom("utils", "edit")
to your NAMESPACE file.
SS.ID: no visible global function definition for ‘var’
SS.sim.chol: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
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.
File ‘stable/libs/stable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.ls.objects: no visible binding for global variable ‘object.size’
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
.expandLevels: no visible global function definition for ‘na.omit’
.ffStack: no visible global function definition for ‘na.omit’
.ffffStack: no visible global function definition for ‘na.omit’
Stack : <anonymous>: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-data.frame: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-ffdf: no visible global function definition for ‘na.omit’
ffStack,ffdf-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.
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 ‘plot’
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 ‘plot’
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 plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
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.

Found the following calls to attach():
File ‘stam/R/stkde.sig.r’:
  attach(samdata)
See section ‘Good practice’ in ‘?attach’.
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.
Error in re-building vignettes:
  ...
Quitting from lines 47-52 (staple_example.Rmd) 
Error: processing vignette ‘staple_example.Rmd’ failed with diagnostics:
incorrect number of dimensions
Execution halted
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.
'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.
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘StatCharrms.tex’ failed.
LaTeX errors:
! Too many }'s.
l.351 ...tion}{Other Endpoints Specification Tab}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! Too many }'s.
l.455 ...oc}{subsection}{Other Endpoints Results}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.##
                   ##..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.####
                     ..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘statcomp/libs/statcomp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  print.corsign
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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 ‘plot’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
auc: no visible global function definition for ‘plot’
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 ‘plot’
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 ‘plot’
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 plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
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.
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.
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.
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘plot’
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 plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  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.
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.
Found the following apparent S3 methods exported but not registered:
  anova.stepplr predict.plr predict.stepplr print.plr print.stepplr
  summary.plr summary.stepplr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cv.step.plr: no visible global function definition for ‘binomial’
cv.step.plr: no visible global function definition for ‘predict’
cv.step.plr: no visible binding for global variable ‘var’
plr: no visible global function definition for ‘binomial’
predict.stepplr: no visible global function definition for ‘predict’
summary.plr: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binomial pnorm predict var
Consider adding
  importFrom("stats", "binomial", "pnorm", "predict", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plr-internal':
  ‘anova.stepplr’ ‘print.plr’ ‘print.stepplr’ ‘summary.plr’
  ‘summary.stepplr’

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

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

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 ‘stepPlr/libs/stepPlr.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘cg_descent.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘_gfortran_stop_string’, possibly from ‘stop’ (Fortran)
    Object: ‘cg_descent.o’
File ‘stepPlr/libs/stepPlr.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.
File ‘stepp/libs/stepp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘stepwise/libs/stepwise.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
d1spectrum: no visible global function definition for ‘fft’
d2spectrum: no visible global function definition for ‘fft’
plot.d1nat: no visible global function definition for ‘plot’
plot.d1nat: no visible global function definition for ‘lines’
plot.d1nat: no visible global function definition for ‘legend’
plot.d1nat: no visible global function definition for ‘title’
plot.d1spec: no visible global function definition for ‘plot’
plot.d1spec: no visible global function definition for ‘lines’
plot.d1spec: no visible global function definition for ‘legend’
plot.d1spec: no visible global function definition for ‘title’
plot.d2spec: no visible global function definition for ‘plot’
plot.d2spec: no visible global function definition for ‘lines’
plot.d2spec: no visible global function definition for ‘legend’
plot.d2spec: no visible global function definition for ‘title’
plot.pvalign: no visible global function definition for ‘plot’
plot.pvalign: no visible global function definition for ‘lines’
plot.pvalign: no visible global function definition for ‘legend’
plot.pvalign: no visible global function definition for ‘title’
print.d1nat: no visible global function definition for ‘plot’
print.d1spec: no visible global function definition for ‘plot’
print.d2spec: no visible global function definition for ‘plot’
print.pvalign: no visible global function definition for ‘plot’
utild1bin: no visible global function definition for ‘median’
utild1bin: no visible global function definition for ‘sd’
utild1clean: no visible global function definition for ‘sd’
utild1filt: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Found the following apparent S3 methods exported but not registered:
  na.stinterp.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
na.stinterp.default: no visible global function definition for ‘time’
na.stinterp.default: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpEjeqQv’, resetting
myQQNorm: no visible global function definition for ‘mad’
myQQNorm: no visible global function definition for ‘qnorm’
myQQNorm: no visible global function definition for ‘plot’
myQQNorm: no visible global function definition for ‘matlines’
myQQNorm: no visible global function definition for ‘points’
myQQNorm: no visible global function definition for ‘qqline’
myQQNorm: no visible global function definition for ‘box’
qqnormSim,lm: no visible global function definition for ‘resid’
Undefined global functions or variables:
  box mad matlines plot points qnorm qqline resid
Consider adding
  importFrom("graphics", "box", "matlines", "plot", "points")
  importFrom("stats", "mad", "qnorm", "qqline", "resid")
to your NAMESPACE file.
File ‘StMoSim/libs/StMoSim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
sharpe: no visible global function definition for ‘sd’
sortino: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
File ‘stocks/libs/stocks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 '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.
Namespace with empty importFrom: ‘tcltk2’
DetailOpLines: no visible global function definition for
  ‘tkProgressBar’
DetailOpLines: no visible global function definition for
  ‘setTkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘tkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘setTkProgressBar’
SimHistory: no visible global function definition for ‘tkProgressBar’
SimHistory: no visible global function definition for
  ‘setTkProgressBar’
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
File ‘stosim/libs/stosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘cubature’ ‘deldir’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.devresid plot.gridresid plot.stpp plot.superthin plot.supresid
  plot.tessdev plot.tessresid plot.thinresid print.devresid
  print.gridresid print.stgrid print.stpp print.stwin print.superthin
  print.supresid print.tessdev print.tessresid print.thinresid
  summary.superthin summary.supresid summary.thinresid
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'gridresid.Rd':
  \usage lines wider than 90 characters:
     gridresid(X, cifunction, theta = NULL, lambda = NULL, grid = c(10, 10), gf = NULL, resid = c("raw", "pearson", "inverse"), algthm = c(" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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.
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.
Found the following apparent S3 methods exported but not registered:
  plot.icweib print.icweib
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
HRatio: no visible global function definition for ‘qnorm’
icweib: no visible global function definition for ‘model.frame’
icweib: no visible binding for global variable ‘na.pass’
icweib: no visible global function definition for ‘complete.cases’
icweib: no visible global function definition for ‘model.matrix’
icweib: no visible global function definition for ‘optim’
icweib: no visible global function definition for ‘pchisq’
icweib: no visible global function definition for ‘pnorm’
plot.icweib : getstat: no visible global function definition for
  ‘qnorm’
plot.icweib: no visible global function definition for ‘plot’
plot.icweib: no visible global function definition for ‘lines’
plot.icweib: no visible global function definition for ‘legend’
print.icweib: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘ROAuth’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘stremr/libs/stremr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 which contains pragma(s) suppressing important diagnostics:
  ‘src/icu55/i18n/decNumber.c’
breakpoints.formula: no visible global function definition for
  ‘%dopar%’
breakpoints.formula: no visible binding for global variable ‘i’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
sctest.default: no visible global function definition for ‘tail’
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
PlotHypTree: no visible global function definition for ‘browseURL’
treePValues: no visible global function definition for ‘lm’
treePValues: no visible global function definition for ‘pf’
plot,GBH-ANY: no visible binding for global variable ‘sorted.hyp’
plot,GBH-ANY: no visible binding for global variable ‘pval’
plot,GBH-ANY: no visible binding for global variable ‘group’
plot,GBH-ANY: no visible binding for global variable ‘type’
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
File ‘strum/libs/strum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: 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.
Found the following apparent S3 methods exported but not registered:
  predict.sublasso
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
SubLasso: no visible global function definition for ‘predict’
SubLasso: no visible global function definition for ‘coef’
SubLasso: no visible global function definition for ‘dev.new’
SubLasso: no visible global function definition for ‘cor’
SubLasso: no visible global function definition for ‘boxplot’
predict.sublasso: no visible global function definition for ‘predict’
Undefined global functions or variables:
  boxplot coef cor dev.new predict
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "boxplot")
  importFrom("stats", "coef", "cor", "predict")
to your NAMESPACE file.
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
plotGraph: no visible global function definition for ‘plot’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  RMcrt.cpp:20:83: warning: field 'gdt' will be initialized after field 'unreliable' [-Wreorder]
  RVcrt.cpp:37:97: warning: field 'e' will be initialized after field 'unreliable' [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/subselect.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  predict.subsemble
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
predict.subsemble: no visible global function definition for ‘predict’
predict.subsemble: no visible binding for global variable ‘family’
subsemble: no visible global function definition for ‘gaussian’
subsemble: no visible global function definition for ‘detectCores’
subsemble : .make_Z_l: no visible global function definition for
  ‘parSapply’
subsemble : .make_Z_l: no visible global function definition for
  ‘makeCluster’
subsemble : .make_Z_l: no visible global function definition for
  ‘stopCluster’
subsemble: no visible global function definition for ‘parSapply’
subsemble: no visible global function definition for ‘makeCluster’
subsemble: no visible global function definition for ‘stopCluster’
subsemble: no visible global function definition for ‘predict’
Undefined global functions or variables:
  detectCores family gaussian makeCluster parSapply predict stopCluster
Consider adding
  importFrom("stats", "family", "gaussian", "predict")
to your NAMESPACE file.
'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.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for ‘plot’
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 plot 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", "plot", "segments", "text")
to your NAMESPACE file.
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.plot: no visible global function definition for ‘plot’
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 plot uniroot
Consider adding
  importFrom("graphics", "plot")
  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.
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.
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.
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.
Package which this enhances but not available for checking: ‘gputools’
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.
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.
File ‘SuperRanker/libs/SuperRanker.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SuppDists.Rcheck/00install.out’ for details.
File ‘SuppDists/libs/SuppDists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/copulas-concordance.tex’
   ‘vignettes/surrosurv.tex’
(Is a VignetteBuilder field missing?)
Found the following apparent S3 methods exported but not registered:
  print.SurvAM
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Est.Var.CCH.trueweights: no visible binding for global variable ‘var’
getEstimatesSP: no visible global function definition for ‘quantile’
getEstimatesSP: no visible global function definition for ‘resid’
prepareDataNP: no visible global function definition for
  ‘complete.cases’
prepareDataSP: no visible global function definition for
  ‘complete.cases’
processRawOutput: no visible global function definition for ‘qnorm’
survAM.estimate: no visible global function definition for ‘median’
survAM.estimate: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  complete.cases median qnorm quantile resid sd var
Consider adding
  importFrom("stats", "complete.cases", "median", "qnorm", "quantile",
             "resid", "sd", "var")
to your NAMESPACE file.
File ‘survAccuracyMeasures/libs/survAccuracyMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘plot’
plot.survAUC: no visible global function definition for ‘lines’
plot.survErr: no visible global function definition for ‘plot’
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 plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  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.
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.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/survClip.Rnw’
(Is a VignetteBuilder field missing?)
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 ‘plot’
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 plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
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.
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 ‘plot’
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 plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "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.
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.
betaEst: no visible global function definition for ‘is’
fullKernel: no visible global function definition for ‘is’
halfKernel: no visible global function definition for ‘is’
kernelAuto: no visible global function definition for ‘quantile’
kernelAuto: no visible global function definition for ‘lm’
kernelAuto: no visible global function definition for ‘pnorm’
kernelFixed: no visible global function definition for ‘pnorm’
lastValue: no visible global function definition for ‘pnorm’
nearValue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  is lm pnorm quantile
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "lm", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
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.
Registered S3 method from a standard package overwritten by 'svars':
  method    from
  plot.boot boot
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.
.jgrRun: no visible global function definition for ‘capture.output’
.macDlgList: no visible global function definition for ‘select.list’
.unixDlgForm: no visible global function definition for ‘as’
.unixDlgMessage: no visible global function definition for ‘alarm’
.winDlgList: no visible global function definition for ‘select.list’
dlgForm.textCLI: no visible global function definition for ‘as’
dlgList.textCLI: no visible global function definition for
  ‘select.list’
dlgMessage.textCLI: no visible global function definition for
  ‘select.list’
dlgSave.textCLI: no visible global function definition for
  ‘select.list’
Undefined global functions or variables:
  alarm as capture.output select.list
Consider adding
  importFrom("methods", "as")
  importFrom("utils", "alarm", "capture.output", "select.list")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/svd.Rcheck/00install.out’ for details.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
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.
.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 ‘svmadmm/libs/svmadmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
completion : finalize : <anonymous>: no visible global function
  definition for ‘existsFunction’
listMethods: no visible global function definition for ‘findFunction’
tempvar: no visible global function definition for ‘runif’
Undefined global functions or variables:
  existsFunction findFunction runif
Consider adding
  importFrom("methods", "existsFunction", "findFunction")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘svMisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: toRjson
> ### Title: Convert R object to and from RJSON specification
> ### Aliases: toRjson evalRjson listToJson
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## A complex R object
> Robj <- structure(list(
+ 	a = as.double(c(1:5, 6)),
+ 	LETTERS,
+ 	c = c(c1 = 4.5, c2 = 7.8, c3 = Inf, c4 = -Inf, NA, c6 = NaN),
+ 	c(TRUE, FALSE, NA),
+ 	e = factor(c("a", "b", "a")),
+ 	f = "this is a \"string\"\nwith\tspecial chars",
+ 	g = matrix(rnorm(4), ncol = 2),
+ 	`h&'$@` = data.frame(x = 1:3, y = rnorm(3),
+ 		fact = factor(c("b", "a", "b"))),
+ 	i = Sys.Date(),
+     j = list(1:5, y = "another item")),
+     comment = "My comment\n\"",
+     anAttrib = 1:10,
+     anotherAttrib = list(TRUE, y = 1:4))
> 
> ## Convert to simplest RJSON, without attributes
> Rjson1 <- toRjson(Robj)
> Rjson1
[1] list(c(1., 2., 3., 4., 5., 6.), c("A", "B", "C", "D", "E", "F",                              
[2] "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S",                             
[3] "T", "U", "V", "W", "X", "Y", "Z"), c(4.5, 7.8, Inf, -Inf, NA,                               
[4] NaN), c(TRUE, FALSE, NA), c("a", "b", "a"), "this is a \\"string\\"\\nwith\\tspecial chars", 
[5]     c(-0.626453810742332, 0.183643324222082, -0.835628612410047,                             
[6]     1.59528080213779), list(seq(1, 3), c(0.329507771815361, -0.820468384118015,              
[7]     0.487429052428485), c("b", "a", "b")), "2018-01-10", list(                               
[8]         seq(1, 5), "another item"))                                                          
> evalRjson(Rjson1)
Error in .getClassesFromCache(Class) : 
  class should be either a character-string name or a class definition
Calls: evalRjson ... new -> getClass -> getClassDef -> .getClassesFromCache
Execution halted
Package in Depends field not imported from: ‘kernlab’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'svmmajcrossval.Rd':
  \usage lines wider than 90 characters:
     svmmajcrossval(X,y,search.grid=list(lambda=2^seq(5,-5,length.out=19)),...,convergence=1e-4, 
                       weights.obs=1, check.positive = TRUE, print.progress=FALSE, ngroup = 5, groups = NULL)

These lines will be truncated in the PDF manual.
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.
processSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
completeCol: no visible global function definition for ‘colors’
completeCol: no visible global function definition for ‘col2rgb’
completeCol: no visible global function definition for ‘palette’
Undefined global functions or variables:
  col2rgb colors palette
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "palette")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  ‘str’
createLog: no visible global function definition for ‘sessionInfo’
protocol_junit.svSuiteData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svSuiteData: no visible global function definition for
  ‘addChildren’
protocol_junit.svSuiteData: no visible global function definition for
  ‘saveXML’
protocol_junit.svTestData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svTestData: no visible global function definition for
  ‘addChildren’
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
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 ‘plot’
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 plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  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.
File ‘SwarmSVM/libs/SwarmSVM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
readSWAT: no visible global function definition for ‘read.fortran’
runSWAT2005: no visible global function definition for ‘read.fortran’
runSWAT2009: no visible global function definition for ‘read.fortran’
runSWAT2012: no visible global function definition for ‘read.fortran’
Undefined global functions or variables:
  read.fortran
Consider adding
  importFrom("utils", "read.fortran")
to your NAMESPACE file.
Rd file 'build_swat_basic.Rd':
  \examples lines wider than 100 characters:
     build_swat_basic(dirname="test", iyr="1979", nbyr=13, wsarea=40, elev=200, declat=45, declon=-72, hist_wx=hist_wx) 

Rd file 'readSWAT.Rd':
  \examples lines wider than 100 characters:
       } else { print ("You need to add your file type to this function if it is not output.sub or output.rch")}

These lines will be truncated in the PDF manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
  src/SWAT2005/Makefile
  src/SWAT2005/Makefile.win
  src/SWAT2009/Makefile
  src/SWAT2009/Makefile.win
  src/SWAT2012/Makefile
  src/SWAT2012/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'.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(swirlify)
  > library(swirl)
  
  | Hi! Type swirl() when you are ready to begin.
  
  
  Attaching package: 'swirl'
  
  The following object is masked from 'package:testthat':
  
      skip
  
  > 
  > test_check("swirlify")
  ── 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R
  all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
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.
calc_MW: no visible global function definition for ‘read.table’
cfba_moment: no visible global function definition for ‘median’
cfba_moment: no visible global function definition for ‘write.csv’
cfba_moment_mr: no visible global function definition for ‘median’
cfba_moment_mr: no visible global function definition for ‘write.csv’
cfba_moment_pw: no visible global function definition for ‘median’
cfba_moment_pw: no visible global function definition for ‘write.csv’
readmodel: no visible global function definition for ‘as’
Undefined global functions or variables:
  as median read.table write.csv
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "median")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
FECorr: no visible global function definition for ‘is’
FECorr: no visible global function definition for ‘write.csv’
FECorr: no visible global function definition for ‘aggregate’
FECorr: no visible global function definition for ‘lm’
FECorr: no visible global function definition for ‘nlm’
eFBA_gene: no visible global function definition for ‘is’
eFBA_gene: no visible global function definition for ‘as’
eFBA_rxn : adjustTol: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘as’
findFluxGeneExpr: no visible global function definition for ‘as’
findMDCFlux: no visible global function definition for ‘is’
findMDCFlux: no visible global function definition for ‘as’
gene2Rule: no visible global function definition for ‘is’
Undefined global functions or variables:
  aggregate as is lm nlm write.csv
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "lm", "nlm")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking:
  ‘sylly.de’ ‘sylly.en’ ‘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.
integrate.polynomial : f: no visible global function definition for
  ‘dmvnorm’
Undefined global functions or variables:
  dmvnorm
Found the following apparent S3 methods exported but not registered:
  [.GenMap [.relationshipMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/interprocess/mapped_region.hpp:351:63: warning: result of comparison 'boost::uintmax_t' (aka 'unsigned long') > 18446744073709551615 is always false [-Wtautological-constant-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/synchronicity.Rcheck/00install.out’ for details.
File ‘synchronicity/libs/synchronicity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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.
ProgressBAR: no visible global function definition for ‘txtProgressBar’
ProgressBAR: no visible global function definition for
  ‘setTxtProgressBar’
cor.matrix: no visible global function definition for ‘cor’
cor.matrix.partial: no visible global function definition for ‘cor’
optimal: no visible global function definition for ‘combn’
optimal: no visible global function definition for ‘cor’
Undefined global functions or variables:
  combn cor setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "cor")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'available_ranges.Rd':
  \usage lines wider than 90 characters:
       available_ranges(authority = "ensembl", species = "Homo sapiens", domain = "hgnc_symbol")

Rd file 'synergizer.Rd':
  \usage lines wider than 90 characters:
       synergizer(authority = "ensembl", species = "Homo sapiens", domain = "hgnc_symbol", range = "entrezgene", ids = NULL, file = NULL)
  \examples lines wider than 100 characters:
     symbols.ids <- synergizer( authority = "ensembl", species = "Homo sapiens", domain="affy_hg_u95av2", range="hgnc_symbol",ids=c("1939_at ... [TRUNCATED]
     entrez.ids <- synergizer( authority = "ensembl", species = "Homo sapiens", domain="hgnc_symbol", range="entrezgene",ids=c("snph", "pja1 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

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.
Namespaces with empty importFrom:
  ‘Rcpp’ ‘methods’
File ‘synlik/libs/synlik.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘plot’
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’
plotPR: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘plot’
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 plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
File ‘synthACS/libs/synthACS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 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.
Found the following significant warnings:
  lib_FeasibleMatrix.cpp:53:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:168:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:176:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_sample_kcycle.cpp:141:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/systemicrisk.Rcheck/00install.out’ for details.
.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 apparent S3 methods exported but not registered:
  rbind.tableList rbind.tableMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'rbind.tableList':
  ‘rbind.tableList’

S3 methods shown with full name in documentation object 'rbind.tableMatrix':
  ‘rbind.tableMatrix’

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.
'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.
Found the following apparent S3 methods exported but not registered:
  print.plist
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TCRsink: no visible global function definition for ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
itabplot : <anonymous>: no visible global function definition for
  ‘capture.output’
itabplot: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL capture.output
Consider adding
  importFrom("utils", "browseURL", "capture.output")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.tabu summary.tabu
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tabu: no visible global function definition for ‘image’
plot.tabu: no visible global function definition for ‘gray’
plot.tabu: no visible global function definition for ‘par’
plot.tabu: no visible global function definition for ‘layout’
plot.tabu: no visible global function definition for ‘plot’
Undefined global functions or variables:
  gray image layout par plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image", "layout", "par", "plot")
to your NAMESPACE file.
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.
File ‘tailDepFun/libs/tailDepFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  proj.data proj.dir proj.dir2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
NANOVA.test: no visible global function definition for ‘ecdf’
NANOVA.test2: no visible global function definition for ‘ecdf’
NANOVA.test3: no visible global function definition for ‘ecdf’
fdr.table: no visible global function definition for ‘median’
fdr.table: no visible global function definition for ‘quantile’
gene.classifier1: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  ecdf median quantile write.table
Consider adding
  importFrom("stats", "ecdf", "median", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'NANOVA.test.Rd':
  \usage lines wider than 90 characters:
     NANOVA.test2(data,f1,f2,type,time.course,equal.size=FALSE,B=100,robustify=FALSE,eb=FALSE,df=0)

Rd file 'tanova.Rd':
  \usage lines wider than 90 characters:
     tanova(data, f1, f2, tp, B=100, FDR=0.05,robustify=FALSE, equal.size=FALSE, qt=-1, longitudinal=TRUE, test.type=0,eb=FALSE,df=0)
     gene.classifier1(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, eb=FALSE,qt=-1)
     gene.classifier2(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, time.course, qt=-1,eb=FALSE,df=1)

These lines will be truncated in the PDF manual.
File ‘TAQMNGR/libs/TAQMNGR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  as.matrix.by stack.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
AnalyzeLVZ: no visible global function definition for ‘approx’
ConvP2Vdepthinv: no visible global function definition for ‘approx’
DistSummary: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘par’
Earthplot: no visible global function definition for ‘plot’
Earthplot: no visible global function definition for ‘approx’
Earthplot: no visible global function definition for ‘image’
Earthplot: no visible binding for global variable ‘lines’
FindRoots: no visible global function definition for ‘uniroot’
InterpModel: no visible global function definition for ‘approx’
LinInterp: no visible global function definition for ‘approx’
PolarPlot: no visible binding for global variable ‘plot’
Rayfan: no visible binding for global variable ‘lines’
polaraxis: no visible global function definition for ‘text’
Undefined global functions or variables:
  approx heat.colors image lines par plot text uniroot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "lines", "par", "plot", "text")
  importFrom("stats", "approx", "uniroot")
to your NAMESPACE file.
Rd file 'DistSummary.Rd':
  \usage lines wider than 90 characters:
     DistSummary(delta, h, model, phaselist = 'default', prop = "vp", image.col = heat.colors(500), n = 200, ...)

Rd file 'Rayfan.Rd':
  \usage lines wider than 90 characters:
     Rayfan(phaselist, h, model, deltalist = 1:17 * 20, minp = 0.5, plot = TRUE, add = TRUE, col = rep("black", length(phaselist)), verbose  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  end.TawnyPortfolio start.TawnyPortfolio
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
end.TawnyPortfolio: no visible global function definition for ‘end’
start.TawnyPortfolio: no visible global function definition for ‘start’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
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.
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’
plot.best: no visible global function definition for ‘plot’
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 plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Package suggested but not available for checking: ‘radiomics’
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Found the following apparent S3 methods exported but not registered:
  slice.fun
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'top.fun':
  ‘slice.fun’

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 ‘tcR/libs/tcR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following significant warnings:
  ./CGAL/GMP/Gmpq_type.h:118:11: warning: result of comparison 'unsigned long long' <= 18446744073709551615 is always true [-Wtautological-constant-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TDA.Rcheck/00install.out’ for details.
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.
makeCircles: no visible global function definition for ‘quantile’
targetDiagram: no visible global function definition for ‘as.formula’
targetDiagram: no visible global function definition for ‘modifyList’
targetDiagram: no visible global function definition for ‘extendrange’
tdStats : sdo: no visible global function definition for ‘sd’
tdStats : sdm: no visible global function definition for ‘sd’
tdStats : r2: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.formula cor extendrange modifyList quantile sd
Consider adding
  importFrom("grDevices", "extendrange")
  importFrom("stats", "as.formula", "cor", "quantile", "sd")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
tdt.quad: no visible global function definition for ‘runif’
tdt.rr: no visible global function definition for ‘pf’
tdt.rr: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  pf qbeta runif
Consider adding
  importFrom("stats", "pf", "qbeta", "runif")
to your NAMESPACE file.
File ‘tdthap/libs/tdthap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
E.2SI: no visible binding for global variable ‘var’
E.2SI: no visible global function definition for ‘var’
E.BE: no visible global function definition for ‘var’
E.Beta: no visible global function definition for ‘var’
E.PO: no visible global function definition for ‘var’
E.PPS: no visible global function definition for ‘var’
E.SI: no visible global function definition for ‘var’
E.STPPS: no visible global function definition for ‘var’
E.STSI: no visible global function definition for ‘var’
E.STpiPS: no visible global function definition for ‘var’
E.SY: no visible global function definition for ‘var’
E.WR: no visible global function definition for ‘var’
E.piPS: no visible global function definition for ‘var’
GREG.SI: no visible global function definition for ‘var’
S.BE: no visible global function definition for ‘runif’
S.PO: no visible global function definition for ‘runif’
S.PPS: no visible global function definition for ‘runif’
S.SI: no visible global function definition for ‘runif’
S.STPPS: no visible global function definition for ‘runif’
S.WR: no visible global function definition for ‘rbinom’
S.piPS: no visible global function definition for ‘runif’
p.WR: no visible global function definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.Weights predict.Weights2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TeachNet: no visible global function definition for ‘predict’
createWeights1: no visible global function definition for ‘rnorm’
createWeights2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
File ‘teigen/libs/teigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  $.tensor ^.tensor as.contravariate.character as.covariate.character
  as.tensor.default as.tensor.tensor is.contravariate.character
  is.contravariate.numeric is.contravariate.tensor
  is.covariate.character is.covariate.numeric is.covariate.tensor
  mean.tensor |.tensor
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
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
Found the following apparent S3 methods exported but not registered:
  plot.df_curves plot.dyntermstrc_nss plot.dyntermstrc_param
  plot.dyntermstrc_yields plot.error plot.fwr_curves plot.ir_curve
  plot.s_curves plot.spot_curves plot.spsearch plot.termstrc_cs
  plot.termstrc_nss plot.zeroyields print.couponbonds
  print.dyncouponbonds print.dyntermstrc_nss print.dyntermstrc_yields
  print.summary.dyntermstrc_nss print.summary.dyntermstrc_param
  print.summary.dyntermstrc_yields print.summary.termstrc_cs
  print.summary.termstrc_nss print.termstrc_cs print.termstrc_nss
  print.zeroyields summary.dyntermstrc_nss summary.dyntermstrc_param
  summary.dyntermstrc_yields summary.termstrc_cs summary.termstrc_nss
  summary.zeroyields
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘termstrc/libs/termstrc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Depends: includes the non-default packages:
  ‘grid’ ‘quadprog’ ‘maps’ ‘maptools’ ‘mapdata’ ‘dichromat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘dichromat’ ‘grid’ ‘mapdata’ ‘maps’ ‘maptools’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.tverify tverify.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tesseract.Rcheck/00install.out’ for details.
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.
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.
File which contains pragma(s) suppressing diagnostics:
  ‘inst/include/testthat/vendor/catch.h’
Found the following apparent S3 methods exported but not registered:
  print.tepAssign print.tepBADA print.tepDICA print.tepGPLS
  print.tepGraphs print.tepPLS print.tepPLSCA print.texpoOutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘plot’
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 ‘plot’
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 plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
File ‘textreg/libs/textreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘textreuse/libs/textreuse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘tgcd/libs/tgcd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
Package unavailable to check Rd xrefs: ‘dada2’
Calls with DUP:
   .C("zstat_pathway_perm", as.double(g), as.integer(m), as.integer(length(m)), 
       as.double(aff), as.integer(length(aff)), as.double(thresh), 
       as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)), 
       as.integer(use_sign), as.integer(use_weight), as.integer(strategy), 
       as.integer(nperm), ret_pvalue, DUP = FALSE)
   .C("zstat_perm", as.double(g), as.integer(m), as.integer(length(m)), 
       as.double(aff), as.integer(length(aff)), as.double(thresh), 
       as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)), 
       as.integer(use_sign), as.integer(use_weight), as.integer(strategy), 
       as.integer(nperm), ret_pvalue, DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘thgenetics/libs/thgenetics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘plot’
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 plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "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.
.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.
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').
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.
Found the following significant warnings:
  common.c:121:16: warning: result of comparison of unsigned expression < 0 is always false [-Wtautological-unsigned-zero-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tiff.Rcheck/00install.out’ for details.
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.
Found the following apparent S3 methods exported but not registered:
  plot.tight.clust
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tight.clust: no visible global function definition for ‘hclust’
plot.tight.clust: no visible global function definition for ‘dist’
plot.tight.clust: no visible global function definition for ‘image’
plot.tight.clust: no visible global function definition for
  ‘colorRampPalette’
plot.tight.clust: no visible global function definition for ‘axis’
plot.tight.clust: no visible global function definition for ‘lines’
tight.clust : find.candidates : kmeans.classify: no visible global
  function definition for ‘kmeans’
write.tight.clust: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  axis colorRampPalette dist hclust image kmeans lines write.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "image", "lines")
  importFrom("stats", "dist", "hclust", "kmeans")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'tight.clust.Rd':
  \usage lines wider than 90 characters:
     tight.clust(x, target, k.min, alpha = 0.1, beta = 0.6, top.can = 7, seq.num = 2, resamp.num = 10, samp.p = 0.7, nstart = 1, remain.p =  ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Quitting from lines 675-675 (tikzDevice.Rnw) 
Error: processing vignette ‘tikzDevice.Rnw’ failed with diagnostics:
there is no package called 'formatR'
Execution halted
.viterbiTrainingEmission,contHMM-list-list: no visible global function
  definition for ‘var’
sampleObs,tDist-numeric: no visible global function definition for ‘rt’
Undefined global functions or variables:
  rt var
Consider adding
  importFrom("stats", "rt", "var")
to your NAMESPACE file.
File ‘tileHMM/libs/tileHMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  Warning: working directory was changed to ‘/tmp/RtmpZ1eZ0W’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpZ1eZ0W’, resetting
'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
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TimeMachine.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  density.tm mean.tm print.tm quantile.tm summary.tm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
density.tm: no visible global function definition for ‘density’
mu.mle: no visible global function definition for ‘optimize’
pophistory.tm: no visible binding for global variable ‘quantile’
quantile.tm: no visible global function definition for ‘quantile’
sample.pop: no visible global function definition for ‘runif’
summary.tm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
File ‘TimeMachine/libs/TimeMachine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
generatelatencies: no visible binding for global variable ‘allNames’
generatetimedeltas: no visible global function definition for ‘head’
generatetimedeltas: no visible global function definition for ‘tail’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘head’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘tail’
plotnetworkslices: no visible global function definition for ‘par’
plotnetworkslices: no visible global function definition for ‘text’
plottanet: no visible global function definition for ‘plot’
plottonet: no visible global function definition for ‘plot’
shortesttimepath : <anonymous>: no visible global function definition
  for ‘tail’
Undefined global functions or variables:
  allNames head par plot tail text
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("methods", "allNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'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
Found the following apparent S3 methods exported but not registered:
  [.Event
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
createHstore.ts: no visible global function definition for ‘time’
exploreDb : <anonymous>: no visible global function definition for
  ‘plot’
exportTsList : <anonymous>: no visible global function definition for
  ‘time’
exportTsList: no visible global function definition for ‘write.csv2’
importTsList: no visible global function definition for ‘read.csv2’
importTsList : <anonymous>: no visible global function definition for
  ‘as.ts’
plot.tslist: no visible global function definition for ‘plot’
plot.tslist : <anonymous>: no visible global function definition for
  ‘time’
plot.tslist: no visible global function definition for ‘par’
plot.tslist: no visible global function definition for ‘legend’
readTimeSeries : <anonymous>: no visible global function definition for
  ‘ts’
resolveOverlap: no visible global function definition for ‘is.ts’
resolveOverlap: no visible global function definition for ‘frequency’
resolveOverlap: no visible global function definition for ‘time’
resolveOverlap: no visible global function definition for ‘ts’
storeTimeSeries: no visible binding for global variable ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘time’
zooLikeDateConvert: no visible global function definition for
  ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘cycle’
Undefined global functions or variables:
  as.ts cycle frequency is.ts legend par plot read.csv2 time ts
  write.csv2
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "as.ts", "cycle", "frequency", "is.ts", "time",
             "ts")
  importFrom("utils", "read.csv2", "write.csv2")
to your NAMESPACE file.
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.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
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 plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "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.
File ‘TIMP/libs/TIMP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘timsac/libs/timsac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘ExPosition’ ‘InPosition’ ‘TExPosition’ ‘prettyGraphs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.tepBADA.inference.battery print.tepDICA.inference.battery
  print.tinpoAllBoots print.tinpoBoot print.tinpoBootTests
  print.tinpoComponents print.tinpoLOO print.tinpoOmni
  print.tinpoOutput print.tinpoR2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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 ‘plot’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'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.
Packages in Depends field not imported from:
  ‘rgl’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'par3dsave.Rd':
  \usage lines wider than 90 characters:
     par3dsave(params = c("userMatrix", "scale", "zoom", "FOV"), times = FALSE, dev = rgl.cur())

These lines will be truncated in the PDF 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.
.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
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.
'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.
search_collection: no visible global function definition for
  ‘URLencode’
search_company: no visible global function definition for ‘URLencode’
search_keyword: no visible global function definition for ‘URLencode’
search_list: no visible global function definition for ‘URLencode’
search_movie: no visible global function definition for ‘URLencode’
search_multi: no visible global function definition for ‘URLencode’
search_person: no visible global function definition for ‘URLencode’
search_tv: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
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.
File ‘tmlenet/libs/tmlenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’
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.
File ‘tokenizers/libs/tokenizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘corpus.JSS.papers’
File ‘TopKLists/libs/TopKLists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  river.c:33:9: warning: incompatible pointer types assigning to 'int *' from 'double *' [-Wincompatible-pointer-types]
  river.c:34:9: warning: incompatible pointer types assigning to 'int *' from 'double *' [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/topmodel.Rcheck/00install.out’ for details.
flowlength: no visible global function definition for ‘is’
river: no visible global function definition for ‘is’
sinkfill: no visible global function definition for ‘is’
subcatch: no visible global function definition for ‘is’
topidx: 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').
File ‘topmodel/libs/topmodel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘rmongodb’
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 48-52 (Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd) 
Error: processing vignette ‘Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd’ failed with diagnostics:
'roxygen2' >= 5.0.0 must be installed for this functionality.
Execution halted
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 ‘plot’
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
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
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.
File ‘TP.idm/libs/TP.idm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘TPmsm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.data.frame.survTP
> ### Title: as.data.frame method for a survTP object
> ### Aliases: as.data.frame.survTP
> ### Keywords: manip methods survival
> 
> ### ** Examples
> 
> # Example for the "TPmsm" format
> weiTP <- dgpTP(n=100, corr=1, dist="weibull", dist.par=c(2, 7, 2, 7),
+ model.cens="exponential", cens.par = 6, state2.prob=0.6)
*** invalid %N$ use detected ***
Aborted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tpr.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
DeadReckoning: no visible global function definition for ‘filter’
DeadReckoning: no visible global function definition for ‘approx’
DeadReckoning: no visible global function definition for ‘lm’
Mapper: no visible global function definition for ‘colorRampPalette’
Mapper: no visible global function definition for ‘terrain.colors’
Mapper: no visible global function definition for ‘points’
Mapper: no visible global function definition for ‘axis’
Standardize: no visible global function definition for ‘lm’
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
File ‘TransferEntropy/libs/TransferEntropy.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following significant warnings:
  binaryIO.c:412:9: warning: result of comparison 'uint64_t' (aka 'unsigned long') > 18446744073709551615 is always false [-Wtautological-constant-compare]
  binaryIO.c:667:19: warning: result of comparison 'uint64_t' (aka 'unsigned long') > 18446744073709551615 is always false [-Wtautological-constant-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/treatSens.Rcheck/00install.out’ for details.
File ‘treeclim/libs/treeclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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 ‘plot’
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 plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  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.
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.
Running examples in ‘trib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trib.CoF
> ### Title: 'trib.CoF' gets file name length and returns coeficient of
> ###   friction in bar plot generates global var CF
> ### Aliases: trib.CoF
> 
> ### ** Examples
> 
> setwd(paste(path.package("trib"),"/exdata/tribometer",sep=""))
> trib.CoF(2)
> tribDATA<-trib.CoF(2,DATAOUT = TRUE)
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("trib.CoF", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'trib-Ex.timings': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: <Anonymous> -> file
Execution halted
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.
Found the following apparent S3 methods exported but not registered:
  plot.trifield
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.trifield: no visible global function definition for ‘topo.colors’
plot.trifield: no visible global function definition for ‘plot’
plot.trifield: no visible global function definition for ‘image’
plot.trifield: no visible global function definition for ‘contour’
plot.trifield: no visible global function definition for ‘text’
ternary.legend: no visible global function definition for ‘arrows’
ternary.legend: no visible global function definition for ‘text’
triaxes: no visible global function definition for ‘lines’
tribox: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  arrows contour image lines plot polygon text topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "arrows", "contour", "image", "lines", "plot",
             "polygon", "text")
to your NAMESPACE file.
Rd file 'plot.trifield.Rd':
  \usage lines wider than 90 characters:
     plot(x, contours = TRUE, col = topo.colors(256), lab1 = "A = 0", lab2 = "B = 0", lab3 = "C = 0", tribox = TRUE, axis.lines = TRUE, ...)

Rd file 'ternary.legend.Rd':
  \usage lines wider than 90 characters:
     ternary.legend(x0 = 0.2, y0 = 0.8, radius = 0.1, lab1 = "A", lab2 = "B", lab3 = "C", infl = 1.5, cex = 0.75, length = 0.05, ...)

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘fpc’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.tkm print.tkm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tkm: no visible global function definition for ‘plotcluster’
plot.tkm: no visible global function definition for ‘plot’
plot.tkm: no visible global function definition for ‘points’
plot.tkm: no visible global function definition for ‘lines’
plot.tkm: no visible global function definition for ‘discrcoord’
Undefined global functions or variables:
  discrcoord lines plot plotcluster points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
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 ‘plot’
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 plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘tripack/libs/tripack.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 the following apparent S3 methods exported but not registered:
  Ops.VectorAddr print.VectorAddr update.VectorAddr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TRSbook/libs/TRSbook.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.
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').
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 ‘plot’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  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.
File ‘truncnorm/libs/truncnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘changes’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘locfit’ ‘mgcv’
  Please remove these calls from your code.
':::' calls which should be '::':
  ‘stats:::ARMAacf’ ‘stats:::acf’ ‘stats:::arima’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  fitted.Arima plot.Arima plot.armasubsets predict.TAR rstandard.Arima
  summary.armasubsets tsdiag.Arima tsdiag.TAR
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
dmvnb: no visible global function definition for ‘dbinom’
drvts: no visible global function definition for ‘dnorm’
drvts: no visible global function definition for ‘dbinom’
dsvts: no visible global function definition for ‘dnorm’
rescale: no visible global function definition for ‘qlogis’
rescale: no visible global function definition for ‘plogis’
tslogl: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
Found the following significant warnings:
  ./tsBSS.h:10:22: warning: 'varExx_k' has C-linkage specified, but returns user-defined type 'arma::mat' (aka 'Mat<double>') which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tsBSS.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  print.tsbugs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'ar.bugs.Rd':
  \examples lines wider than 100 characters:
     ar2 <- ar.bugs(y = diff(LH), ar.order = 2, ar.prior = "dunif(-1,1)", var.prior = "dgamma(0.001,0.001)")

Rd file 'rv.bugs.Rd':
  \usage lines wider than 90 characters:
                     rv.tol0.prior = "dgamma(0.000001,0.000001)", rv.eps.prior = "dbeta(1, 100)", 
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

Rd file 'sv.bugs.Rd':
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

These lines will be truncated in the PDF manual.
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.
Package suggested but not available for checking: ‘FinTS’
File ‘tsDyn/libs/tsDyn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘deSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.ami plot.d2 plot.false.nearest print.d2 print.false.nearest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'sim.cont.Rd':
  \examples lines wider than 100 characters:
     rossler.ts <- sim.cont(rossler.syst, start=0, end=650, dt=0.1, start.x=c(0,0,0), parms=c(0.15, 0.2, 10))

These lines will be truncated in the PDF manual.
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.
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.
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.
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’
plot.tsdecomp: no visible global function definition for ‘plot’
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 plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
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.
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.
ttScreening: no visible global function definition for ‘gaussian’
ttScreening: no visible global function definition for ‘glm.control’
ttScreening: no visible global function definition for ‘model.response’
ttScreening: no visible global function definition for ‘is.empty.model’
ttScreening: no visible global function definition for ‘model.matrix’
ttScreening: no visible global function definition for ‘na.omit’
ttScreening: no visible global function definition for ‘terms’
ttScreening: no visible global function definition for ‘capture.output’
ttScreening: no visible global function definition for ‘glm’
ttScreening: no visible binding for global variable ‘gaussian’
ttScreening: no visible global function definition for ‘pt’
ttScreening: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  capture.output gaussian glm glm.control is.empty.model model.matrix
  model.response na.omit p.adjust pt terms
Consider adding
  importFrom("stats", "gaussian", "glm", "glm.control", "is.empty.model",
             "model.matrix", "model.response", "na.omit", "p.adjust",
             "pt", "terms")
  importFrom("utils", "capture.output")
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.
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.
':::' calls which should be '::':
  ‘knitr:::is_html_output’ ‘knitr:::is_latex_output’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  TukeyC.aov TukeyC.aovlist TukeyC.default TukeyC.nest TukeyC.nest.aov
  TukeyC.nest.aov TukeyC.nest.aovlist TukeyC.nest.aovlist
  TukeyC.nest.default TukeyC.nest.default plot.TukeyC summary.TukeyC
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
http.connection: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘gsl’ ‘igraph’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  predict.TuneParetoModel print.TuneParetoClassifier
  print.TuneParetoModel print.TuneParetoResult
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TunePareto/libs/TunePareto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
accelerate: no visible global function definition for ‘modifyList’
boxplot.turbosim: no visible global function definition for ‘par’
boxplot.turbosim: no visible global function definition for ‘axis’
boxplot.turbosim: no visible global function definition for ‘mtext’
dataprof.turbosim: no visible global function definition for ‘quantile’
dataprof.turbosim: no visible global function definition for ‘par’
dataprof.turbosim: no visible global function definition for ‘plot’
dataprof.turbosim: no visible global function definition for ‘lines’
dataprof.turbosim: no visible global function definition for ‘segments’
dataprof.turbosim: no visible global function definition for ‘legend’
line.search: no visible global function definition for ‘optimize’
pairs.turbosim: no visible global function definition for ‘par’
pairs.turbosim: no visible global function definition for ‘plot’
pairs.turbosim: no visible global function definition for ‘legend’
pairs.turbosim: no visible global function definition for ‘axis’
pairs.turbosim: no visible global function definition for ‘title’
pairs.turbosim: no visible global function definition for ‘coef’
pairs.turbosim: no visible global function definition for ‘abline’
pairs.turbosim: no visible global function definition for ‘text’
plot.turbo: no visible global function definition for ‘plot’
plot.turbo: no visible global function definition for ‘lines’
plot.turbo: no visible global function definition for ‘legend’
turboSim: no visible binding for global variable ‘par’
turboem: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  abline axis coef legend lines modifyList mtext optimize par plot
  quantile segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "plot", "segments", "text", "title")
  importFrom("stats", "coef", "optimize", "quantile")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
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 ‘TUWmodel/libs/TUWmodel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
File ‘tweenr/libs/tweenr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 apparent S3 methods exported but not registered:
  print.twoStageGwasPower print.twoStageNull
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
condnorm: no visible global function definition for ‘pnorm’
condnorm: no visible global function definition for ‘dnorm’
find.p.joint: no visible global function definition for ‘integrate’
find.p.joint.alt: no visible global function definition for ‘integrate’
termsInt: no visible global function definition for ‘pnorm’
termsInt.alt: no visible global function definition for ‘pnorm’
twoStageNull: no visible global function definition for ‘qnorm’
twoStageNull: no visible global function definition for ‘optimize’
twoStagePower: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm integrate optimize pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "integrate", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
Rd file 'twoStageGwasPower.Rd':
  \usage lines wider than 90 characters:
     twoStageGwasPower(pD, pG, grr, inheritance = "multiplicative", pi.samples, pi.markers, alpha.marker, n.cases, n.controls)

These lines will be truncated in the PDF manual.
txtacf: no visible binding for global variable ‘na.fail’
txtacf: no visible global function definition for ‘acf’
txtboxplot : <anonymous>: no visible global function definition for
  ‘boxplot.stats’
txtboxplot: no visible global function definition for ‘boxplot.stats’
txtdensity: no visible global function definition for ‘density’
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpGWBYza/treePos/2018_01_10/run’, resetting
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 ‘plot’
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 plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
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.
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.
Rd file 'dataItemExplorer.Rd':
  \usage lines wider than 90 characters:
       apiurl = "http://marketinformation.natgrid.co.uk/MIPIws-public/public/publicwebservice.asmx")

These lines will be truncated in the PDF manual.
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.
Found the following apparent S3 methods exported but not registered:
  predict.uniCox print.uniCoxCVFit print.uniCoxFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
permute.rows: no visible global function definition for ‘runif’
uniCox: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘coxph’
uniCoxCV: no visible binding for global variable ‘var’
Undefined global functions or variables:
  coxph quantile runif var
Consider adding
  importFrom("stats", "quantile", "runif", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.uniCox':
  ‘predict.uniCox’

S3 methods shown with full name in documentation object 'uniCox-internal':
  ‘print.uniCoxCVFit’ ‘print.uniCoxFit’

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 ‘uniCox/libs/uniCox.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
File ‘unsystation/libs/unsystation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  +.census +.count plot.census plot.count plot.preston print.preston
  print.summary.count summary.census summary.count
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  plot.upclassfit print.upclassfit summary.upclassfit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.upclassfit: no visible global function definition for ‘frame’
plot.upclassfit: no visible global function definition for ‘par’
plot.upclassfit: no visible global function definition for ‘axis’
plot.upclassfit: no visible global function definition for ‘matplot’
plot.upclassfit: no visible global function definition for ‘legend’
plot.upclassfit: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
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.
File ‘urltools/libs/urltools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘uroot/libs/uroot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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.
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'.
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'.
'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.
File ‘utf8latex/libs/utf8latex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’
File ‘uuid/libs/uuid.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.
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.
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
File ‘validatejsonr/libs/validatejsonr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
File ‘valuer/libs/valuer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/News.Rmd’
(Is a VignetteBuilder field missing?)
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.
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 ‘plot’
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 plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
File ‘VariABEL/libs/VariABEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘Todo’
Packages in Depends field not imported from:
  ‘MASS’ ‘strucchange’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
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.
File ‘VBLPCM/libs/VBLPCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
cv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘VDA/libs/VDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 ‘plot’
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 ‘plot’
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 ‘plot’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘plot’
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 plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "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.
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.
vsetdiff : <anonymous>: no visible global function definition for
  ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
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.
File ‘vegan/libs/vegan.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘cepin.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘cepin.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘cepin.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.
'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
Undocumented S4 methods:
  generic 'merge_taxa' and siglist 'vegtable,numeric,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
File ‘vertexenum/libs/vertexenum.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.
File ‘VideoComparison/libs/VideoComparison.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
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.
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
Package in Depends field not imported from: ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vioplot: no visible global function definition for ‘quantile’
vioplot: no visible global function definition for ‘median’
vioplot: no visible global function definition for ‘plot.new’
vioplot: no visible global function definition for ‘plot.window’
vioplot: no visible global function definition for ‘axis’
vioplot: no visible global function definition for ‘box’
vioplot: no visible global function definition for ‘polygon’
vioplot: no visible global function definition for ‘lines’
vioplot: no visible global function definition for ‘rect’
vioplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis box lines median plot.new plot.window points polygon quantile
  rect
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "points", "polygon", "rect")
  importFrom("stats", "median", "quantile")
to your NAMESPACE file.
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.
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.
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 ‘plot’
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 plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
RCplot: no visible global function definition for ‘residuals’
RCplot: no visible global function definition for ‘predict’
RCplot: no visible global function definition for ‘par’
RCplot: no visible global function definition for ‘plot.new’
RCplot: no visible global function definition for ‘plot.window’
RCplot: no visible global function definition for ‘strwidth’
RCplot: no visible global function definition for ‘plot’
RCplot: no visible global function definition for ‘abline’
RCplot: no visible global function definition for ‘text’
RCplot: no visible global function definition for ‘mtext’
fitted.vlmc: no visible global function definition for ‘predict’
print.vlmc: no visible global function definition for ‘AIC’
residuals.vlmc: no visible global function definition for ‘predict’
simulate.vlmc: no visible global function definition for ‘runif’
summary.vlmc: no visible global function definition for ‘predict’
vlmc: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  AIC abline mtext par plot plot.new plot.window predict qchisq
  residuals runif strwidth text
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "strwidth", "text")
  importFrom("stats", "AIC", "predict", "qchisq", "residuals", "runif")
to your NAMESPACE file.
File ‘VLMC/libs/VLMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
voss1d: no visible global function definition for ‘approx’
voss1d: no visible global function definition for ‘rnorm’
voss1g: no visible global function definition for ‘dchisq’
voss1g: no visible global function definition for ‘approx’
voss1g: no visible global function definition for ‘rnorm’
voss2d: no visible global function definition for ‘rnorm’
voss2g: no visible global function definition for ‘dchisq’
voss2g: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
add.spread.vowelplot: no visible global function definition for
  ‘points’
add.spread.vowelplot: no visible binding for global variable ‘mtext’
add.spread.vowelplot: no visible global function definition for ‘lines’
add.spread.vowelplot: no visible global function definition for
  ‘prcomp’
add.spread.vowelplot: no visible global function definition for
  ‘arrows’
add.spread.vowelplot: no visible global function definition for
  ‘legend’
add.spread.vowelplot: no visible global function definition for ‘text’
add.vowelplot: no visible global function definition for ‘points’
add.vowelplot: no visible binding for global variable ‘mtext’
add.vowelplot: no visible global function definition for ‘arrows’
add.vowelplot: no visible global function definition for ‘text’
compute.medians: no visible global function definition for ‘median’
compute.sds: no visible global function definition for ‘sd’
load.vowels: no visible global function definition for ‘read.table’
norm.lobanov: no visible global function definition for ‘sd’
vowelplot: no visible global function definition for ‘plot’
vowelplot: no visible global function definition for ‘legend’
vowelplot: no visible global function definition for ‘arrows’
vowelplot: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows legend lines median mtext plot points prcomp read.table sd
  text
Consider adding
  importFrom("graphics", "arrows", "legend", "lines", "mtext", "plot",
             "points", "text")
  importFrom("stats", "median", "prcomp", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘raster’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for ‘quantile’
obj.rec: no visible global function definition for ‘txtProgressBar’
obj.rec: no visible global function definition for ‘setTxtProgressBar’
project: no visible global function definition for ‘aggregate’
raster.proj: no visible global function definition for ‘quantile’
raster.proj: no visible global function definition for ‘rasterFromXYZ’
raster.proj: no visible global function definition for ‘plot.new’
raster.proj: no visible global function definition for ‘plot’
raster.proj: no visible global function definition for ‘legend’
sub.obj: no visible global function definition for ‘aggregate’
sub.obj: no visible global function definition for ‘txtProgressBar’
sub.obj: no visible global function definition for ‘setTxtProgressBar’
surface: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'waffect-package.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 5 individuals, 2 cases, 3 controls, the probab ... [TRUNCATED]
     ## Not run: Simulation of phenotypes in the multiclass case (in this example: 4 individuals and  3 classes, 1 individual in class 1, 2  ... [TRUNCATED]

Rd file 'waffect.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 12 individuals, 7 cases, 5 controls, the proba ... [TRUNCATED]
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=7, label=c(1,0))
     ## Not run: If prob is not specified then a constant vector of probabilities is assumed by default. This is equivalent to simulate phen ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’
File ‘waffect/libs/waffect.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.
summary.whc: no visible global function definition for ‘printCoefmat’
wahc.fit: no visible global function definition for ‘pt’
wahc.fit: no visible global function definition for ‘cor’
whc: no visible global function definition for ‘model.frame’
whc: no visible global function definition for ‘model.matrix’
whc: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
File ‘wand/libs/wand.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpNjn3Q3’, resetting
Examples with CPU or elapsed time > 5s
           user system elapsed
coor.test 8.663  0.016   8.679
Rd file 'p.storage.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

Rd file 'read.results.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]

Rd file 'wasim-package.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  plot.wb
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.wb: no visible global function definition for ‘plot’
plot.wb: no visible global function definition for ‘lines’
power.sum: no visible global function definition for ‘plot’
power.sum: no visible global function definition for ‘lines’
test.data: no visible global function definition for ‘var’
test.data: no visible global function definition for ‘rnorm’
test.data: no visible global function definition for ‘plot’
test.data: no visible global function definition for ‘lines’
wave.band: no visible binding for global variable ‘var’
wave.band: no visible global function definition for ‘pnorm’
wave.band: no visible global function definition for ‘qnorm’
wave.band: no visible global function definition for ‘plot’
wave.band: no visible global function definition for ‘lines’
wb.johnson.lims: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  lines plot pnorm qnorm rnorm var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
File ‘waveband/libs/waveband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  plot.wvd summary.wvd
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'FWaveD.Rd':
  \usage lines wider than 90 characters:
     FWaveD(y, g = 1, L = 3, deg = 3, F = (log2(length(y)) - 1), thr = rep(0, log2(length(y))), SOFT = FALSE)

Rd file 'WaveD.Rd':
  \usage lines wider than 90 characters:
     WaveD(yobs, g = c(1, rep(0, (length(yobs) - 1))), MC = FALSE, SOFT = FALSE, F = find.j1(g, scale(yobs))[2], L = 3, deg = 3, eta = sqrt( ... [TRUNCATED]

Rd file 'multires.Rd':
  \usage lines wider than 90 characters:
     multires(wcUntrimmed, lowest = 3, coarse = 3, highestplot = NULL, descending = FALSE, sc = 1)

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  plot.dwt plot.dwt.multiple plot.modwt print.dwt print.modwt
  print.wt.filter summary.dwt summary.modwt summary.wt.filter
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  plot.dwt.2d
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘waveslim/libs/waveslim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘wavethresh/libs/wavethresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
changepoints.sbs: no visible global function definition for ‘mad’
changepoints.wbs: no visible global function definition for ‘var’
changepoints.wbs: no visible global function definition for ‘quantile’
plot.sbs: no visible global function definition for ‘ts.plot’
plot.sbs: no visible global function definition for ‘lines’
plot.sbs: no visible global function definition for ‘title’
random.intervals: no visible global function definition for ‘runif’
sbs.default: no visible global function definition for ‘var’
wbs.default: no visible global function definition for ‘var’
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
File ‘wbs/libs/wbs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘wbsts/libs/wbsts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  knots.WCE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
onesamplemeantest: no visible global function definition for ‘pnorm’
twosamplemeantest: no visible global function definition for ‘pnorm’
wcq: no visible global function definition for ‘var’
wcq: no visible global function definition for ‘pnorm’
wcq.fdrc: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
WDI: no visible binding for global variable ‘WDI_data’
WDIcache: no visible global function definition for ‘fromJSON’
WDIsearch: no visible binding for global variable ‘WDI_data’
Undefined global functions or variables:
  WDI_data fromJSON
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
Deprecated license: BSD
Non-standard file/directory found at top level:
  ‘webvis_0.0.1.tar.gz’
Found the following apparent S3 methods exported but not registered:
  +.webvis
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘webvis/R/zzz.R’:
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

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

[1] "Welcome to the webvis pacakge."
render.webvis: no visible global function definition for ‘browseURL’
unfold.webvis : <anonymous>: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  browseURL runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.webvis':
  ‘plot.webvis’

S3 methods shown with full name in documentation object '"+.webvis"':
  ‘+.webvis’

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 ‘weco/libs/weco.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘sbw’
File ‘weights/libs/weights.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
print.palette: no visible global function definition for ‘par’
print.palette: no visible global function definition for ‘image’
print.palette: no visible global function definition for ‘rect’
print.palette: no visible global function definition for ‘rgb’
print.palette: no visible global function definition for ‘text’
wes_palette: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette image par rect rgb text
Consider adding
  importFrom("grDevices", "colorRampPalette", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
Package in Depends field not imported from: ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for ‘sd’
Z.value: no visible global function definition for ‘pnorm’
pairtest: no visible global function definition for ‘is’
pairtest: no visible global function definition for ‘new’
pairtest: no visible global function definition for ‘rbind2’
pairtest: no visible global function definition for ‘p.value’
pairtest: no visible global function definition for ‘single.snp.tests’
scoretest: no visible global function definition for ‘pchisq’
varplot : <anonymous>: no visible global function definition for ‘var’
varplot: no visible global function definition for ‘plot’
varplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to ‘markdown’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Quitting from lines 34-37 (Running_WhiteStripe.Rmd) 
Error: processing vignette ‘Running_WhiteStripe.Rmd’ failed with diagnostics:
File(s) not found!
Execution halted
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
dlog.norm: no visible global function definition for ‘rnorm’
fun.load.hals.a: no visible global function definition for ‘sfExport’
fun.load.hals.a: no visible global function definition for ‘sfLibrary’
fun.load.hals.fill: no visible global function definition for
  ‘sfExport’
fun.load.hals.fill: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.a: no visible global function definition for ‘sfExport’
fun.load.widals.a: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.fill: no visible global function definition for
  ‘sfExport’
fun.load.widals.fill: no visible global function definition for
  ‘sfLibrary’
unif.mh: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘widals/libs/widals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 in package code:
  ‘genefilter’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  ‘packageDescription’
.relax.cvcompute: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.elnet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.lognet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.elnet: no visible global function definition for ‘predict’
.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.lognet: no visible global function definition for ‘predict’
.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
predict.widenet: no visible global function definition for ‘predict’
screen.cor : <anonymous>: no visible global function definition for
  ‘var’
screen.cor : <anonymous>: no visible global function definition for
  ‘cor.test’
screen.ttest: no visible global function definition for ‘colttests’
widenet: no visible global function definition for ‘mc.reset.stream’
widenet: no visible global function definition for ‘mclapply’
widenet: no visible global function definition for ‘predict’
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
File ‘widenet/libs/widenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for ‘wilcox.test’
Don: no visible global function definition for ‘points’
Don: no visible global function definition for ‘chisq.test’
Lixn: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘wle/libs/wle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘WMCapacity/libs/WMCapacity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
File ‘wnominate/libs/wnominate.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘wnominate.o’
File ‘wnominate/libs/wnominate.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.
prepareData: no visible global function definition for ‘tokenize’
Undefined global functions or variables:
  tokenize
'library' or 'require' call to ‘tm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘wordcloud/libs/wordcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for ‘llply’
wordmatch : <anonymous>: no visible global function definition for
  ‘llply’
wordmatch: no visible global function definition for ‘melt’
wordmatch: no visible global function definition for ‘count’
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: 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.
Running examples in ‘WordR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addFlexTables
> ### Title: Read Word document with bookmarks and create other Word document
> ###   with rendered tables in place.
> ### Aliases: addFlexTables
> 
> ### ** Examples
> 
> library(ReporteRs)
Loading required package: ReporteRsjars
> ft_mtcars <- vanilla.table(mtcars)
> ft_iris <- vanilla.table(iris)
> FT <- list(ft_mtcars=ft_mtcars,ft_iris=ft_iris)
> addFlexTables(
+   paste(examplePath(),'templates/templateFT.docx',sep = ''),
+   paste(examplePath(),'results/resultFT.docx',sep = ''),
+   FT)
Error in writeDoc.docx(doc, docxOut) : 
  writeDoc: Cannot write to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/WordR/examples/results/resultFT.docx
Calls: addFlexTables -> <Anonymous> -> writeDoc.docx
Execution halted
File ‘wordspace/libs/wordspace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘wrassp/libs/wrassp.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.
File ‘wrswoR/libs/wrswoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Quitting from lines 57-82 (wrswoR.Rmd) 
Error: processing vignette ‘wrswoR.Rmd’ failed with diagnostics:
there is no package called 'cluster'
Execution halted
File ‘wskm/libs/wskm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
simul.wsvm: no visible binding for global variable ‘mixture.example’
wsvm.boost: no visible global function definition for ‘plot’
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Rd file 'simul.wsvm.Rd':
  \usage lines wider than 90 characters:
         simul.wsvm(set.seeds = 123, obs.num = 1000, mu = c(0,0), cov.mat = 0.2*diag(2), X = NULL, Y = NULL)

Rd file 'wsvm.boost.Rd':
  \usage lines wider than 90 characters:
         wsvm.boost(X, Y, new.X, new.Y, c.n, B = 50, kernel.type = list(type = "rbf", par= 0.5), C = 4, eps = 1e-10, plotting = FALSE)

These lines will be truncated in the PDF manual.
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
Rd file 'classroom.Rd':
  \examples lines wider than 100 characters:
     {boxplot(classroom.first8$mathgain[classroom.first8$schoolid==i] ~ classroom.first8$classid[classroom.first8$schoolid==i],ylab="Mathgai ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
quadplot: no visible global function definition for ‘median’
xgobi: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  +.CellStyle CellBlock.default CellStyle.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.xssfcolor: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File ‘xml2/libs/xml2.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’
File ‘xml2/libs/xml2.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.
Running examples in ‘xml2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_xml
> ### Title: Read HTML or XML.
> ### Aliases: read_xml read_html read_xml.character read_xml.raw
> ###   read_xml.connection
> 
> ### ** Examples
> 
> # Literal xml/html is useful for small examples
> read_xml("<foo><bar /></foo>")
{xml_document}
<foo>
[1] <bar/>
> read_html("<html><title>Hi<title></html>")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> read_html("<html><title>Hi")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> 
> # From a local path
> read_html(system.file("extdata", "r-project.html", package = "xml2"))
{xml_document}
<html lang="en">
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
[2] <body>\n    <div class="container page">\n      <div class="row">\n       ...
> 
> # From a url
> cd <- read_xml("http://www.xmlfiles.com/examples/cd_catalog.xml")
Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html,  : 
  Specification mandate value for attribute async [41]
Calls: read_xml ... read_xml.connection -> read_xml.raw -> doc_parse_raw -> .Call
Execution halted
Non-standard files/directories found at top level:
  ‘Bug.R’ ‘Bugs.html’ ‘Check’ ‘CodeDetails’ ‘DESCRIPTION.in’ ‘Docs’
  ‘FAQ.html’ ‘FIXME_NOW’ ‘GNUmakefile’ ‘GNUmakefile.admin’
  ‘Makevars.in’ ‘MemoryBug.R’ ‘NAMESPACE.in’ ‘NodeFuns’ ‘Notes’
  ‘QuestionSolutions’ ‘README.windows’ ‘Rsamples’ ‘TAGS’
  ‘Todo-orig.html’ ‘Todo.xml’ ‘VersionInfo’ ‘addFinalizer’ ‘checkLinks’
  ‘dotCalls’ ‘expat’ ‘index.html’ ‘index.html.in’ ‘libxml’
  ‘libxml2.9.R’ ‘scrapingData.xml’ ‘testRemoveFinalizers.R’
  ‘testRemoveFinalizers.c’ ‘xpathPointer.xml’
newXMLDoc: no visible binding for global variable ‘doc’
source: no visible binding for global variable ‘use_file’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
Rd file 'makeClassTemplate.Rd':
  \examples lines wider than 100 characters:
     "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

Rd file 'xmlClone.Rd':
  \examples lines wider than 100 characters:
     xmlParse('<doc><author id="dtl"><firstname>Duncan</firstname><surname>Temple Lang</surname></author></doc>')

Rd file 'xmlToS4.Rd':
  \examples lines wider than 100 characters:
      "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

These lines will be truncated in the PDF manual.
File ‘XML/libs/XML.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘DocParse.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.
LPGM: no visible global function definition for ‘flush.console’
PGM: no visible global function definition for ‘flush.console’
PGM.path.neighborhood: no visible global function definition for
  ‘runif’
PGMSim: no visible global function definition for ‘rpois’
PGMSim: no visible global function definition for ‘par’
WPGMSim: no visible global function definition for ‘rpois’
XMRF.Sim: no visible global function definition for ‘cov2cor’
XMRF.Sim: no visible global function definition for ‘rbinom’
XMRF.Sim: no visible global function definition for ‘rnorm’
glm.generic: no visible global function definition for ‘flush.console’
mymult: no visible global function definition for ‘rmultinom’
plot.GMS: no visible global function definition for ‘pdf’
plot.GMS: no visible global function definition for ‘dev.off’
plotNet: no visible global function definition for ‘pdf’
plotNet: no visible global function definition for ‘dev.off’
print.GMS: no visible global function definition for ‘str’
processSeq: no visible binding for global variable ‘quantile’
processSeq: no visible binding for global variable ‘var’
processSeq: no visible global function definition for ‘ks.test’
rmpois : <anonymous>: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘xoi/libs/xoi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘xseq/libs/xseq.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.
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
Found the following apparent S3 methods exported but not registered:
  plot.cca print.F.test.cca print.cca print.summary.cca summary.cca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘yCrypticRNAs/libs/yCrypticRNAs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘yCrypticRNAs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

Rd file 'FedYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat, FedYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
File ‘YplantQMC/libs/YplantQMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘deSolve’ ‘triangle’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Deprecated license: CC BY-SA 2.0 + file LICENSE
Package suggested but not available for checking: ‘zdat’
Found the following apparent S3 methods exported but not registered:
  cbind.zoocat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'merge':
  ‘cbind.zoocat’

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.
.getPath: no visible global function definition for ‘predict’
ZIClass: no visible binding for global variable ‘na.omit’
ZIClass: no visible global function definition for ‘predict’
analyzeClass: no visible global function definition for ‘plot’
calibrate : findmax: no visible global function definition for ‘lowess’
calibrate: no visible global function definition for ‘lm’
calibrate: no visible global function definition for ‘anova’
calibrate: no visible global function definition for ‘coef’
focusGraph: no visible global function definition for ‘dev.list’
getTrain: no visible global function definition for ‘na.omit’
makeClass : selectVars: no visible global function definition for
  ‘as.formula’
predict.ZIClass: no visible global function definition for ‘predict’
processSampleAll: no visible global function definition for ‘predict’
viewResults: no visible global function definition for ‘par’
viewResults: no visible global function definition for ‘plot’
viewResults: no visible global function definition for ‘points’
viewResults: no visible global function definition for ‘text’
zidbDrawVignette: no visible global function definition for ‘dev.size’
zidbDrawVignette: no visible global function definition for ‘par’
zidbDrawVignette: no visible global function definition for ‘dev.cur’
zidbDrawVignette: no visible global function definition for
  ‘rasterImage’
zidbPlotNew: no visible global function definition for ‘par’
zidbPlotNew: no visible global function definition for ‘plot’
Undefined global functions or variables:
  anova as.formula coef dev.cur dev.list dev.size lm lowess na.omit par
  plot points predict rasterImage text
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "dev.size")
  importFrom("graphics", "par", "plot", "points", "rasterImage", "text")
  importFrom("stats", "anova", "as.formula", "coef", "lm", "lowess",
             "na.omit", "predict")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  ‘src/third_party/zstd-1.2.0/lib/dictBuilder/divsufsort.c’
ztable.glm: no visible global function definition for ‘confint’
ztable.glm: no visible global function definition for ‘coef’
ztable.nls: no visible global function definition for ‘formula’
Undefined global functions or variables:
  coef confint formula
Consider adding
  importFrom("stats", "coef", "confint", "formula")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  confint.zyp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
confint.zyp: no visible global function definition for ‘qnorm’
confint.zyp: no visible global function definition for ‘var’
zyp.sen: no visible global function definition for ‘terms’
zyp.sen: no visible global function definition for ‘median’
zyp.trend.csv: no visible global function definition for ‘read.csv’
zyp.trend.csv: no visible global function definition for ‘write.csv’
zyp.yuepilon: no visible global function definition for ‘acf’
zyp.yuepilon: no visible binding for global variable ‘na.pass’
zyp.yuepilon: no visible global function definition for ‘confint’
zyp.yuepilon: no visible global function definition for ‘lm’
zyp.zhang: no visible global function definition for ‘acf’
zyp.zhang: no visible binding for global variable ‘na.pass’
zyp.zhang: no visible global function definition for ‘confint’
zyp.zhang: no visible global function definition for ‘lm’
Undefined global functions or variables:
  acf confint lm median na.pass qnorm read.csv terms var write.csv
Consider adding
  importFrom("stats", "acf", "confint", "lm", "median", "na.pass",
             "qnorm", "terms", "var")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmplLdZLK/filematrices’, resetting
Examples with CPU or elapsed time > 5s
                 user system elapsed
multithreadACME 0.666  0.063  22.694
Running examples in ‘ApacheLogProcessor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.multiple.apache.access.log
> ### Title: Reads multiple files of apache web server.
> ### Aliases: read.multiple.apache.access.log
> 
> ### ** Examples
> 
> path <- system.file("examples", package="ApacheLogProcessor")
> path <- paste(path, "/", sep="")
> 
> #read multiple gziped logs with the prefix m_access_log_combined_
> dfLog <- read.multiple.apache.access.log(path, "m_access_log_combined_")
[1] "Starting the log processing. This may take a long time..."
[1] "Processing file  m_access_log_combined_1.log.gz"
[1] "Unziping  m_access_log_combined_1.log.gz"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ApacheLogProcessor/examples/m_access_log_combined_1.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: read.multiple.apache.access.log -> write -> cat -> file
Execution halted
Running examples in ‘ASIP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arvi
> ### Title: Atmospherically Resistant Vegetation Index
> ### Aliases: arvi
> 
> ### ** Examples
> 
> library (raster)
Loading required package: sp
> library (rgdal)
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-6 
> # Finding the path of the sample satellite image directory.
> # User may define paths directly like "/home/ur_folder" or "C:/ur_folder"
> path <- system.file ("TM_sample", package = "ASIP")
> shapefil <- paste0 (path, "/test.shp")
> arvi (directory = path, crop = "y", ext2crop = shapefil)
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ASIP/TM_sample/test.shp", layer: "test"
with 1 features
It has 1 fields
Integer64 fields read as strings:  id 
Error in .local(.Object, ...) : Dataset copy failed
Calls: arvi ... <Anonymous> -> new -> initialize -> initialize -> .local -> .Call
Execution halted
Running examples in ‘atsd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: save_connection
> ### Title: Write connection parameters to configuration file.
> ### Aliases: save_connection
> 
> ### ** Examples
> 
> # Write the current values of the connection parameters to the configuration file
> save_connection()
Warning in writeLines(l, fileConn) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/atsd/connection.config': Read-only file system
Error in writeLines(l, fileConn) : cannot open the connection
Calls: save_connection -> writeLines
Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesMCClust.Rcheck/bayesMCClust-wd’, resetting
Examples with CPU or elapsed time > 5s
               user system elapsed
mcClustering 11.816  0.062  15.855
Found the following significant warnings:
  Gspline.cpp:1064:29: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 41 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  Gspline.cpp:1065:29: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 49 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  Gspline.cpp:1066:29: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 39 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  classCovMatrix.cpp:231:27: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 16 bytes into a region of size 15 overflows the destination [-Wstringop-overflow=]
  classRandomEff.cpp:248:24: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 14 bytes into a region of size 10 overflows the destination [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesSurv.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in gzfile(file, "wb") :
  cannot open compressed file ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Bchron/data/intcal09.rda’, probable reason ‘Read-only file system’
Quitting from lines 279-283 (Bchron.Rmd) 
Error: processing vignette ‘Bchron.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  bcrypt/bcrypt.c:144:24: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
  bcrypt/bcrypt.c:254:29: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bcrypt.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  ── 1. Failure: bib2df() throws error messages (@tests.R#53)  ───────────────────
  `bib2df("https://www.ottlngr.de/data/x.bib")` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 15 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘biclique-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi.format
> ### Title: Add number of vertices and edges to the input file
> ### Aliases: bi.format
> 
> ### ** Examples
> 
> bi.format(system.file("extdata", "example2.el", package = "biclique"))
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/biclique/extdata/example2.el': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: bi.format -> cat -> file
Execution halted
Running examples in ‘bigstatsr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: asPlotlyText
> ### Title: Plotly text
> ### Aliases: asPlotlyText
> 
> ### ** Examples
> 
> set.seed(1)
> 
> X <- big_attachExtdata()
> svd <- big_SVD(X, big_scale(), k = 10)
Error in getXPtrFBM(.self$backingfile, .self$nrow, .self$ncol, .self$type) : 
  File '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/extdata/example.bk' not found.
Calls: big_SVD ... extractVec -> $ -> $ -> get -> <Anonymous> -> getXPtrFBM
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biorxivr.Rcheck/vign_test/biorxivr") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/index.Rmd’
(Is a VignetteBuilder field missing?)
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 17-20 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
failed to load external entity "http://www.biorxiv.org/search/Ecology?page=0"
Execution halted
Running examples in ‘Brundle-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jg.plotDeSeqCombined
> ### Title: jg.plotDeSeqCombined
> ### Aliases: jg.plotDeSeqCombined
> ### Keywords: DESeq2 data plot
> 
> ### ** Examples
> 
> data(jg.controlResultsDeseq,package="Brundle")
> data(jg.experimentResultsDeseq,package="Brundle")
> 
> jg.plotDeSeqCombined(jg.controlResultsDeseq,
+                     jg.experimentResultsDeseq,
+                     title.main="ER and CTCF Binding Folding changes on ER treatment",
+                     p=0.01,flip=TRUE)
Error in concatenateObjects(x, objects, ignore.mcols = ignore.mcols) : 
  the objects to concatenate must be DESeqResults objects (or NULLs)
Calls: jg.plotDeSeqCombined ... c -> .local -> concatenateObjects -> concatenateObjects
Execution halted
Running ‘testthat.R’ [5s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(callr)
  > 
  > Sys.unsetenv("R_TESTS")
  > 
  > test_check("callr")
  ── 1. Error: debugger is called (@test-error.R#45)  ────────────────────────────
  Can't mock functions in base packages (utils)
  1: with_mock(`utils::debugger` = function(...) called <<- TRUE, r(function() {
         1 + "A"
     }, error = "debugger")) at testthat/test-error.R:45
  2: extract_mocks(new_values = new_values[!code_pos], .env = .env, eval_env = parent.frame())
  3: lapply(stats::setNames(nm = mock_qual_names), function(qual_name) {
         pkg_name <- gsub(pkg_and_name_rx, "\\1", qual_name)
         if (is_base_pkg(pkg_name)) {
             stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
         }
         name <- gsub(pkg_and_name_rx, "\\2", qual_name)
         if (pkg_name == "") 
             pkg_name <- .env
         env <- asNamespace(pkg_name)
         if (!exists(name, envir = env, mode = "function")) 
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: debugger is called (@test-error.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cda.Rcheck/00install.out’ for details.
Found the following significant warnings:
  BlockCEM.h:52:44: warning: ‘BlockCEM<double>::Y’ will be initialized after [-Wreorder]
  BlockCEM.h:51:44: warning:   ‘FortranLinalg::DenseMatrix<double> BlockCEM<double>::X’ [-Wreorder]
  BlockCEM.h:152:5: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cems.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS’, resetting
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clust.bin.pair)
  > 
  > test_check("clust.bin.pair")
  ── 1. Error: McNemar scores datasets correctly (@test_clust_bin_pair.R#11)  ────
  'check.attributes' must be logical
  1: expect_equal(.mcnemar.impl(psychiatry$bh, psychiatry$ch), 11.85, tolerance = 0.1, 
         scale = NULL, "psychiatry") at testthat/test_clust_bin_pair.R:11
  2: compare(act$val, exp$val, ...)
  3: compare.numeric(act$val, exp$val, ...)
  4: all.equal(x, y, tolerance = tolerance, check.attributes = check.attributes, ...)
  5: all.equal.numeric(x, y, tolerance = tolerance, check.attributes = check.attributes, 
         ...)
  6: stop(gettextf("'%s' must be logical", "check.attributes"), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Error: McNemar scores datasets correctly (@test_clust_bin_pair.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  bdsmatrix_stub.h:41:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:44:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:50:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:53:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:97:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:100:12: warning: return from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/coxme.Rcheck/00install.out’ for details.
Running examples in ‘CREAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CREAM
> ### Title: CREAM is the main function for CORE identification
> ### Aliases: CREAM
> 
> ### ** Examples
> 
> CREAM(system.file("extdata", "A549_Chr21.bed", package = "CREAM"),
+ system.file("extdata", "A549_Chr21_COREs.bed", package = "CREAM"),
+ MinLength = 1000, peakNumMin = 2)
[1] "Please make sure there is no overlap between the input genomic regions. Overlap between the input regions may cause error."
[1] "Identifying window size for each Order"
[1] "Identifying COREs"
[1] "Filtering clusters of low order"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CREAM/extdata/A549_Chr21_COREs.bed': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: CREAM -> write.table -> file
Execution halted
Found the following significant warnings:
  BIC_comp_dposv.c:1813:44: warning: passing argument 4 of ‘qsort’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dagbag.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DatABEL.Rcheck/00install.out’ for details.
Compilation used the following non-portable flag(s):
  ‘-Werror’
Error in re-building vignettes:
  ...
Loading required package: Rcpp

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

Joining, by = "gene"
Joining, by = "cell"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Have 35 cells after filtering
Joining, by = "cell"
Have 20 genes after filtering
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Compiling model
the number of chains is less than 1; sampling not done
Saving compiled model to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/DeLorean/extdata/exact-sizes.rds
Quitting from lines 145-146 (DeLorean.Rmd) 
Error: processing vignette ‘DeLorean.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Running ‘has-devel.R’ [1s/3s]
  Running ‘test-that.R’ [48s/100s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  
  Attaching package: 'devtools'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  ── 1. Failure: Github repos with submodules are identified correctly (@test-gith
  github_has_remotes(github_remote("armstrtw/rzmq")) not equal to TRUE.
  1 element mismatch
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 395 SKIPPED: 9 FAILED: 1
  1. Failure: Github repos with submodules are identified correctly (@test-github.r#82) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  DPPmcmc.h:91:16: warning: ‘DPPmcmc::model’ will be initialized after [-Wreorder]
  DPPmcmc.h:82:12: warning:   ‘Rcpp::Function DPPmcmc::effectiveSizeFunction’ [-Wreorder]
  DPPmcmc.cpp:11:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DPP.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(earthtones)
  > 
  > test_check("earthtones")
  ── 1. Error: returns normal (@test-earth.R#6)  ─────────────────────────────────
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=50.759,-125.673&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false'
  1: expect_is(get_earthtones(method = "kmeans"), "palette") at testthat/test-earth.R:6
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: get_earthtones(method = "kmeans")
  5: ggmap::get_map(location = c(longitude, latitude), maptype = "satellite", zoom = zoom, 
         ...)
  6: get_googlemap(center = location, zoom = zoom, maptype = maptype, scale = scale, messaging = messaging, 
         urlonly = urlonly, force = force, filename = filename, color = color, language = language)
  7: download.file(url, destfile = tmp, quiet = !messaging, mode = "wb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Error: returns normal (@test-earth.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 26-28 (earthtones.rmd) 
Error: processing vignette ‘earthtones.rmd’ failed with diagnostics:
cannot open URL ‘http://maps.googleapis.com/maps/api/staticmap?center=36.094994,-111.837962&zoom=12&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false’
Execution halted
Running examples in ‘EasyStrata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EasyStrata
> ### Title: Function to run EasyStrata (v8.6).
> ### Aliases: EasyStrata
> 
> ### ** Examples
> 
> extDataDir=system.file("extdata", package="EasyStrata")
> ## Example Pipeline:
> ecfPipe=paste(extDataDir,"example_pipeline.ecf",sep="/")
> EasyStrata(ecfPipe)
Warning message:
In file(fileLog, open = "a") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/EasyStrata/extdata/example_pipeline.ecf.out': Read-only file system
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpBILHTz’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpBILHTz’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpBILHTz’, resetting
Examples with CPU or elapsed time > 5s
              user system elapsed
partitioning 5.314  0.012   6.757
expansion    4.680  0.012   6.737
Found the following significant warnings:
  Matrix.h:42:7: warning: ‘myMatrix::numrow’ will be initialized after [-Wreorder]
  Matrix.h:41:7: warning:   ‘int myMatrix::numcol’ [-Wreorder]
  Matrix.h:8:12: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Emcdf.Rcheck/00install.out’ for details.
Running examples in ‘empiricalFDR.DESeq2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: empiricalFDR.DESeq2-package
> ### Title: Simulation-Based False Discovery Rate in RNA-Seq
> ### Aliases: empiricalFDR.DESeq2-package empiricalFDR.DESeq2
> 
> ### ** Examples
> 
> 
> dds = makeExampleDESeqDataSet(betaSD=1, n=100)
> dds = DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated fitted dispersions, removing these
fitting model and testing
> sims = simulateCounts(dds)
simulating...
================================================================================converting counts to integer mode
> sims = DESeq(sims)
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated fitted dispersions, removing these
fitting model and testing
> res = results(dds)
Error in concatenateObjects(x, objects, ignore.mcols = ignore.mcols) : 
  the objects to concatenate must be DESeqResults objects (or NULLs)
Calls: results ... c -> .local -> concatenateObjects -> concatenateObjects
Execution halted
Running examples in ‘ETLUtils-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write.dbi.ffdf
> ### Title: Write ffdf data to a database table by using a DBI connection.
> ### Aliases: write.dbi.ffdf
> 
> ### ** Examples
> 
> require(ff)
> 
> ##
> ## Example query using data in sqlite
> ##
> require(RSQLite)
Loading required package: RSQLite
> dbfile <- system.file("smalldb.sqlite3", package="ETLUtils")
> drv <- dbDriver("SQLite")
> query <- "select * from testdata limit 10000"
> x <- read.dbi.ffdf(query = query, dbConnect.args = list(drv = drv, dbname = dbfile),
+ first.rows = 100, next.rows = 1000, VERBOSE=TRUE)
read.dbi.ffdf 1..100 (100)  dbi-read=0.001sec ffdf-write=0.007sec
read.dbi.ffdf 101..1100 (1000)  dbi-read=0.002sec ffdf-write=0.004sec
read.dbi.ffdf 1101..2100 (1000)  dbi-read=0.002sec ffdf-write=0.005sec
read.dbi.ffdf 2101..2860 (760)  dbi-read=0.002sec ffdf-write=0.02sec
 dbi-read=0.007sec  ffdf-write=0.036sec  TOTAL=0.043sec
> 
> write.dbi.ffdf(x = x, name = "helloworld", row.names = FALSE, overwrite = TRUE,
+   dbConnect.args = list(drv = drv, dbname = dbfile),
+   by = 1000, VERBOSE=TRUE)
2018-01-11 16:07:44 dbWriteTable chunk 1/3
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Calls: write.dbi.ffdf ... initialize -> initialize -> rsqlite_send_query -> .Call
Execution halted
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/expoRkit.Rcheck/00install.out’ for details.
Compilation used the following non-portable flag(s):
  ‘-Wmisleading-indentation’
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [14s/20s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library('testthat')
  > library('finch')
  > 
  > test_check('finch')
  ── 1. Error: dwca_get - works with a zip file - read=FALSE (@test-dwca_get.R#21)
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/finch/examples/0000154-150116162929234/multimedia.txt': Read-only file system
  1: dwca_read(zip, read = FALSE) at testthat/test-dwca_get.R:21
  2: process(x)
  3: utils::unzip(x, exdir = dirpath)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 29 SKIPPED: 2 FAILED: 1
  1. Error: dwca_get - works with a zip file - read=FALSE (@test-dwca_get.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘boot.R’ [3s/5s]
  Running ‘disttests.R’ [1s/1s]
Running the tests in ‘tests/disttests.R’ failed.
Complete output:
  > library(flexclust)
  Loading required package: grid
  Loading required package: lattice
  Loading required package: modeltools
  Loading required package: stats4
  > 
  > ## create a random matrix
  > x <- matrix(rnorm(1000), ncol=4)
  > rownames(x) <- 1:nrow(x)
  > 
  > ## test canberra at margin
  > x[1:10,1] <- 0
  > x[1:20,2] <- 0
  > x[1:30,3] <- 0
  > 
  > stopifnot(all.equal(dist2(x,x,"eucl"), as.matrix(dist(x, "eucl"))))
  > stopifnot(all.equal(dist2(x,x,"man"), as.matrix(dist(x, "man"))))
  > stopifnot(all.equal(dist2(x,x,"max"), as.matrix(dist(x, "max"))))
  > stopifnot(all.equal(dist2(x,x,"bin"), as.matrix(dist(x, "bin"))))
  > stopifnot(all.equal(dist2(x,x,"can"), as.matrix(dist(x, "can"))))
  Error: dist2(x, x, "can") and as.matrix(dist(x, "can")) are not equal:
    Mean relative difference: 0.9074364
  Execution halted
Running ‘testthat.R’ [41s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  ── 1. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id1 not equal to c(1, 1, 2, 2, 3).
  Lengths differ: 6 is not 5
  
  ── 2. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id2 not equal to c(1, 2, 1, 2, 3).
  Lengths differ: 6 is not 5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 224 SKIPPED: 0 FAILED: 2
  1. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#50) 
  2. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  m4_prod2_ms.cpp:19:12: warning: ‘paraPro2::v’ will be initialized after [-Wreorder]
  m4_prod2_ms.cpp:18:16: warning:   ‘const size_t paraPro2::r’ [-Wreorder]
  m4_prod2_ms.cpp:24:3: warning:   when initialized here [-Wreorder]
  m4_prod2_ms.cpp:30:3: warning:   when initialized here [-Wreorder]
  m4_prod2_p.cpp:18:12: warning: ‘paraPro2_p::v’ will be initialized after [-Wreorder]
  m4_prod2_p.cpp:17:16: warning:   ‘const size_t paraPro2_p::r’ [-Wreorder]
  m4_prod2_p.cpp:23:3: warning:   when initialized here [-Wreorder]
  m4_prod2_p.cpp:30:3: warning:   when initialized here [-Wreorder]
  m4_prod_ms.cpp:19:18: warning: ‘paraPro_ms::v’ will be initialized after [-Wreorder]
  m4_prod_ms.cpp:18:16: warning:   ‘const size_t paraPro_ms::r’ [-Wreorder]
  m4_prod_ms.cpp:25:3: warning:   when initialized here [-Wreorder]
  m4_prod_p.cpp:18:18: warning: ‘paraPro_p::v’ will be initialized after [-Wreorder]
  m4_prod_p.cpp:17:16: warning:   ‘const size_t paraPro_p::r’ [-Wreorder]
  m4_prod_p.cpp:24:3: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gaston.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:1665:9: warning: specified bound 256 equals the size of the destination [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GenABEL.Rcheck/00install.out’ for details.
Running ‘runTests.R’ [8s/12s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
  > BiocGenerics:::testPackage("geno2proteo")
  Timing stopped at: 1.467 0.02 2.148
  Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  In addition: Warning message:
  In file(file, ifelse(append, "a", "w")) :
    cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geno2proteo/extdata/Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz_CDS_transcript.txt': Read-only file system
  Timing stopped at: 0.459 0 0.683
  Error in getWritablePathname.Arguments(static, ...) : 
    No write permission for directory: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geno2proteo/extdata
  
  
  RUNIT TEST PROTOCOL -- Thu Jan 11 18:33:23 2018 
  *********************************************** 
  Number of test functions: 6 
  Number of errors: 2 
  Number of failures: 0 
  
   
  1 Test Suite : 
  geno2proteo RUnit Tests - 6 test functions, 2 errors, 0 failures
  ERROR in test_generatingCDSaaFile: Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  ERROR in test_genomicLocToWholeDNASequence: Error in getWritablePathname.Arguments(static, ...) : 
    No write permission for directory: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geno2proteo/extdata
  
  Test files with failing tests
  
     test_functionsInGeno2proteo.R 
       test_generatingCDSaaFile 
       test_genomicLocToWholeDNASequence 
  
  
  Error in BiocGenerics:::testPackage("geno2proteo") : 
    unit tests failed for package geno2proteo
  Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘geno2proteoIntroduction.Rnw’ failed with diagnostics:
 chunk 3 (label = example_generatingCDSaaFile) 
Error in getWritablePathname.Arguments(static, ...) : 
  No write permission for directory: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geno2proteo/extdata
Execution halted
Running examples in ‘GetDFPData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gdfpd.fix.DFP.dataframes
> ### Title: Fix dataframe for version issues and inflation measures
> ###   (internal)
> ### Aliases: gdfpd.fix.DFP.dataframes
> 
> ### ** Examples
> 
> #'
> # get example data from RData file
> my.f <- system.file('extdata/Example_DFP_Report_Petrobras.RData', package = 'GetDFPData')
> load(my.f)
> 
> df.assets <- df.reports$fr.assets[[1]]
> df.inflation <- gdfpd.get.inflation.data('dollar', do.cache = FALSE)
Error in open.connection(con, "rb") : HTTP error 500.
Calls: gdfpd.get.inflation.data ... read_delimited -> read_connection -> open -> open.connection
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-53 (gdfpd-vignette-introduction.Rmd) 
Error: processing vignette ‘gdfpd-vignette-introduction.Rmd’ failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/msperlin/GetitrData_auxiliary/master/LastUpdate.txt'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 46-49 (gitrd-vignette-introduction.Rmd) 
Error: processing vignette ‘gitrd-vignette-introduction.Rmd’ failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/msperlin/GetitrData_auxiliary/master/LastUpdate.txt'
Execution halted
Running examples in ‘ggmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_map
> ### Title: Grab a map.
> ### Aliases: get_map
> 
> ### ** Examples
> 
> map <- get_map()
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=29.763284,-95.363271&zoom=10&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Error in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") : 
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=29.763284,-95.363271&zoom=10&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
Calls: get_map -> get_googlemap -> download.file
Execution halted
Error in re-building vignettes:
  ...
trying URL ‘https://hughparsonage.github.io/drat/src/contrib/taxstats_0.0.4.1314.tar.gz’
Content type 'application/gzip' length 52654612 bytes (50.2 MB)
==================================================
downloaded 50.2 MB

* installing *source* package ‘taxstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (taxstats)

The downloaded source packages are in
	'/tmp/Rtmpti7Vtx/downloaded_packages'
Quitting from lines 437-441 (companion-to-sample-file-1314.Rmd) 
Error: processing vignette ‘companion-to-sample-file-1314.Rmd’ failed with diagnostics:
there is no package called 'mgcv'
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tensorflow)
  > library(greta)
  
  
    greta requires TensorFlow version 1.0.0 or higher, but TensorFlow isn't installed.
    Use install_tensorflow() to install the latest version.
  
  
  
  Attaching package: 'greta'
  
  The following objects are masked from 'package:stats':
  
      binomial, poisson
  
  The following objects are masked from 'package:base':
  
      %*%, beta, diag, gamma, sweep
  
  > 
  > test_check("greta")
  Error: 'dnst' is not an exported object from 'namespace:extraDistr'
  Execution halted
Found the following significant warnings:
  readstat/sas/readstat_xport_write.c:339:13: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
  readstat/sas/readstat_xport_write.c:306:13: warning: ‘%-40s’ directive output may be truncated writing between 40 and 99 bytes into a region of size 49 [-Wformat-truncation=]
  readstat/sas/readstat_sas.c:304:14: warning: ‘%1ld’ directive output may be truncated writing between 1 and 16 bytes into a region of size 8 [-Wformat-truncation=]
  readstat/sas/readstat_sas7bdat_read.c:517:101: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size between 435 and 954 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:610:52: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:638:56: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:697:51: warning: ‘%05d’ directive output may be truncated writing between 5 and 11 bytes into a region of size between 1 and 10 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:716:51: warning: ‘%05d’ directive output may be truncated writing between 5 and 11 bytes into a region of size between 1 and 10 [-Wformat-truncation=]
  readstat/spss/readstat_spss.c:139:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lassoModels/IPenalizedSolver.h:221:28: warning: ‘HD::IPenalizedSolver::p_y_’ will be initialized after [-Wreorder]
  lassoModels/IPenalizedSolver.h:217:18: warning:   ‘STK::Real HD::IPenalizedSolver::threshold_’ [-Wreorder]
  lassoModels/IPenalizedSolver.h:112:7: warning:   when initialized here [-Wreorder]
  lassoModels/IPenalizedSolver.h:126:7: warning:   when initialized here [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.h:154:21: warning: ‘HD::LogisticFusedLassoSolver::cginit_’ will be initialized after [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.h:147:26: warning:   ‘HD::FusedLassoPenalty* HD::LogisticFusedLassoSolver::p_penalty_’ [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.cpp:51:3: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HDPenReg.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [170s/229s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(heemod)
  > 
  > ## the Sys.setenv fixes a problem running tests
  > ##   with parallel processing; related to
  > ##   https://github.com/hadley/testthat/issues/86 and
  > ##   https://github.com/hadley/testthat/issues/144
  > 
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("heemod")
  ── 1. Error: absolute path works (@test_tabular_input.R#501)  ──────────────────
  cannot open the connection
  1: write.csv(ref_edit, paste(system.file("tabular/test", package = "heemod"), "edited_ref.csv", 
         sep = "/"), row.names = FALSE) at testthat/test_tabular_input.R:501
  2: eval.parent(Call)
  3: eval(expr, p)
  4: eval(expr, p)
  5: write.table(ref_edit, paste(system.file("tabular/test", package = "heemod"), "edited_ref.csv", 
         sep = "/"), row.names = FALSE, col.names = TRUE, sep = ",", dec = ".", qmethod = "double")
  6: file(file, ifelse(append, "a", "w"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 476 SKIPPED: 0 FAILED: 1
  1. Error: absolute path works (@test_tabular_input.R#501) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [2s/3s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("hrbrthemes")
  Loading required package: hrbrthemes
  ── 1. Error: we can do something (@test-hrbrthemes.R#60)  ──────────────────────
  cannot open the connection
  1: import_roboto_condensed() at testthat/test-hrbrthemes.R:60
  2: suppressWarnings(suppressMessages(extrafont::font_import(rc_font_dir, prompt = FALSE)))
  3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  4: suppressMessages(extrafont::font_import(rc_font_dir, prompt = FALSE))
  5: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  6: extrafont::font_import(rc_font_dir, prompt = FALSE)
  7: ttf_import(paths, recursive, pattern)
  8: ttf_extract(ttfiles)
  9: gzcopy_exclude(paste(tmpfiles[i], ".afm", sep = ""), paste(outfiles[i], ".afm.gz", 
         sep = ""), delete = TRUE, exclusions = c("^Characters"))
  10: gzfile(dest, "w")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: we can do something (@test-hrbrthemes.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Compilation used the following non-portable flag(s):
  ‘-Wno-unused-parameter’
including flag(s) suppressing warnings
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpfbkQmH’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpfbkQmH’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpfbkQmH’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpfbkQmH’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpfbkQmH’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpfbkQmH’, resetting
Examples with CPU or elapsed time > 5s
                   user system elapsed
chip.support     49.201  0.163  72.371
nearest.snp      14.317  0.019  19.093
get.GO.for.genes  1.111  0.028   6.418
Running ‘testthat.R’ [28s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(huxtable)
  
  Attaching package: 'huxtable'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > 
  > we_are_in_R_CMD_check <- TRUE
  > test_check("huxtable")
  ── 1. Failure: Quick output functions work (@test-output.R#135)  ───────────────
  `quick_pdf(m, dfr, ht, file = tf)` threw an error.
  Message: Could not move pdf file to /tmp/Rtmp7zfe25/file623425a2f385. The pdf file remains at "file623448541803.pdf" in the current working directory.
  Class:   simpleError/error/condition
  
  ── 2. Failure: Quick output functions work (@test-output.R#136)  ───────────────
  file.exists(tf) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 301 SKIPPED: 48 FAILED: 2
  1. Failure: Quick output functions work (@test-output.R#135) 
  2. Failure: Quick output functions work (@test-output.R#136) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  s_hull_pro.h:75:9: warning: ‘Shx::ro’ will be initialized after [-Wreorder]
  s_hull_pro.h:74:14: warning:   ‘float Shx::tr’ [-Wreorder]
  s_hull_pro.h:77:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:74:17: warning: ‘Shx::tc’ will be initialized after [-Wreorder]
  s_hull_pro.h:73:7: warning:   ‘int Shx::id’ [-Wreorder]
  s_hull_pro.h:78:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:112:11: warning: ‘Dupex::c’ will be initialized after [-Wreorder]
  s_hull_pro.h:111:7: warning:   ‘int Dupex::id’ [-Wreorder]
  s_hull_pro.h:115:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:116:3: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/interp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  as_output.c:323:24: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iotools.Rcheck/00install.out’ for details.
Running ‘test.R’ [2s/3s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > # Use the default data to avoid token requirement for testing purposes
  > # Generate markdown text string
  > library(issueReporter)
  > setwd(tempdir())
  > 
  > testMD <- issuesData2md()
  > 
  > # Use default data to generate PDF
  > issuesGenPDF(style = "tint",
  +              RmdLocation =  system.file("rmarkdown/templates/", "tint.Rmd",
  +                                         package = "issueReporter"),
  +              outputFile = tempfile(pattern="ir", fileext=".pdf"),
  +              outputDir = tempdir(),
  +              md = testMD,
  +              setTitle = "Example Notes",
  +              setAuthor = "Author Name")
  
  
  processing file: tint.Rmd
     inline R code fragments
  
  label: setup (with options) 
  List of 1
   $ include: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-1 (with options) 
  List of 2
   $ results: chr "asis"
   $ echo   : logi FALSE
  
    ordinary text without R code
  
  Error in file(con, "w") : cannot open the connection
  Calls: issuesGenPDF -> <Anonymous> -> <Anonymous> -> writeLines -> file
  In addition: Warning messages:
  1: In block_exec(params) : failed to tidy R code in chunk <setup>
  reason: Error in loadNamespace(name) : there is no package called 'formatR'
  
  2: In file(con, "w") :
    cannot open file 'tint.knit.md': Read-only file system
  Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/KATforDCEMRI.Rcheck/KATforDCEMRI_benchmark_test’, resetting
Running examples in ‘knitr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spin
> ### Title: Spin goat's hair into wool
> ### Aliases: spin
> 
> ### ** Examples
> 
> #' write normal text like this and chunk options like below
> 
> #+ label, opt=value
> 
> # /*
> #' these lines are treated as comments in spin()
> 1 + 1
[1] 2
> # */
> 
> (s = system.file("examples", "knitr-spin.R", package = "knitr"))
[1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/knitr/examples/knitr-spin.R"
> spin(s)  # default markdown
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/knitr/examples/knitr-spin.Rmd': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: spin -> cat -> file
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lazyWeave.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
pandoc: Could not determine mime type for `https://raw.githubusercontent.com/AlexiaJM/LEGIT/master/images/GxE_testing_strong.png'
CallStack (from HasCallStack):
  error, called at src/Text/Pandoc/SelfContained.hs:156:35 in pandoc-1.19.2.4-7yudG8wfqBNHS2KzoOxWqS:Text.Pandoc.SelfContained
Error: processing vignette ‘GxE_testing.Rmd’ failed with diagnostics:
pandoc document conversion failed with error 1
Execution halted
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/localdepth.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cvrout.c:286:32: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LogicOpt.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [22s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  ── 1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ── 2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2456 SKIPPED: 36 FAILED: 2
  1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88) 
  2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘MAGNAMWAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FormatMCLFastas
> ### Title: Format all raw GenBank fastas to single OrthoMCL compatible
> ###   fasta file
> ### Aliases: FormatMCLFastas
> 
> ### ** Examples
> 
> 
> dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
> dir <- paste(dir,'/',sep='')
> formatted_file <- FormatMCLFastas(dir)
Warning in file.remove(outfile) :
  cannot remove file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta', reason 'Read-only file system'
Writing out to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta 
Warning in file(description = file.out, open = open) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta': Read-only file system
Error in file(description = file.out, open = open) : 
  cannot open the connection
Calls: FormatMCLFastas -> <Anonymous> -> file
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/markmyassignment.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpFhh5Rh’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpFhh5Rh’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpFhh5Rh’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpFhh5Rh’, resetting
Examples with CPU or elapsed time > 5s
                 user system elapsed
ind.analysis   18.623  0.047  26.794
MetaDE.rawdata  4.702  0.050   7.096
Running examples in ‘MetaSubtract-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meta.subtract
> ### Title: Subtracts GWAS results from one or more cohorts from the
> ###   meta-GWAS results
> ### Aliases: meta.subtract
> ### Keywords: Correct meta-GWAS results Leave-one-out
> 
> ### ** Examples
> 
> metafile="meta_results.txt"
> cohortfiles=c("cohort1_results.txt","cohort2_results.txt")
> # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
> # Genomic control correction of the imported meta summary statistics will be undone using 
> # lambda.meta. Genomic control will be applied to the corrected meta summary statistics 
> # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics 
> # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first 
> # corrected for genomic control before subtracting them from the meta summary statistics. By 
> # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
> m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, 
+       dir=system.file("extdata", package="MetaSubtract"))
[1] "Thu Jan 11 16:35:49 2018"
Reading meta_results.txt 
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'MetaSubtract.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: meta.subtract -> write.table -> file
Execution halted
Warning in utils::download.file(extDB, destfile = localDB, quiet = T) :
  URL https://github.com/cflagg/metScanR/raw/master/data/metScanR_DB.rda: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/metScanR/data/metScanR_DB.rda', reason 'Read-only file system'
Warning in utils::download.file(extDB, destfile = localDB, quiet = T) :
  download had nonzero exit status
Warning in utils::download.file(extTermsDB, destfile = localTermsDB, quiet = T) :
  URL https://github.com/cflagg/metScanR/raw/master/data/metScanR_terms.rda: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/metScanR/data/metScanR_terms.rda', reason 'Read-only file system'
Warning in utils::download.file(extTermsDB, destfile = localTermsDB, quiet = T) :
  download had nonzero exit status

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.
Running examples in ‘micropan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bDist
> ### Title: Computes distances between sequences based on BLAST results
> ### Aliases: bDist
> 
> ### ** Examples
> 
> # Using BLAST result files in this package...
> # We need to uncompress them first:
> extdata.path <- file.path(path.package("micropan"),"extdata")
> filenames <- c("GID1_vs_GID1.txt",
+ "GID1_vs_GID2.txt",
+ "GID1_vs_GID3.txt",
+ "GID2_vs_GID1.txt",
+ "GID2_vs_GID2.txt",
+ "GID2_vs_GID3.txt",
+ "GID3_vs_GID1.txt",
+ "GID3_vs_GID2.txt",
+ "GID3_vs_GID3.txt")
> pth <- lapply( file.path( extdata.path, paste( filenames, ".xz", sep="" ) ), xzuncompress )
Warning in file(destname, open = "wb") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/micropan/extdata/GID1_vs_GID1.txt': Read-only file system
Error in file(destname, open = "wb") : cannot open the connection
Calls: lapply -> FUN -> file
Execution halted
Found an obsolete/platform-specific call in the following functions:
  ‘microplot.trellis’ ‘win.metafileMicroplot_yfactorGgplot’
Found the platform-specific device:
  ‘win.metafile’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Found the following significant warnings:
  ../inst/projects/MixAll/ILauncher.h:103:27: warning: ‘STK::ILauncher::v_models_’ will be initialized after [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:99:18: warning:   ‘STK::RDataHandler STK::ILauncher::handler_’ [-Wreorder]
  ILauncher.cpp:47:1: warning:   when initialized here [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:99:18: warning: ‘STK::ILauncher::handler_’ will be initialized after [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:88:46: warning:   ‘STK::DiagGaussianMixtureManager<STK::RDataHandler> STK::ILauncher::diagGaussianManager_’ [-Wreorder]
  ILauncher.cpp:63:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MixAll.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nelder_mead_min.c:180:21: warning: ‘%5d’ directive writing between 5 and 10 bytes into a region of size 6 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlegp.Rcheck/00install.out’ for details.
Running examples in ‘mlmm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlmc
> ### Title: mlmc for missing and censored response in multilevel model.
> ### Aliases: mlmc
> 
> ### ** Examples
> 
> ## Don't show: 
> testfun=function()
+ {set.seed(100)
+  var2=abs(rnorm(50,0,1))
+  var1=(1/0.85)*var2;
+  geneid=rep(c(1:10),5);sid=c(rep(c(1:25),2),rep(c(26:50),2));
+  censor=rep(0,50)
+  pidname="geneid";sidname="sid";
+  miss_logit=var2*(-0.9);
+  miss=rbinom(50,1,exp(miss_logit)/(exp(miss_logit)+1));
+  censor=rep(0,50)
+  for (i in 1:50) {if (var1[i]<0.05) censor[i]=1}
+  for ( i in 1:50) {if ((miss[i]==1) & (censor[i]==1)) miss[i]=0};
+  for ( i in 1:50) {if (miss[i]==1) var1[i]=NA;
+  if (censor[i]==1) var1[i]=0.05}
+  pdata=data.frame(var1,var2,miss,censor,geneid,sid)
+  pathdir=getwd()
+  if (R.Version()$arch=="i386") fp=system.file("chunks","mlmc_i32.rds",package="mlmm")
+  if (R.Version()$arch=="x86_64") fp=system.file("chunks","mlmc_i64.rds",package="mlmm")
+  mcfit=readRDS(fp)
+  model1=mlmc(formula_completed=var1~var2,formula_missing=miss~var2,
+              formula_censor=censor~1,formula_subject=~var2,pdata=pdata,response_censorlim=0.05,
+              respond_dep_missing=TRUE,pidname="geneid",sidname="sid",pathname=pathdir,
+              iterno=10,chains=2,savefile=FALSE,usefit=TRUE,stanfit=mcfit)
+  }
> system.time(testfun())
Error in prep_call_sampler(object) : 
  the compiled object from C++ code for this model is invalid, possible reasons:
  - compiled with save_dso=FALSE;
  - compiled on a different platform;
  - does not exist (created from reading csv files).
Calls: system.time ... sampling -> .local -> <Anonymous> -> prep_call_sampler
Timing stopped at: 0.15 0 0.201
Execution halted
Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modmarg)
  > 
  > test_check("modmarg")
  ── 1. Error: Collinear cols treated right (@test_glm.R#288)  ───────────────────
  non-conformable arguments
  1: marg(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 30, 
         5))) at testthat/test_glm.R:288
  2: marg.glm(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 
         30, 5)))
  3: .marg(mod = mod, var_interest = var_interest, data = data, weights = weights, ...)
  4: lapply(data, function(x) {
         df_levels <- at_transforms(model_df = x, at_list = gen_at_list(df = x, var_interest = var_interest, 
             at_var_interest = at_var_interest))
         pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
             weights = weights, link_func = NULL, deriv_func = NULL)
     })
  5: FUN(X[[i]], ...)
  6: pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  7: pred_se.glm(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  8: .pred_se(model = model, deriv_func = model$family$mu.eta, link_func = model$family$linkinv, 
         ...)
  9: calc_pred_se(vcov_mat, jacobs)
  10: diag(jac %*% vcov_model %*% t(jac))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 303 SKIPPED: 0 FAILED: 1
  1. Error: Collinear cols treated right (@test_glm.R#288) 
  
  Error: testthat unit tests failed
  Execution halted
Compilation used the following non-portable flag(s):
  ‘-Wno-format’
including flag(s) suppressing warnings
Running examples in ‘neurovault-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download_nv_atlas
> ### Title: Download Neurovault Atlas and Label file
> ### Aliases: download_nv_atlas
> 
> ### ** Examples
> 
> res = download_nv_atlas(id = 1408)
GET command is:
Response [https://neurovault.org/api/atlases/1408/]
  Date: 2018-01-11 18:21
  Status: 200
  Content-Type: application/json; charset=utf-8
  Size: 751 B


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Unrecognized content encoding type. libcurl understands deflate, gzip content encodings.
Calls: download_nv_atlas ... request_fetch -> request_fetch.write_disk -> <Anonymous> -> .Call
Execution halted
Running ‘testthat.R’ [27s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NLMR)
  > 
  > test_check("NLMR")
  ── 1. Failure: basic functionality (@test_utilimportrobotocondensed.R#5)  ──────
  `util_import_roboto_condensed()` threw an error.
  Message: cannot open the connection
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 118 SKIPPED: 1 FAILED: 1
  1. Failure: basic functionality (@test_utilimportrobotocondensed.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  cc1: warning: ‘__builtin_memset’: writing between 256 and 17179869176 bytes into a region of size 248 overflows the destination [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/npsf.Rcheck/00install.out’ for details.
Running examples in ‘ODMconverter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CDA2ODM
> ### Title: CDA2ODM
> ### Aliases: CDA2ODM
> ### Keywords: ODM
> 
> ### ** Examples
> 
> CDA2ODM(CDAfile=file.path(path.package("ODMconverter"),"extdata","CDA_letter_basic.xml"))
[1] "Generating /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ODMconverter/extdata/CDA_letter_basic.xml.odm.xml"
Warning in file(file, if (append) "a" else "w") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ODMconverter/extdata/CDA_letter_basic.xml.odm.xml': Read-only file system
Error in file(file, if (append) "a" else "w") : 
  cannot open the connection
Calls: CDA2ODM -> sink -> file
Execution halted
Compilation used the following non-portable flag(s):
  ‘-Wno-deprecated-declarations’ ‘-Wno-ignored-attributes’
  ‘-Wno-int-in-bool-context’ ‘-Wno-misleading-indentation’
  ‘-Wno-pragmas’ ‘-Wno-unknown-pragmas’ ‘-Wno-unused-function’
  ‘-Wno-unused-local-typedefs’ ‘-Wno-unused-parameter’ ‘-Wvla’
including flag(s) suppressing warnings
Running ‘testthat.R’ [18s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optimus)
  This is optimus 0.1.0, roll out!
  > 
  > test_check("optimus")
  ── 1. Error: find_optimal() stops with wrong data or arguments (@test-find_optim
  argument "quo" is missing, with no default
  1: expect_error(expr = optimus::find_optimal(data = mixed, clustering = counts_cutree, 
         family = "poisson"), message = "some.*") at testthat/test-find_optimal.R:38
  2: quasi_capture(enquo(object), capture_error, label = label)
  3: label %||% quo_label(quo)
  4: quo_label(quo)
  5: expr_label(quo_expr(quo))
  6: quo_expr(quo)
  7: quo_splice(duplicate(quo), warn = warn)
  8: switch_expr(x, language = {
         if (is_quosure(x)) {
             if (!is_false(warn)) {
                 if (is_string(warn)) {
                     msg <- warn
                 }
                 else {
                     msg <- "Collapsing inner quosure"
                 }
                 warn(msg)
                 warn <- FALSE
             }
             while (is_quosure(x)) {
                 x <- f_rhs(x)
             }
             if (!is_null(parent)) {
                 mut_node_car(parent, x)
             }
             quo_splice(x, parent, warn = warn)
         }
         else {
             quo_splice(node_cdr(x), warn = warn)
         }
     }, pairlist = {
         while (!is_null(x)) {
             quo_splice(node_car(x), x, warn = warn)
             x <- node_cdr(x)
         }
     })
  9: expr_type_of(.x)
  10: typeof(x)
  11: duplicate(quo)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Error: find_optimal() stops with wrong data or arguments (@test-find_optimal.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [10s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(palm)
  Loading required package: Rcpp
  > 
  > test_check("palm")
  
  ── 1. Failure: Matern fitting (@test-fits.r#55)  ───────────────────────────────
  `par.fit.matern` not equal to c(38.76459565, 0.73561864, 0.05327295).
  2/3 mismatches (average diff: 0.0646)
  [1] 38.892 - 38.765 ==  0.12698
  [2]  0.733 -  0.736 == -0.00229
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 1
  1. Failure: Matern fitting (@test-fits.r#55) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  export_blacs/pkg_tools.c:32:26: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pbdBASE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  sparse.c:926:16: warning: self-comparison always evaluates to false [-Wtautological-compare]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PET.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PGICA.Rcheck/Sim’, resetting
Running examples in ‘PlasmaMutationDetector-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BuildCtrlErrorRate
> ### Title: function BuildCtrlErrorRate
> ### Aliases: BuildCtrlErrorRate
> 
> ### ** Examples
> 
>    ctrl.dir = system.file("extdata", "4test_only/ctrl/", package = "PlasmaMutationDetector")
>    if (substr(ctrl.dir,nchar(ctrl.dir),nchar(ctrl.dir))!='/')
+      ctrl.dir = paste0(ctrl.dir,'/') # TO RUN UNDER WINDOWS
>    BuildCtrlErrorRate(ctrl.dir)
[1] "Looking for bam and bai in /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PlasmaMutationDetector/extdata/4test_only/ctrl/rBAM/ ..."
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PlasmaMutationDetector/extdata/4test_only/ctrl/BER/ctrl1-downsample-05_MAF.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: BuildCtrlErrorRate -> MAF_from_BAM -> write.table -> file
Execution halted
Found the following significant warnings:
  gaussianProcesses/GaussianProcess.h:66:7: warning: ‘GaussianProcess::Observations’ will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning:   ‘CovarianceFunction& GaussianProcess::covFunc’ [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:3:1: warning:   when initialized here [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning: ‘GaussianProcess::covFunc’ will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:6:12: warning:   base ‘ForwardModel’ [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psgp.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pxweb)
  pxweb: R tools for PX-WEB API.
  Copyright (C) 2014 Mans Magnusson, Leo Lahti, Love Hansson
  https://github.com/ropengov/pxweb
  
  New PXWEB API(s):
   - prognos.konj.se
   - data.ssb.no
   - pxweb.asub.ax
   - makstat.stat.gov.mk
   - data.csb.gov.lv
  
  Use update_pxweb_apis() to update the api catalogue.
  > test_check("pxweb")
  ── 1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20)  ───────────────────
  NOT(success)
  
  ── 2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22)  ───────────────────
  "foo.bar" %in% unlist(lapply(api_catalogue(), function(X) X$api)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 98 SKIPPED: 16 FAILED: 2
  1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20) 
  2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Compilation used the following non-portable flag(s):
  ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’
Running ‘panel.R’ [2s/3s]
  Running ‘rq.R’ [2s/3s]
  Running ‘rq.fit.panel.R’ [0s/1s]
  Running ‘run-demos.R’ [2s/2s]
Running the tests in ‘tests/run-demos.R’ failed.
Complete output:
  > library(quantreg)
  Loading required package: SparseM
  
  Attaching package: 'SparseM'
  
  The following object is masked from 'package:base':
  
      backsolve
  
  > 
  > (dDIR <- system.file("demo", package = "quantreg"))
  [1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/quantreg/demo"
  > setwd(dDIR)
  > set.seed(1) # since some demos randomly generate
  > 
  > cat("Running demos from package 'quantreg' : \n\n")
  Running demos from package 'quantreg' : 
  
  > for(ff in list.files(dDIR, pattern="\\.R$", full.names = TRUE)) {
  +    f <- basename(ff)
  +    cat("\n", f," :\n", paste(rep.int("-", nchar(f)), collapse=''),
  +        "\n", sep='')
  + 
  +    source(ff, echo = TRUE)
  + }
  
  Frank.R :
  -------
  
  > vFrank <- function(x, df, delta, u) -log(1 - (1 - 
  +     exp(-delta))/(1 + exp(-delta * pt(x, df)) * ((1/u) - 1)))/delta
  
  > FrankModel <- function(x, delta, mu, sigma, df, tau) {
  +     z <- qt(vFrank(x, df, delta, u = tau), df)
  +     mu + sigma * z
  + }
  
  > n <- 200
  
  > df <- 8
  
  > delta <- 8
  
  > set.seed(1989)
  
  > x <- sort(rt(n, df))
  
  > v <- vFrank(x, df, delta, u = runif(n))
  
  > y <- qt(v, df)
  
  > plot(x, y, pch = "o", col = "blue", cex = 0.25)
  Error in (function (file = if (onefile) "Rplots.pdf" else "Rplot%03d.pdf",  : 
    cannot open file 'Rplots.pdf'
  Calls: source ... eval -> plot -> plot.default -> dev.hold -> <Anonymous>
  Execution halted
Running examples in ‘R2GUESS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.ESS.object
> ### Title: Compiles the main input and output files from a previous run of
> ###   'R2GUESS' and creates an ESS object.
> ### Aliases: as.ESS.object
> 
> ### ** Examples
> 
> dataX <- "data-X-C-CODE.txt"
> dataY <- "data-Y-ALL-C-CODE.txt"
> 
> path.input <- system.file("Input", package="R2GUESS")
> path.output <- system.file("Output", package="R2GUESS")
> path.par <- system.file("extdata", package="R2GUESS")
> file.par <- "Par_file_example_Hopx.xml"
> root.file.output <- "Example-GUESS-Y-Hopx"
> label.Y <- c("ADR","Fat","Heart","Kidney")
> my.env <- new.env()
> data(MAP.file,envir=my.env)
> MAP.file <- my.env$MAP.file
> modelY_Hopx <-as.ESS.object(dataY=dataY,dataX=dataX,path.input=path.input,
+     path.output=path.output,root.file.output=root.file.output,label.X=NULL,
+     label.Y=label.Y,path.par=path.par,file.par=file.par,MAP.file=MAP.file)
Warning in gzfile(file, "wb") :
  cannot open compressed file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/R2GUESS/Output/Example-GUESS-Y-Hopx_output_best_visited_models.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: as.ESS.object -> get.best.models -> save -> gzfile
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS’, resetting
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/r2lh.Rcheck/tmp’, resetting
Found the following significant warnings:
  randtoolbox.c:271:37: warning: passing argument 1 of ‘get_seed_congruRand’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/randtoolbox.Rcheck/00install.out’ for details.
Found the following significant warnings:
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 41 [-Wformat-overflow=]
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 42 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RCALI.Rcheck/00install.out’ for details.
Compilation used the following non-portable flag(s):
  ‘-Wno-non-virtual-dtor’ ‘-Wno-parentheses’
including flag(s) suppressing warnings
Running ‘testthat.R’ [72s/101s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  ── 1. Error: dmoz cat (@test-dmoz-cat.R#5)  ────────────────────────────────────
  HTTP error 404.
  1: get_dmoz_data() at testthat/test-dmoz-cat.R:5
  2: curl_download("https://github.com/soodoku/domain_classifier/blob/master/rdomains/data-raw/dmoz/dmoz_domain_category.zip?raw=true", 
         tmp)
  
  Shallalist Data saved to the following destination: ./ 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: dmoz cat (@test-dmoz-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/redcapAPI.Rcheck/00install.out’ for details.
Running examples in ‘Reol-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PingAPI
> ### Title: Test the working order of the EOL API
> ### Aliases: PingAPI
> 
> ### ** Examples
> 
> 	PingAPI()
Opening and ending tag mismatch: hr line 5 and body
Opening and ending tag mismatch: body line 3 and html
Premature end of data in tag html line 1
Error: 1: Opening and ending tag mismatch: hr line 5 and body
2: Opening and ending tag mismatch: body line 3 and html
3: Premature end of data in tag html line 1
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 209-226 (revdbayes-vignette.Rmd) 
Error: processing vignette ‘revdbayes-vignette.Rmd’ failed with diagnostics:
non-finite finite-difference value [1]
Execution halted
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGtk2.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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.
Found the following significant warnings:
  readPEDfile.c:321:74: warning: ‘%s’ directive output may be truncated writing up to 63 bytes into a region of size between 46 and 109 [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rJPSGCS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  LASlib/laswriter_las.cpp:126:6: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  LASzip/laszip.cpp:275:6: warning: ‘ bytes’ directive writing 6 bytes into a region of size between 5 and 18 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlas.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmixmod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rph_tfbs.c:811:26: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpiyv9EF’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpiyv9EF’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpiyv9EF’, resetting
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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.
Running examples in ‘RSMET-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meteofrance
> ### Title: Snow Weather Data in France
> ### Aliases: meteofrance
> 
> ### ** Examples
> 
>  
> 
> library(ggmap)
Loading required package: ggplot2
> data(meteofrance)
> 
> dates <- as.Date(meteofrance$timestamp)
> 
> data=meteofrance[dates==dates[1],]
> 
> 
> 
> map <- get_map(location ="France", zoom = 6)
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=France&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=France&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "France"
Error in data.frame(ll.lat = ll[1], ll.lon = ll[2], ur.lat = ur[1], ur.lon = ur[2]) : 
  arguments imply differing number of rows: 0, 1
Calls: get_map -> get_googlemap -> data.frame
Execution halted
Found the following significant warnings:
  rph_tfbs.c:811:26: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Running examples in ‘rvalues-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FDRCurve
> ### Title: FDR Curve
> ### Aliases: FDRCurve
> ### Keywords: dplot hstat
> 
> ### ** Examples
> 
> n <- 500
> theta <- rnorm(n)
> ses <- sqrt(rgamma(n,shape=1,scale=1))
> XX <- theta + ses*rnorm(n)
> dd <- cbind(XX,ses)
> 
> rvs <- rvalues(dd, family = gaussian)
> 
> FDRCurve(rvs, q = .1, threshold = .3, cex.main = 1.5)
Error in approxfun(threshgrid, fdr) : 
  need at least two non-NA values to interpolate
Calls: FDRCurve -> approxfun
Execution halted
Running examples in ‘RVowpalWabbit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vw
> ### Title: Run the Vowpal Wabbit fast out-of-core learner
> ### Aliases: vw
> ### Keywords: misc
> 
> ### ** Examples
> 
>   ## also see demo(vw) from which this is a subset
> 
>   library(RVowpalWabbit)
> 
>   # Test 3: without -d, training only
>   # {VW} train-sets/0002.dat    -f models/0002.model
>   test3 <- c("-t", system.file("test", "train-sets", "0002.dat", package="RVowpalWabbit"),
+              "-f", system.file("test", "models", "0002.model", package="RVowpalWabbit"))
> 
>   res <- vw(test3)
Error in Rvw(args) : 
  can't open: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RVowpalWabbit/test/models/0002.model.writing for writing, exiting
Calls: vw -> Rvw -> .Call
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SASxport.Rcheck/00install.out’ for details.
Running examples in ‘satscanMapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: satscanMapper
> ### Title: Function to map Results data produced by a SaTScan (TM) cluster
> ###   analysis
> ### Aliases: satscanMapper
> 
> ### ** Examples
> 
> ######
> #
> #  These examples focus on mapping the SaTScan (TM) data after the analysis
> #  has been completed.
> #  See the section on the CreateGeo4SS function for an example of how 
> #  to build a coordinates file (.geo) that matches the satscanMapper 
> #  boundary data.
> #
> ######
> 
> ######
> #
> #  Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
> #     Make sure SaTScan (TM) results files are still located in the directories
> #     documented in the session saved (.prm) file.
> #
> #     This example maps data for the US States containing circular clusters.
> #
> #   Get location of .prm file and location to write mapping output files
> #
> 
> SSMInstDir <- system.file(package="satscanMapper", "extdata")
> 
> TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
> 
> satscanMapper(resDir=SSMInstDir,                # path to .prm file location for output files. 
+                      prmFile  = "stateLung.prm", 
+                      title    = TT          )
Error in pdf(file = OutputFNpdf, width = vW, height = vH) : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/satscanMapper/extdata/stateLung-R01.pdf'
Calls: satscanMapper -> pdf
Execution halted
Found the following significant warnings:
  BGPscan.h:63:10: warning: ‘BGPscan::m_beta_alt’ will be initialized after [-Wreorder]
  BGPscan.h:49:15: warning:   ‘arma::uword BGPscan::m_inc_idx’ [-Wreorder]
  BGPscan.h:96:8: warning:   when initialized here [-Wreorder]
  USTscan.h:28:15: warning: ‘USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_counts’ will be initialized after [-Wreorder]
  USTscan.h:23:15: warning:   ‘arma::uword USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_num_locs’ [-Wreorder]
  USTscan.h:62:8: warning:   when initialized here [-Wreorder]
  USTscan.h:30:15: warning: ‘USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_zone_lengths’ will be initialized after [-Wreorder]
  USTscan.h:26:15: warning:   ‘bool USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_store_everything’ [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scanstatistics.Rcheck/00install.out’ for details.
Running ‘betabin.R’ [2s/3s]
  Comparing ‘betabin.Rout’ to ‘betabin.Rout.save’ ... OK
  Running ‘discrim.R’ [2s/2s]
  Comparing ‘discrim.Rout’ to ‘discrim.Rout.save’ ... OK
  Running ‘test-all.R’ [6s/10s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > 
  > if(require(testthat) && require(sensR)) {
  +     test_check("sensR")
  + }
  Loading required package: testthat
  Loading required package: sensR
  ── 1. Failure: dod estimates are stable (@test-dod.R#39)  ──────────────────────
  coef(fm) not equal to `coefExpect`.
  2/4 mismatches (average diff: 6.2e-07)
  [1] 0.952 - 0.952 == -9.67e-07
  [2] 0.309 - 0.309 ==  2.72e-07
  
  ── 2. Failure: dod works for extreme data settings (@test-dod.R#47)  ───────────
  `dod(data[1, ], data[2, ])` produced unexpected warnings.
  Expected match: Cannot assess convergence: non-finite gradient
  Actual values:
  * Cannot determine upper confidence bound
  
  ── 3. Failure: dod works for extreme data settings (@test-dod.R#49)  ───────────
  `dod_fit(data[1, ], data[2, ])` did not produce any warnings.
  
  ── 4. Failure: dod works for extreme data settings (@test-dod.R#61)  ───────────
  `dod(data[1, ], data[2, ])` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 234 SKIPPED: 1 FAILED: 4
  1. Failure: dod estimates are stable (@test-dod.R#39) 
  2. Failure: dod works for extreme data settings (@test-dod.R#47) 
  3. Failure: dod works for extreme data settings (@test-dod.R#49) 
  4. Failure: dod works for extreme data settings (@test-dod.R#61) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  data/data_set.h:79:25: warning: ‘data_set::xpMat_’ will be initialized after [-Wreorder]
  data/data_set.h:64:7: warning:   ‘arma::mat data_set::Y’ [-Wreorder]
  data/data_set.h:23:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:30:10: warning: ‘onedim_learn_rate::scale_’ will be initialized after [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:27:10: warning:   ‘double onedim_learn_rate::gamma_’ [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:18:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:51:10: warning: ‘ddim_learn_rate::eta_’ will be initialized after [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:48:10: warning:   ‘double ddim_learn_rate::a_’ [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:24:3: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sgd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  expression.h:80:10: warning: ‘ev3::Operand::exponent’ will be initialized after [-Wreorder]
  expression.h:58:7: warning:   ‘int ev3::Operand::dependency’ [-Wreorder]
  expression.cpp:271:1: warning:   when initialized here [-Wreorder]
  expression.cpp:276:1: warning:   when initialized here [-Wreorder]
  expression.cpp:281:1: warning:   when initialized here [-Wreorder]
  expression.cpp:286:1: warning:   when initialized here [-Wreorder]
  expression.h:83:11: warning: ‘ev3::Operand::depexponent’ will be initialized after [-Wreorder]
  expression.cpp:317:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/simplr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  NelderMead.c:140:24: warning: ‘%5d’ directive writing between 5 and 10 bytes into a region of size 6 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sme.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: items ‘package:smotefamily’ were removed from the search path
Examples with CPU or elapsed time > 5s
        user system elapsed
DBSMOTE 3.62  0.023   5.602
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: sp
loading reproducible     0.1.3
loading quickPlot        0.1.2
loading SpaDES.core      0.1.0
loading SpaDES.tools     0.1.0
loading SpaDES.addins    0.1.0

Default paths for SpaDES directories set to:
  cachePath:  /tmp/RtmpeCAMcc/SpaDES/cache
  inputPath:  /tmp/RtmpeCAMcc/SpaDES/inputs
  modulePath: /tmp/RtmpeCAMcc/SpaDES/modules
  outputPath: /tmp/RtmpeCAMcc/SpaDES/outputs
These can be changed using 'setPaths()'. See '?setPaths'.
Quitting from lines 48-61 (iii-cache.Rmd) 
Error: processing vignette ‘iii-cache.Rmd’ failed with diagnostics:
Some packages required for the simulation are not installed:
    tkrplot
Execution halted
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpwn2I7y’, resetting
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "georgia"
Quitting from lines 220-233 (Details.Rmd) 
Error: processing vignette ‘Details.Rmd’ failed with diagnostics:
arguments imply differing number of rows: 0, 1
Execution halted
Found the following significant warnings:
  RMcrt.h:80:13: warning: ‘extendedleaps::rmdata::gdt’ will be initialized after [-Wreorder]
  RMcrt.h:76:10: warning:   ‘bool extendedleaps::rmdata::unreliable’ [-Wreorder]
  RMcrt.cpp:19:1: warning:   when initialized here [-Wreorder]
  RVcrt.h:101:18: warning: ‘extendedleaps::rvdata::e’ will be initialized after [-Wreorder]
  RVcrt.h:99:10: warning:   ‘bool extendedleaps::rvdata::unreliable’ [-Wreorder]
  RVcrt.cpp:36:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/subselect.Rcheck/00install.out’ for details.
Running examples in ‘svMisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: toRjson
> ### Title: Convert R object to and from RJSON specification
> ### Aliases: toRjson evalRjson listToJson
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## A complex R object
> Robj <- structure(list(
+ 	a = as.double(c(1:5, 6)),
+ 	LETTERS,
+ 	c = c(c1 = 4.5, c2 = 7.8, c3 = Inf, c4 = -Inf, NA, c6 = NaN),
+ 	c(TRUE, FALSE, NA),
+ 	e = factor(c("a", "b", "a")),
+ 	f = "this is a \"string\"\nwith\tspecial chars",
+ 	g = matrix(rnorm(4), ncol = 2),
+ 	`h&'$@` = data.frame(x = 1:3, y = rnorm(3),
+ 		fact = factor(c("b", "a", "b"))),
+ 	i = Sys.Date(),
+     j = list(1:5, y = "another item")),
+     comment = "My comment\n\"",
+     anAttrib = 1:10,
+     anotherAttrib = list(TRUE, y = 1:4))
> 
> ## Convert to simplest RJSON, without attributes
> Rjson1 <- toRjson(Robj)
> Rjson1
[1] list(c(1., 2., 3., 4., 5., 6.), c("A", "B", "C", "D", "E", "F",                              
[2] "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S",                             
[3] "T", "U", "V", "W", "X", "Y", "Z"), c(4.5, 7.8, Inf, -Inf, NA,                               
[4] NaN), c(TRUE, FALSE, NA), c("a", "b", "a"), "this is a \\"string\\"\\nwith\\tspecial chars", 
[5]     c(-0.626453810742332, 0.183643324222082, -0.835628612410047,                             
[6]     1.59528080213779), list(seq(1, 3), c(0.329507771815361, -0.820468384118015,              
[7]     0.487429052428485), c("b", "a", "b")), "2018-01-11", list(                               
[8]         seq(1, 5), "another item"))                                                          
> evalRjson(Rjson1)
Error in .getClassesFromCache(Class) : 
  class should be either a character-string name or a class definition
Calls: evalRjson ... new -> getClass -> getClassDef -> .getClassesFromCache
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(swirlify)
  > library(swirl)
  
  | Hi! Type swirl() when you are ready to begin.
  
  
  Attaching package: 'swirl'
  
  The following object is masked from 'package:testthat':
  
      skip
  
  > 
  > test_check("swirlify")
  ── 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R
  all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  sybilSBML.c:2236:32: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
  sybilSBML.c:2247:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sybilSBML.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tesseract.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp41Sl16’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp41Sl16’, resetting
Found the following significant warnings:
  river.c:33:9: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  river.c:34:9: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/topmodel.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘lgtdl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for ‘gaussian’
ci.plot: no visible global function definition for ‘qnorm’
ci.plot: no visible global function definition for ‘plot’
ci.plot: no visible global function definition for ‘lines’
cst.fit.ff: no visible global function definition for ‘pnorm’
cstfit.1: no visible global function definition for ‘var’
gof.test.boots.pf: no visible binding for global variable ‘sd’
gof.test.int.1.ff: no visible global function definition for ‘quantile’
gof.test.int.1.ff: no visible global function definition for ‘var’
gof.test.int.ff: no visible global function definition for ‘pnorm’
gofTest: no visible binding for global variable ‘sd’
plotGof: no visible global function definition for ‘plot’
plotGof : <anonymous>: no visible global function definition for
  ‘lines’
plotGof: no visible global function definition for ‘lines’
sig.test.int.1.ff: no visible global function definition for ‘quantile’
sig.test.int.1.ff: no visible global function definition for ‘var’
sig.test.int.ff: no visible global function definition for ‘pnorm’
test.boots.1: no visible binding for global variable ‘sd’
tpr: no visible global function definition for ‘poisson’
tpr: no visible global function definition for ‘glm.fit’
tpr: no visible global function definition for ‘coef’
tpr: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
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 ‘_ZSt4cerr’, 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.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp5mVs28/treePos/2018_01_11/run’, resetting
Found the following significant warnings:
  libunrtf/convert.c:1397:21: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/unrtf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VariABEL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  EM.c:386:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
  EM.c:391:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VBmix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpxfr5am’, resetting
Examples with CPU or elapsed time > 5s
           user system elapsed
coor.test 5.523  0.016   6.515
Running examples in ‘WordR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addFlexTables
> ### Title: Read Word document with bookmarks and create other Word document
> ###   with rendered tables in place.
> ### Aliases: addFlexTables
> 
> ### ** Examples
> 
> library(ReporteRs)
Loading required package: ReporteRsjars
> ft_mtcars <- vanilla.table(mtcars)
> ft_iris <- vanilla.table(iris)
> FT <- list(ft_mtcars=ft_mtcars,ft_iris=ft_iris)
> addFlexTables(
+   paste(examplePath(),'templates/templateFT.docx',sep = ''),
+   paste(examplePath(),'results/resultFT.docx',sep = ''),
+   FT)
Error in writeDoc.docx(doc, docxOut) : 
  writeDoc: Cannot write to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/WordR/examples/results/resultFT.docx
Calls: addFlexTables -> <Anonymous> -> writeDoc.docx
Execution halted
Running examples in ‘yCrypticRNAs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
Namespaces in Imports field not imported from:
  ‘devtools’ ‘httr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpjvP1P5/filematrices’, resetting
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 175-189 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
RANN required
Execution halted
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Found the following significant warnings:
  ADM3.c:34:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:31: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:61: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:73: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:57: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:52:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:42: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ADM3.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Found the following significant warnings:
  matrix.c:629:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:631:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:632:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/amei.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘unmarked’
  All declared Imports should be used.
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘caret’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Error in re-building vignettes:
  ...




More than one TSN found for taxon 'Canis lupus'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Canis latrans'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Acer saccharum'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Castor canadensis'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Alces alces'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Acer rubrum'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Vulpes vulpes'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Salix babylonica'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Odocoileus virginianus'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Betula alleghaniensis'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Rangifer tarandus'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Juniperus occidentalis'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Pinus strobus'!

            Enter rownumber of taxon (other inputs will return 'NA'):
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘abind’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 233-254 (full-example.Rmd) 
Error: processing vignette 'full-example.Rmd' failed with diagnostics:
package e1071 is required
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.7Mb
Error in re-building vignettes:
  ...

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'backtestGraphics.tex' failed.
LaTeX errors:
! Package inputenc Error: Unicode char ⁵ (U+2075)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char ⁵ (U+2075)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char ⁷ (U+2077)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char ⁶ (U+2076)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char ⁶ (U+2076)
(inputenc)                not set up for use with LaTeX
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/BAMBI.Rcheck/00install.out’ for details.
installed size is 101.5Mb
  sub-directories of 1Mb or more:
    libs  101.1Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.3Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following significant warnings:
  Blasso.cpp:451:51: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/bayesCL.Rcheck/00install.out’ for details.
Running examples in ‘bayesCL-Ex.R’ failed
The error most likely occurred in:

> ### Name: lasso
> ### Title: Bayesian Lasso
> ### Aliases: lasso
> ### Keywords: regression
> 
> ### ** Examples
> 
> 
> set.seed(0)
> n_samples  <- 500
> n_features <- 40
> X <- matrix(rnorm(n_features * n_samples), nrow = n_samples)
> y <- 2 * X[,1] - 3 * X[,2] + rnorm(n_samples) # only features 1 & 2 are relevant
> 
> X_train <- X[1:400,]
> y_train <- y[1:400]
> X_test  <- X[401:500,]
> y_test  <- y[401:500]
> 
> 
> # START ------------------------------------------------------------------------
> 
> # first, standardize data !!!
> X_train <- scale(X_train)
> 
> tmp00 <- bayesCL::lasso(X = X_train, 
+                           y = y_train, 
+                           T = 500,  # number of Gibbs sampling iterations
+                           icept = T,
+                           device=0  ) # use constant term (intercept), we do
------------------------------
Platform and device selection

 *** caught segfault ***
address 0x19280390, cause 'memory not mapped'

Traceback:
 1: .Call("prepareCL", as.integer(platf), as.integer(device_id),     as.character(paste(.libPaths()[1], "/bayesCL", .Platform$file.sep,         "polyaGammaf.cl", sep = "")), as.character(paste(.libPaths()[1],         "/bayesCL", .Platform$file.sep, "polyaGammaf-", platf,         "-", device_id, ".bin", sep = "")), as.integer(params))
 2: prepare(precision = 0, device = device, parameters = parameters)
 3: bayesCL::lasso(X = X_train, y = y_train, T = 500, icept = T,     device = 0)
An irrecoverable exception occurred. R is aborting now ...
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  15.1Mb
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    libs  56.8Mb
Namespace in Imports field not imported from: ‘inline’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/bayesMCClust.Rcheck/bayesMCClust-wd’, resetting
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  23.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   3.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
installed size is 69.2Mb
  sub-directories of 1Mb or more:
    libs  69.1Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 52.6Mb
  sub-directories of 1Mb or more:
    libs  51.2Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crochet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
installed size is 141.6Mb
  sub-directories of 1Mb or more:
    include  141.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  ── 1. Failure: bib2df() throws error messages (@tests.R#53)  ───────────────────
  `bib2df("https://www.ottlngr.de/data/x.bib")` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 15 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      7.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   7.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/biorxivr.Rcheck/vign_test/biorxivr") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/index.Rmd’
(Is a VignetteBuilder field missing?)
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 17-20 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
failed to load external entity "http://www.biorxiv.org/search/Ecology?page=0"
Execution halted
Package suggested but not available for checking: ‘IHW’
Package suggested but not available for checking: ‘RQuantLib’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs  38.1Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
File ‘BMN/libs/BMN.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’
File ‘BMN/libs/BMN.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 significant warnings:
  least.squares.c:250:24: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnlearn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./sampling.h:84:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BNSP.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘yaml’
  All declared Imports should be used.
installed size is 264.8Mb
  sub-directories of 1Mb or more:
    include    2.9Mb
    lib      261.7Mb
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    libs  46.6Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  rBGWM.cc:240:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rBGWM.cc:599:18: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rBGWM.cc:799:18: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Branching.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     2.2Mb
    doc   2.4Mb
Running examples in ‘Brundle-Ex.R’ failed
The error most likely occurred in:

> ### Name: jg.plotDeSeqCombined
> ### Title: jg.plotDeSeqCombined
> ### Aliases: jg.plotDeSeqCombined
> ### Keywords: DESeq2 data plot
> 
> ### ** Examples
> 
> data(jg.controlResultsDeseq,package="Brundle")
> data(jg.experimentResultsDeseq,package="Brundle")
> 
> jg.plotDeSeqCombined(jg.controlResultsDeseq,
+                     jg.experimentResultsDeseq,
+                     title.main="ER and CTCF Binding Folding changes on ER treatment",
+                     p=0.01,flip=TRUE)
Error in concatenateObjects(x, objects, ignore.mcols = ignore.mcols) : 
  the objects to concatenate must be DESeqResults objects (or NULLs)
Calls: jg.plotDeSeqCombined ... c -> .local -> concatenateObjects -> concatenateObjects
Execution halted
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BSquare.Rcheck/00install.out’ for details.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Error in re-building vignettes:
  ...
Quitting from lines 95-97 (growth_model.Rmd) 
Error: processing vignette 'growth_model.Rmd' failed with diagnostics:
Package 'ramcmc' referenced from Rcpp::depends in source file growth_model_functions.cpp is not available.
Execution halted
installed size is 54.9Mb
  sub-directories of 1Mb or more:
    libs  54.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
Running examples in ‘cablecuttr-Ex.R’ failed
The error most likely occurred in:

> ### Name: can_i_stream
> ### Title: Query CanIStream.It
> ### Aliases: can_i_stream can_i_stream_id can_i_stream_it
> 
> ### ** Examples
> 
> can_i_stream_id("4eb0173df5f8079d29000002", "purchase")
Error in as.POSIXlt.character(x, tz, ...) : 
  character string is not in a standard unambiguous format
Calls: can_i_stream_id ... as.POSIXct.default -> as.POSIXct -> as.POSIXlt -> as.POSIXlt.character
Execution halted
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(callr)
  > 
  > Sys.unsetenv("R_TESTS")
  > 
  > test_check("callr")
  ── 1. Error: debugger is called (@test-error.R#45)  ────────────────────────────
  Can't mock functions in base packages (utils)
  1: with_mock(`utils::debugger` = function(...) called <<- TRUE, r(function() {
         1 + "A"
     }, error = "debugger")) at testthat/test-error.R:45
  2: extract_mocks(new_values = new_values[!code_pos], .env = .env, eval_env = parent.frame())
  3: lapply(stats::setNames(nm = mock_qual_names), function(qual_name) {
         pkg_name <- gsub(pkg_and_name_rx, "\\1", qual_name)
         if (is_base_pkg(pkg_name)) {
             stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
         }
         name <- gsub(pkg_and_name_rx, "\\2", qual_name)
         if (pkg_name == "") 
             pkg_name <- .env
         env <- asNamespace(pkg_name)
         if (!exists(name, envir = env, mode = "function")) 
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: debugger is called (@test-error.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
data(thermo): attached environment "CHNOSZ"
thermo$obigt: 1911 aqueous, 3588 total species
data(canprot): attached environment "canprot"
human_base: 21006 proteins
human_additional: 71173 proteins
human_extra: 337 proteins
Quitting from lines 58-72 (basis_comparison.Rmd) 
Error: processing vignette 'basis_comparison.Rmd' failed with diagnostics:
there is no package called 'KernSmooth'
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data     1.5Mb
    models   2.4Mb
Found the following significant warnings:
  slpcovis.cpp:381:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/catlearn.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Retrieving tables from http://opendata.cbs.nl/ODataCatalog/Tables?$format=json&$filter=(Language%20eq%20'en')
Quitting from lines 29-34 (cbsodata.Rmd) 
Error: processing vignette 'cbsodata.Rmd' failed with diagnostics:
Required package curl not found. Please run: install.packages('curl')
Execution halted
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/CCMnet.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/cda.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘rgdal’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Found the following significant warnings:
  ./BlockCEM.h:154:71: warning: field 'Y' will be initialized after field 'X' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/cems.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang’, resetting
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tools’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base64enc’ ‘rgl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.4Mb
Running examples in ‘climtrends-Ex.R’ failed
The error most likely occurred in:

> ### Name: ReadEtmgegFile
> ### Title: Read USHCN files
> ### Aliases: ReadEtmgegFile
> ### Keywords: programming
> 
> ### ** Examples
> 
> # data from the ECA station series of Eelde (The Netherlands) from 1900 to 2000
> EtmgegData<-ReadEtmgegFile('etmgeg_280.txt',c(2,12,13,15))
Warning in file(file, "rt") :
  cannot open file 'etmgeg_280.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: ReadEtmgegFile -> read.csv -> read.table -> file
Execution halted
Running examples in ‘CLME-Ex.R’ failed
The error most likely occurred in:

> ### Name: VarCorr
> ### Title: Variance components
> ### Aliases: VarCorr VarCorr.summary.clme VarCorr.clme
> 
> ### ** Examples
> 
> 
> data( rat.blood )
> cons <- list(order = "simple", decreasing = FALSE, node = 1 )
> clme.out <- clme(mcv ~ time + temp + sex + (1|id), data = rat.blood , 
+                  constraints = cons, seed = 42, nsim = 0)
>                  
> VarCorr( clme.out )
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
Calls: VarCorr -> VarCorr.clme -> rownames<-
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clust.bin.pair)
  > 
  > test_check("clust.bin.pair")
  ── 1. Error: McNemar scores datasets correctly (@test_clust_bin_pair.R#11)  ────
  'check.attributes' must be logical
  1: expect_equal(.mcnemar.impl(psychiatry$bh, psychiatry$ch), 11.85, tolerance = 0.1, 
         scale = NULL, "psychiatry") at testthat/test_clust_bin_pair.R:11
  2: compare(act$val, exp$val, ...)
  3: compare.numeric(act$val, exp$val, ...)
  4: all.equal(x, y, tolerance = tolerance, check.attributes = check.attributes, ...)
  5: all.equal.numeric(x, y, tolerance = tolerance, check.attributes = check.attributes, 
         ...)
  6: stop(gettextf("'%s' must be logical", "check.attributes"), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Error: McNemar scores datasets correctly (@test_clust_bin_pair.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘infuser’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
Package suggested but not available for checking: ‘CNVtools’
Error in re-building vignettes:
  ...
Quitting from lines 478-486 (codingMatrices.Rnw) 
Error: processing vignette 'codingMatrices.Rnw' failed with diagnostics:
xtable not installed.
Execution halted
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rscala’
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app   2.6Mb
    doc   2.2Mb
Running examples in ‘compareGroups-Ex.R’ failed
The error most likely occurred in:

> ### Name: compareGroups
> ### Title: Descriptives by groups
> ### Aliases: compareGroups compareGroups.default compareGroups.formula
> ###   print.compareGroups plot.compareGroups update.compareGroups
> ###   summary.compareGroups print.summary.compareGroups
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> require(compareGroups)
> 
> # load REGICOR data
> data(regicor)
> 
> # compute a time-to-cardiovascular event variable
> regicor$tcv <- with(regicor, Surv(tocv, as.integer(cv=='Yes')))
> label(regicor$tcv)<-"Cardiovascular"
Error in UseMethod("label<-") : 
  no applicable method for 'label<-' applied to an object of class "Surv"
Calls: label<-
Execution halted
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-2>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

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

    nobs

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

    object.size

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

    startsWith

Loading required package: xtable

Attaching package: 'xtable'

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

    label, label<-

Loading required package: SNPassoc
Loading required package: haplo.stats
Loading required package: mvtnorm
Loading required package: parallel
Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-3>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 151-158 (compareGroups_vignette.Rmd) 
Error: processing vignette 'compareGroups_vignette.Rmd' failed with diagnostics:
no applicable method for 'label' applied to an object of class "c('labelled', 'factor')"
Execution halted
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompRandFld.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Namespaces in Imports field not imported from:
  ‘Rtsne’ ‘scatterplot3d’
  All declared Imports should be used.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
Namespace in Imports field not imported from: ‘xtable’
  All declared Imports should be used.
Package in Depends field not imported from: ‘calibrate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
Found the following significant warnings:
  ./bdsmatrix_stub.h:44:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
  ./bdsmatrix_stub.h:53:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
  ./bdsmatrix_stub.h:100:11: warning: incompatible pointer types returning 'double *' from a function with result type 'double **' [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-clang/coxme.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 38.5Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Namespace in Imports field not imported from: ‘httpcode’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Found the following significant warnings:
  ./ctl.h:38:23: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  ./ctl.h:36:25: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
See ‘/data/gannet/ripley/R/packages/tests-clang/ctl.Rcheck/00install.out’ for details.
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Found the following significant warnings:
  BIC_comp_dposv.c:1813:44: warning: incompatible pointer types passing 'int (const struct gshdm *, const struct gshdm *)' to parameter of type '__compar_fn_t' (aka 'int (*)(const void *, const void *)') [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-clang/dagbag.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘Demerelate’ ‘misc3d’ ‘plotly’ ‘quadprog’ ‘rgl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is 72.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  70.5Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
browse: no visible global function definition for ‘slot’
browse: no visible global function definition for ‘page’
default.options: no visible binding for global variable ‘object.size’
heat.view: no visible global function definition for ‘head’
heat.view: no visible global function definition for ‘tail’
whos: no visible global function definition for ‘slotNames’
whos : <anonymous> : <anonymous>: no visible global function definition
  for ‘slot’
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘dat-Ex.R’ failed
The error most likely occurred in:

> ### Name: DataFrame
> ### Title: DataFrame and methods
> ### Aliases: DataFrame DataFrame as.DataFrame as.DataFrame.default
> ###   as.DataFrame.data.frame [.DataFrame
> 
> ### ** Examples
> 
> data("airquality")
> dat <- as.DataFrame(airquality)
> dat[~ Month > 4, ][meanWind ~ mean(Wind), sby = "Month"]["meanWind"]
Error in initialize(value, ...) : length(.Object) == 2 is not TRUE
Calls: [ ... eval -> new -> initialize -> initialize -> stopifnot
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 64-66 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
length(.Object) == 2 is not TRUE
Execution halted
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   6.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Note: found 83 marked Latin-1 strings
  Note: found 71 marked UTF-8 strings
Bootstrapping.CI: no visible global function definition for ‘quantile’
D.Jost: no visible global function definition for ‘read.table’
D.Jost: no visible global function definition for ‘write.table’
Dv.locis.corrected.calc: no visible global function definition for
  ‘p.adjust’
Gst.Nei: no visible global function definition for ‘read.table’
Gst.Nei: no visible global function definition for ‘write.table’
H.out: no visible global function definition for ‘write.table’
Hardy.calc: no visible global function definition for ‘chisq.test’
critical.ci.values: no visible global function definition for
  ‘quantile’
inputformat: no visible global function definition for ‘read.table’
inputformat: no visible global function definition for ‘write.table’
over.all.pops: no visible global function definition for ‘write.table’
p.value.correcture: no visible global function definition for
  ‘p.adjust’
pair.pops: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 13-16 (denoiSeq-vignette.Rmd) 
Error: processing vignette 'denoiSeq-vignette.Rmd' failed with diagnostics:
'roxygen2' >= 5.0.0 must be installed for this functionality.
Execution halted
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  DEploid/updateHap.cpp:670:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:678:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:681:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:682:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DEploid.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Error in re-building vignettes:
  ...
Quitting from lines 133-140 (DescriptiveStatsObeu.Rmd) 
Error: processing vignette 'DescriptiveStatsObeu.Rmd' failed with diagnostics:
Required package curl not found. Please run: install.packages('curl')
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.3Mb
    libs   1.3Mb
Packages suggested but not available for checking: ‘gurobi’ ‘Rcplex’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Namespace in Imports field not imported from: ‘ijtiff’
  All declared Imports should be used.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    libs  45.3Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  16.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: viridisLite

Attaching package: 'dplyr'

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

    intersect, select, union

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'magrittr'

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

    extract

Quitting from lines 53-92 (dissever-demo.Rmd) 
Error: processing vignette 'dissever-demo.Rmd' failed with diagnostics:
Required package is missing
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    include  19.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: doBy
Loading required package: Matrix
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used

Error: processing vignette 'LSmeans.Rnw' failed with diagnostics:
 chunk 47 
Error in VV %*% kk : non-conformable arguments
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Found the following significant warnings:
  DPPmcmc.cpp:21:10: warning: field 'model' will be initialized after field 'effectiveSizeFunction' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/DPP.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘drc’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘readr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
drtmle: TMLE with doubly robust inference
Version: 1.0.0
Loading required package: nnls
Super Learner
Version: 2.0-22
Package created on 2017-07-18

Loading required package: nloptr
Loading required package: quadprog
Loading required package: gam
Loading required package: splines
Loading required package: foreach
Loaded gam 1.14-4

Loading required package: iterators
Loading required package: parallel
Quitting from lines 408-420 (using_drtmle.Rmd) 
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
there is no package called 'snow'
Execution halted
Namespace in Imports field not imported from: ‘shapefiles’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.9Mb
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
circFBM: no visible global function definition for ‘fft’
circFBM: no visible global function definition for ‘rnorm’
circFBM: no visible global function definition for ‘par’
circFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘filter’
dvFBM: no visible global function definition for ‘quantile’
dvFBM: no visible global function definition for ‘lm’
dvFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘abline’
filt: no visible global function definition for ‘wavDaubechies’
perturbFBM: no visible global function definition for ‘rnorm’
perturbFBM: no visible global function definition for ‘rbinom’
perturbFBM: no visible global function definition for ‘par’
perturbFBM: no visible global function definition for ‘segments’
perturbFBM: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline fft filter lm par plot points quantile rbinom rnorm segments
  wavDaubechies
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "fft", "filter", "lm", "quantile", "rbinom",
             "rnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  15.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    models   4.3Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘corrplot’ ‘scorer’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpsbijeq’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpsbijeq’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpsbijeq’, resetting
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.2Mb
Error in re-building vignettes:
  ...
Loading required package: ggplot2
OMP: Warning #96: Cannot form a team with 4 threads, using 2 instead.
OMP: Hint: Consider unsetting KMP_ALL_THREADS and OMP_THREAD_LIMIT (if either is set).
Quitting from lines 172-181 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Package `maps` required for `map_data`.
Please install and try again.
Execution halted
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    libs  44.4Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Found the following significant warnings:
  ./Matrix.h:8:36: warning: field 'numrow' will be initialized after field 'numcol' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/Emcdf.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘ggmap’ ‘simFrame’
  All declared Imports should be used.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.1Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/EmiStatR.Rcheck/EmiStatR/shiny/EmiStatR_output’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/EmiStatR.Rcheck/EmiStatR/shiny/EmiStatR_output’, resetting
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    xsd   5.4Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Error in re-building vignettes:
  ...
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
there is no package called 'ggtree'
Execution halted
Running examples in ‘empiricalFDR.DESeq2-Ex.R’ failed
The error most likely occurred in:

> ### Name: empiricalFDR.DESeq2-package
> ### Title: Simulation-Based False Discovery Rate in RNA-Seq
> ### Aliases: empiricalFDR.DESeq2-package empiricalFDR.DESeq2
> 
> ### ** Examples
> 
> 
> dds = makeExampleDESeqDataSet(betaSD=1, n=100)
> dds = DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated fitted dispersions, removing these
fitting model and testing
> sims = simulateCounts(dds)
simulating...
================================================================================converting counts to integer mode
> sims = DESeq(sims)
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated fitted dispersions, removing these
fitting model and testing
> res = results(dds)
Error in concatenateObjects(x, objects, ignore.mcols = ignore.mcols) : 
  the objects to concatenate must be DESeqResults objects (or NULLs)
Calls: results ... c -> .local -> concatenateObjects -> concatenateObjects
Execution halted
Note: found 23639 marked Latin-1 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    Sweave   6.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    2.1Mb
Package suggested but not available for checking: ‘faahKO’
Namespace in Imports field not imported from: ‘BiocParallel’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   3.4Mb
Found the following significant warnings:
  input2.c:767:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/epanet2toolkit.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘ROCR’ ‘c060’ ‘methods’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Running examples in ‘Epi-Ex.R’ failed
The error most likely occurred in:

> ### Name: LCa.fit
> ### Title: Fit Lee-Carter-type models for rates to arbitrarily shaped
> ###   observations of rates in a Lexis diagram.
> ### Aliases: LCa.fit print.LCa summary.LCa plot.LCa predict.LCa
> ### Keywords: models regression
> 
> ### ** Examples
> 
> library( Epi )
> # Load the testis cancer data by Lexis triangles
> data( testisDK )
> tc <- subset( testisDK, A>14 & A<60 )
> head( tc )
    A    P D        Y
16 15 1943 0 31188.00
17 16 1943 0 31654.33
18 17 1943 0 32084.33
19 18 1943 0 32681.67
20 19 1943 0 33005.67
21 20 1943 0 33302.67
> 
> # We want to see rates per 100,000 PY
> tc$Y <- tc$Y / 10^5
> 
> # Fit the Lee-Carter model with age-period interaction (default)
> LCa.tc <- LCa.fit( tc, model="ACa", a.ref=30, p.ref=1980, quiet=FALSE, eps=10e-4, maxit=50 )
Error in vM[!is.na(cf), !is.na(cf)] <- vcv : 
  number of items to replace is not a multiple of replacement length
Calls: LCa.fit -> cbind -> ci.lin
Execution halted
Namespaces in Imports field not imported from:
  ‘llogistic’ ‘logitnorm’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/data/gannet/ripley/R/packages/tests-clang/expoRkit.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Running examples in ‘eyetrackingR-Ex.R’ failed
The error most likely occurred in:

> ### Name: analyze_time_clusters
> ### Title: Bootstrap analysis of time-clusters.
> ### Aliases: analyze_time_clusters analyze_time_clusters.time_cluster_data
> 
> ### ** Examples
> 
> data(word_recognition)
> data <- make_eyetrackingr_data(word_recognition, 
+                                participant_column = "ParticipantName",
+                                trial_column = "Trial",
+                                time_column = "TimeFromTrialOnset",
+                                trackloss_column = "TrackLoss",
+                                aoi_columns = c('Animate','Inanimate'),
+                                treat_non_aoi_looks_as_missing = TRUE )
`mutate_each()` is deprecated.
Use `mutate_all()`, `mutate_at()` or `mutate_if()` instead.
To map `funs` over a selection of variables, use `mutate_at()`
> response_window <- subset_by_window(data, window_start_time = 15500, window_end_time = 21000, 
+                                     rezero = FALSE)
Avg. window length in new data will be 5500
> response_time <- make_time_sequence_data(response_window, time_bin_size = 500, aois = "Animate", 
+                                          predictor_columns = "Sex")
> 
> time_cluster_data <- make_time_cluster_data(data = response_time, predictor_column = "SexM", 
+                          aoi = "Animate", test = "lmer", 
+                          threshold = 1.5, 
+                          formula = LogitAdjusted ~ Sex + (1|Trial) + (1|ParticipantName))
Error in UseMethod("analyze_time_bins") : 
  no applicable method for 'analyze_time_bins' applied to an object of class "data.frame"
Calls: make_time_cluster_data ... make_time_cluster_data.time_sequence_data -> do.call -> <Anonymous>
Execution halted
Running ‘testthat.R’ [130s/155s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eyetrackingR)
  > 
  > test_check("eyetrackingR")
  Test Type:	 lmer 
  Predictor:	 (Intercept) 
  Formula:	 Prop ~ AOI + (1 | Trial) 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15500 - 21000 Test Type:	 boot_splines 
  Predictor:	 Target 
  Formula:	 Prop ~ Target 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15800 - 21000 ── 1. Error: (unknown) (@test_cluster_analysis.R#143)  ─────────────────────────
  no applicable method for 'make_time_cluster_data' applied to an object of class "data.frame"
  1: make_time_cluster_data(response_time_by_ppt, predictor_column = "Sex", test = "boot_splines", 
         within_subj = FALSE, smoother = "smooth.spline", alpha = 0.05) at testthat/test_cluster_analysis.R:143
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_cluster_analysis.R#143) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
pandoc: Could not fetch http://ropensci.org/public_images/github_footer.png
HttpExceptionRequest Request {
  host                 = "ropensci.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/public_images/github_footer.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed Error_EOF))
Error: processing vignette 'ezknitr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-clang/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  fasttext.cc:121:27: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  fasttext.cc:137:27: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/fastTextR.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
Found the following significant warnings:
  cgFbat.cpp:222:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  cgFbat.cpp:265:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  cgFbat.cpp:358:40: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  cgFbat.cpp:2210:14: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:23:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:23:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:33:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:33:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rvector.cpp:23:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rvector.cpp:34:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/fbati.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 51.0Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Found the following significant warnings:
  ff.cpp:256:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ff.cpp:256:54: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/ff.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Running ‘boot.R’
  Running ‘disttests.R’
  Running ‘grouping.R’
  Running ‘plots.R’
  Running ‘weights.R’
Running the tests in ‘tests/disttests.R’ failed.
Complete output:
  > library(flexclust)
  Loading required package: grid
  Loading required package: lattice
  Loading required package: modeltools
  Loading required package: stats4
  > 
  > ## create a random matrix
  > x <- matrix(rnorm(1000), ncol=4)
  > rownames(x) <- 1:nrow(x)
  > 
  > ## test canberra at margin
  > x[1:10,1] <- 0
  > x[1:20,2] <- 0
  > x[1:30,3] <- 0
  > 
  > stopifnot(all.equal(dist2(x,x,"eucl"), as.matrix(dist(x, "eucl"))))
  > stopifnot(all.equal(dist2(x,x,"man"), as.matrix(dist(x, "man"))))
  > stopifnot(all.equal(dist2(x,x,"max"), as.matrix(dist(x, "max"))))
  > stopifnot(all.equal(dist2(x,x,"bin"), as.matrix(dist(x, "bin"))))
  > stopifnot(all.equal(dist2(x,x,"can"), as.matrix(dist(x, "can"))))
  Error: dist2(x, x, "can") and as.matrix(dist(x, "can")) are not equal:
    Mean relative difference: 0.8959585
  Execution halted
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
Package required but not available: ‘flowWorkspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Running examples in ‘forega-Ex.R’ failed
The error most likely occurred in:

> ### Name: ForecastArima
> ### Title: Floating-Point Genetic Algorithms with Statistical Forecast
> ###   Based Inheritance Operator
> ### Aliases: ForecastArima
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # Required package forega
> require("forega")
> 
> set.seed(12345)
> 
> # This function has the global minimum at x_1 = pi and x_2 = exp(1)
> f <- function (x){
+ 	return( (x[1]-pi)^2 + (x[2]-2.71828)^2 )
+ }
> 
> # Performing a floating-point genetic algorithm search with forecast probability of 0.10
> res <- forecasting_ga(evalFunc=f, chsize=2, minv=rep(-10.0,2),
+                       maxv=rep(10.0,2), crossprob=0.80, mutationprob=0.01, 
+                       popsize=100, maxiter=1000, MinimumForecastLength=20, 
+                       ForecastFunction=ForecastArima, elitism=2, forecastprob=0.01)
Error in forecasting_ga(evalFunc = f, chsize = 2, minv = rep(-10, 2),  : 
  Evaluation error: only replacement of elements is allowed.
Calls: forecasting_ga -> .Call
Execution halted
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Found the following significant warnings:
  hcubature.c:923:12: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/frailtySurv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  psplines.c:975:16: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  psplines.c:1087:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/freeknotsplines.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package which this enhances but not available for checking: ‘dggrids’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.8Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘grDevices’ ‘graphics’ ‘matrixStats’ ‘stats’
  All declared Imports should be used.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
Running ‘testthat.R’ [67s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  ── 1. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id1 not equal to c(1, 1, 2, 2, 3).
  Lengths differ: 6 is not 5
  
  ── 2. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id2 not equal to c(1, 2, 1, 2, 3).
  Lengths differ: 6 is not 5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 224 SKIPPED: 0 FAILED: 2
  1. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#50) 
  2. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.2Mb
installed size is 62.5Mb
  sub-directories of 1Mb or more:
    libs  62.1Mb
Found the following significant warnings:
  m4_prod2_ms.cpp:25:73: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod2_ms.cpp:31:36: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod2_p.cpp:24:65: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod2_p.cpp:31:36: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod_ms.cpp:26:75: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod_p.cpp:25:64: warning: field 'v' will be initialized after field 'r' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/gaston.Rcheck/00install.out’ for details.
installed size is 70.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     67.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.5Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdmp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Found the following significant warnings:
  mpi.c:3951:10: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/GENLIB.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.4Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   8.7Mb
Error in re-building vignettes:
  ...
pandoc: Could not fetch http://www.ropensci.org/public_images/github_footer.png
HttpExceptionRequest Request {
  host                 = "www.ropensci.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/public_images/github_footer.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed Error_EOF))
Error: processing vignette 'geoparser.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘alluvial’ ‘grid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggmap’ ‘gridExtra’ ‘scales’ ‘tnet’
  All declared Imports should be used.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 259-273 (comparing-graph-drawing-speed.Rmd) 
Error: processing vignette 'comparing-graph-drawing-speed.Rmd' failed with diagnostics:
there is no package called 'mgcv'
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Running examples in ‘ggfortify-Ex.R’ failed
The error most likely occurred in:

> ### Name: gglagplot
> ### Title: Plot time series against lagged versions of themselves
> ### Aliases: gglagplot
> 
> ### ** Examples
> 
> gglagplot(AirPassengers)
Error: `x` must be a vector, not a ts object, do you want `stats::lag()`?
Execution halted
Running ‘test-all.R’ [98s/118s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check('ggfortify')
  Loading required package: ggfortify
  Loading required package: ggplot2
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  ── 1. Error: gglagplot (@test-tslib.R#103)  ────────────────────────────────────
  `x` must be a vector, not a ts object, do you want `stats::lag()`?
  1: gglagplot(AirPassengers) at testthat/test-tslib.R:103
  2: dplyr::bind_rows(lapply(seq(1:lags), .lag))
  3: flatten_bindable(dots_values(...))
  4: dots_values(...)
  5: map(dots, function(dot) eval_bare(dot$expr, dot$env))
  6: lapply(.x, .f, ...)
  7: FUN(X[[i]], ...)
  8: eval_bare(dot$expr, dot$env)
  9: lapply(seq(1:lags), .lag)
  10: FUN(X[[i]], ...)
  11: as.vector(lag(ts, k))
  12: lag(ts, k)
  13: bad_args("x", "must be a vector, not a ts object, do you want `stats::lag()`?")
  14: glubort(fmt_args(args), ..., .envir = .envir)
  15: .abort(text)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1442 SKIPPED: 9 FAILED: 1
  1. Error: gglagplot (@test-tslib.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘XML’ ‘mapproj’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHANES’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plyr’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.0Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’
  ‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’
  ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’
  ‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’
  ‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 332-362 (ggrepel.Rmd) 
Error: processing vignette 'ggrepel.Rmd' failed with diagnostics:
there is no package called 'gridExtra'
Execution halted
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 50.8Mb
  sub-directories of 1Mb or more:
    libs  50.1Mb
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
Package suggested but not available for checking: ‘cplexAPI’
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gnmf.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following significant warnings:
  findEd.c:1061:26: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gRapHD.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Error in re-building vignettes:
  ...
trying URL 'https://hughparsonage.github.io/drat/src/contrib/taxstats_0.0.4.1314.tar.gz'
Content type 'application/gzip' length 52654612 bytes (50.2 MB)
==================================================
downloaded 50.2 MB

* installing *source* package ‘taxstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (taxstats)

The downloaded source packages are in
	'/tmp/RtmpRAy4Rh/downloaded_packages'
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint: Consider unsetting KMP_ALL_THREADS and OMP_THREAD_LIMIT (if either is set).
Quitting from lines 437-441 (companion-to-sample-file-1314.Rmd) 
Error: processing vignette 'companion-to-sample-file-1314.Rmd' failed with diagnostics:
there is no package called 'mgcv'
Execution halted
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tensorflow)
  > library(greta)
  
  
    greta requires TensorFlow version 1.0.0 or higher, but TensorFlow isn't installed.
    Use install_tensorflow() to install the latest version.
  
  
  
  Attaching package: 'greta'
  
  The following objects are masked from 'package:stats':
  
      binomial, poisson
  
  The following objects are masked from 'package:base':
  
      %*%, beta, diag, gamma, sweep
  
  > 
  > test_check("greta")
  Error: 'dnst' is not an exported object from 'namespace:extraDistr'
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘raster’ ‘rgeos’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘deldir’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
installed size is 126.0Mb
  sub-directories of 1Mb or more:
    java  124.6Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  SNPHWEX.cpp:50:31: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  SNPHWEX.cpp:51:65: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/HardyWeinberg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./City.h:82:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:93:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:94:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:95:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:96:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:87:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:89:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:267:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:268:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ./Spooky.h:285:36: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashFunction.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/hashmap/sparsepp/spp.h:2342:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/hashmap/sparsepp/spp.h:2365:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashmap.Rcheck/00install.out’ for details.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Found the following significant warnings:
  lassoModels/IPenalizedSolver.h:117:27: warning: field 'p_y_' will be initialized after field 'threshold_' [-Wreorder]
  lassoModels/IPenalizedSolver.h:136:25: warning: field 'p_y_' will be initialized after field 'threshold_' [-Wreorder]
  ./lassoModels/IPenalizedSolver.h:117:27: warning: field 'p_y_' will be initialized after field 'threshold_' [-Wreorder]
  ./lassoModels/IPenalizedSolver.h:136:25: warning: field 'p_y_' will be initialized after field 'threshold_' [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.cpp:59:77: warning: field 'cginit_' will be initialized after field 'p_penalty_' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/HDPenReg.Rcheck/00install.out’ for details.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        6.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.0Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
print.summary.hotspots: warning in sort(x$data, dec = TRUE): partial
  argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$positive, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$negative, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
Lchs: no visible global function definition for ‘plot’
Lchs: no visible global function definition for ‘points’
disprop: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘qnorm’
hotspots: no visible global function definition for ‘qt’
plot.hotspots: no visible global function definition for ‘par’
summary.hotspots: no visible global function definition for ‘median’
Undefined global functions or variables:
  median par plot points qnorm qt
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "median", "qnorm", "qt")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Found the following significant warnings:
  language.c:41:5: warning: flexible array initialization is a GNU extension [-Wgnu-flexible-array-initializer]
See ‘/data/gannet/ripley/R/packages/tests-clang/htmltidy.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    data  12.3Mb
    doc    1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpFZsH0T’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpFZsH0T’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpFZsH0T’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpFZsH0T’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpFZsH0T’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpFZsH0T’, resetting
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.4Mb
Running ‘testthat.R’ [41s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(huxtable)
  
  Attaching package: 'huxtable'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > 
  > we_are_in_R_CMD_check <- TRUE
  > test_check("huxtable")
  ── 1. Failure: Quick output functions work (@test-output.R#135)  ───────────────
  `quick_pdf(m, dfr, ht, file = tf)` threw an error.
  Message: Could not move pdf file to /tmp/Rtmphn9yrE/file1d07418a74cf. The pdf file remains at "file1d074c7cdab1.pdf" in the current working directory.
  Class:   simpleError/error/condition
  
  ── 2. Failure: Quick output functions work (@test-output.R#136)  ───────────────
  file.exists(tf) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 301 SKIPPED: 48 FAILED: 2
  1. Failure: Quick output functions work (@test-output.R#135) 
  2. Failure: Quick output functions work (@test-output.R#136) 
  
  Error: testthat unit tests failed
  Execution halted
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'lo' to 'locut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'hi' to 'hicut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.1Mb
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/IBDsim.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘survival’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.3Mb
    doc    2.2Mb
    libs   1.3Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.0Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  23.7Mb
Found the following significant warnings:
  src/foreign-pajek-parser.y:449:41: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  src/foreign-pajek-parser.y:453:44: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  src/foreign-pajek-parser.y:464:41: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  src/foreign-pajek-parser.y:468:44: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  ./vector.pmt:1971:19: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  ./vector.pmt:1971:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/igraph.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  15.2Mb
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     27.0Mb
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
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’
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prodlim’
  All declared Imports should be used.
Found the following significant warnings:
  ./s_hull_pro.h:77:39: warning: field 'ro' will be initialized after field 'tr' [-Wreorder]
  ./s_hull_pro.h:77:57: warning: field 'tc' will be initialized after field 'id' [-Wreorder]
  ./s_hull_pro.h:78:48: warning: field 'ro' will be initialized after field 'id' [-Wreorder]
  ./s_hull_pro.h:115:35: warning: field 'c' will be initialized after field 'id' [-Wreorder]
  ./s_hull_pro.h:116:42: warning: field 'c' will be initialized after field 'id' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/interp.Rcheck/00install.out’ for details.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘rBayesianOptimization’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘PMCMR’ ‘R6’ ‘afex’ ‘car’
  ‘ggridges’ ‘lavaan’ ‘lsmeans’ ‘multcomp’ ‘mvnormtest’ ‘psych’ ‘vcd’
  ‘vcdExtra’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.3Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/KATforDCEMRI.Rcheck/KATforDCEMRI_benchmark_test’, resetting
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘kirby21.t1’
  All declared Imports should be used.
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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  'dim' to 'dims'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs          13.7Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespace in Imports field not imported from: ‘lavaan’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/lazyWeave.Rcheck/00install.out’ for details.
Found the following significant warnings:
  partial_order.cpp:45:51: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/ldat.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘htmlwidgets’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.5Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘scales’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.8Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'listenv.md.rsp' failed with diagnostics:
there is no package called ‘markdown’
Execution halted
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs      21.9Mb
    testdata   1.5Mb
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.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/localdepth.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  lsdall.c:2078:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2200:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2209:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2219:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2225:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/logspline.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: sglOptim
Loading required package: foreach
Loading required package: doParallel
Loading required package: iterators
Loading required package: parallel
pandoc: Could not determine mime type for `https://raw.github.com/vincent-dk/lsgl/master/fig1.png'
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
Execution halted
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  44.9Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
Running ‘testthat.R’ [32s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  ── 1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ── 2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2456 SKIPPED: 36 FAILED: 2
  1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88) 
  2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data  16.0Mb
Running examples in ‘m4fe-Ex.R’ failed
The error most likely occurred in:

> ### Name: currentStocks
> ### Title: Current Stock Info (Yahoo Finance API)
> ### Aliases: currentStocks
> 
> ### ** Examples
> 
> currentStocks()
Warning in file(file, "rt") :
  URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOGL&f=abb2b3poydr1qc1cc6k2p2d1d2t1c8c3m5m6m7m8m3m4ghk1ll1t8w1w4p1mm2g1g3g4g5g6t7t6i5l2l3v1v7s6kjj5k4j6k5wvj1j3f6nn4ss1xs2ee7e8e9b4j4p5p6rr2r5r6r7s7': status was 'Couldn't resolve host name'
Error in file(file, "rt") : 
  cannot open the connection to 'http://finance.yahoo.com/d/quotes.csv?s=GOOGL&f=abb2b3poydr1qc1cc6k2p2d1d2t1c8c3m5m6m7m8m3m4ghk1ll1t8w1w4p1mm2g1g3g4g5g6t7t6i5l2l3v1v7s6kjj5k4j6k5wvj1j3f6nn4ss1xs2ee7e8e9b4j4p5p6rr2r5r6r7s7'
Calls: currentStocks -> read.csv -> read.table -> file
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
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 11.4Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   4.5Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/ManifoldOptim.Rcheck/00install.out’ for details.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    mapdata  32.6Mb
Found the following significant warnings:
  perspective.c:12:23: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/mapproj.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mapclip.c:321:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/maps.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/markmyassignment.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 264-270 (estimaterates.Rmd) 
Error: processing vignette 'estimaterates.Rmd' failed with diagnostics:
cannot open the connection to 'http://info.mcmaster.ca/~udang/mp_example_data'
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   5.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
File ‘maxent/libs/maxent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 12.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘formattable’ ‘ggplot2’ ‘ggthemes’ ‘mem’
  ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  ‘shinythemes’ ‘stringr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.3Mb
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpfqyebw’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpfqyebw’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpfqyebw’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpfqyebw’, resetting
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘shiny’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mets.Rcheck/00install.out’ for details.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.8Mb
    misc   1.1Mb
File ‘mFilter/R/zzz.R’:
  .onLoad calls:
    writeLines(strwrap(txt, indent = 4, exdent = 4))

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

.onLoad: warning in packageDescription("mFilter", lib = mylib): partial
  argument match of 'lib' to 'lib.loc'
bkfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
cffilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
Package suggested but not available for checking: ‘grasp2db’
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘jpeg’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  ggum_derivs.cpp:299:47: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:299:51: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:301:49: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:301:53: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:306:50: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:306:54: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1800:58: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1800:62: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1841:58: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1841:62: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mirt.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   5.3Mb
Error in re-building vignettes:
  ...
pandoc: Could not fetch https://fonts.googleapis.com/css?family=Open+Sans:400,700,900
HttpExceptionRequest Request {
  host                 = "fonts.googleapis.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/css"
  queryString          = "?family=Open+Sans:400,700,900"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed Error_EOF))
Error: processing vignette 'misreport-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Found the following significant warnings:
  simcensor.cpp:91:16: warning: comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ILauncher.cpp:50:31: warning: field 'v_models_' will be initialized after field 'handler_' [-Wreorder]
  ILauncher.cpp:51:31: warning: field 'handler_' will be initialized after field 'diagGaussianManager_' [-Wreorder]
  ILauncher.cpp:66:31: warning: field 'v_models_' will be initialized after field 'handler_' [-Wreorder]
  ILauncher.cpp:67:31: warning: field 'handler_' will be initialized after field 'diagGaussianManager_' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/MixAll.Rcheck/00install.out’ for details.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘foreach’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    chunks   3.4Mb
    libs    38.7Mb
Running examples in ‘mlmm-Ex.R’ failed
The error most likely occurred in:

> ### Name: mlmc
> ### Title: mlmc for missing and censored response in multilevel model.
> ### Aliases: mlmc
> 
> ### ** Examples
> 
> ## Don't show: 
> testfun=function()
+ {set.seed(100)
+  var2=abs(rnorm(50,0,1))
+  var1=(1/0.85)*var2;
+  geneid=rep(c(1:10),5);sid=c(rep(c(1:25),2),rep(c(26:50),2));
+  censor=rep(0,50)
+  pidname="geneid";sidname="sid";
+  miss_logit=var2*(-0.9);
+  miss=rbinom(50,1,exp(miss_logit)/(exp(miss_logit)+1));
+  censor=rep(0,50)
+  for (i in 1:50) {if (var1[i]<0.05) censor[i]=1}
+  for ( i in 1:50) {if ((miss[i]==1) & (censor[i]==1)) miss[i]=0};
+  for ( i in 1:50) {if (miss[i]==1) var1[i]=NA;
+  if (censor[i]==1) var1[i]=0.05}
+  pdata=data.frame(var1,var2,miss,censor,geneid,sid)
+  pathdir=getwd()
+  if (R.Version()$arch=="i386") fp=system.file("chunks","mlmc_i32.rds",package="mlmm")
+  if (R.Version()$arch=="x86_64") fp=system.file("chunks","mlmc_i64.rds",package="mlmm")
+  mcfit=readRDS(fp)
+  model1=mlmc(formula_completed=var1~var2,formula_missing=miss~var2,
+              formula_censor=censor~1,formula_subject=~var2,pdata=pdata,response_censorlim=0.05,
+              respond_dep_missing=TRUE,pidname="geneid",sidname="sid",pathname=pathdir,
+              iterno=10,chains=2,savefile=FALSE,usefit=TRUE,stanfit=mcfit)
+  }
> system.time(testfun())
Error in prep_call_sampler(object) : 
  the compiled object from C++ code for this model is invalid, possible reasons:
  - compiled with save_dso=FALSE;
  - compiled on a different platform;
  - does not exist (created from reading csv files).
Calls: system.time ... sampling -> .local -> <Anonymous> -> prep_call_sampler
Timing stopped at: 0.224 0.002 0.416
Execution halted
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Running ‘testthat.R’ [21s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modmarg)
  > 
  > test_check("modmarg")
  ── 1. Error: Collinear cols treated right (@test_glm.R#288)  ───────────────────
  non-conformable arguments
  1: marg(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 30, 
         5))) at testthat/test_glm.R:288
  2: marg.glm(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 
         30, 5)))
  3: .marg(mod = mod, var_interest = var_interest, data = data, weights = weights, ...)
  4: lapply(data, function(x) {
         df_levels <- at_transforms(model_df = x, at_list = gen_at_list(df = x, var_interest = var_interest, 
             at_var_interest = at_var_interest))
         pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
             weights = weights, link_func = NULL, deriv_func = NULL)
     })
  5: FUN(X[[i]], ...)
  6: pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  7: pred_se.glm(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  8: .pred_se(model = model, deriv_func = model$family$mu.eta, link_func = model$family$linkinv, 
         ...)
  9: calc_pred_se(vcov_mat, jacobs)
  10: diag(jac %*% vcov_model %*% t(jac))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 303 SKIPPED: 0 FAILED: 1
  1. Error: Collinear cols treated right (@test_glm.R#288) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘fields’ ‘iterpc’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.6Mb
    libs   2.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Running examples in ‘monogeneaGM-Ex.R’ failed
The error most likely occurred in:

> ### Name: hsplot
> ### Title: Scatter plot with marginal histograms
> ### Aliases: hsplot
> 
> ### ** Examples
> 
> library(phytools)
Loading required package: ape
Loading required package: maps
> 
> data(pwed_pd)
> data(ligotree)
> data(spcolmap)
> 
> #principal component analysis of size variables from ventral and dorsal anchors
> pca2d_pwedv <- pca2d(pwed_pd[,1:55], sgn=-1, labcol=spcolmap$color,
+ phylo=TRUE, phy=ligotree, genus="L. ", bound.y=c(-0.2, 0.2),
+ bound.x1=c(-0.2,0.2), bound.x2 = c(-0.2,0.2))
> pca2d_pwedd <- pca2d(pwed_pd[,56:110], sgn=-1, labcol=spcolmap$color,
+ phylo=TRUE, phy=ligotree, genus="L. ", bound.y=c(-0.2, 0.2),
+ bound.x1=c(-0.2,0.2), bound.x2 = c(-0.2,0.2))
> 
> #comparing size PC1 between ventral and dorsal anchors
> hsplot(cbind(pca2d_pwedv$scores[,1], pca2d_pwedd$scores[,1]),
+ seqx=seq(-0.2,0.15,0.01), seqy=seq(-0.2,0.15,0.01),
+ xbound=c(-0.2,0.15), ybound=c(-0.2,0.15), y.label="Dorsal size PC1",
+ x.label="Ventral size PC1", labcol=spcolmap$color, type="ru",
+ sep1=0.1, sep2=0.1, phylo=FALSE, addline=c(0,1))
Error in hist.default(dat[, 1], breaks = seqx, plot = FALSE) : 
  some 'x' not counted; maybe 'breaks' do not span range of 'x'
Calls: hsplot -> hist -> hist.default
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.7Mb
export.summary.mpm: warning in complex(real = x$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.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  43.5Mb
Error in re-building vignettes:
  ...
pandoc: Could not determine mime type for `https://raw.github.com/vincent-dk/msgl/master/fig1.png'
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
Execution halted
Namespaces in Imports field not imported from:
  ‘hms’ ‘methods’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 70.9Mb
  sub-directories of 1Mb or more:
    libs  70.8Mb
Namespaces in Imports field not imported from:
  ‘boot’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.5Mb
Namespace in Imports field not imported from: ‘ggcorrplot’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘devtools’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    CppCode        1.0Mb
    R              3.4Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.2Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘dparser’ ‘inline’ ‘n1qn1’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/npcp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘mclust’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
Found the following significant warnings:
  libglpk/glpapi06.c:530:26: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpapi06.c:539:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpios01.c:224:17: warning: explicitly assigning value of variable of type 'IOSNPD *' (aka 'struct IOSNPD *') to itself [-Wself-assign]
  libglpk/glpmpl06.c:666:17: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpmpl06.c:825:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpmps.c:1280:19: warning: explicitly assigning value of variable of type 'GLPAIJ *' (aka 'struct GLPAIJ *') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/npsf.Rcheck/00install.out’ for details.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  14.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 13172 marked Latin-1 strings
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
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())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R            1.4Mb
    test_files   4.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/ODMconverter.Rcheck/ODMconverter/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/ODMconverter.Rcheck/ODMconverter/extdata’, resetting
installed size is 92.8Mb
  sub-directories of 1Mb or more:
    libs  92.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/opefimor.Rcheck/opefimor/book’, resetting
installed size is 146.1Mb
  sub-directories of 1Mb or more:
    R         2.3Mb
    libs    136.4Mb
    models    4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 22-24 (openwindfarm-vignette.Rmd) 
Error: processing vignette 'openwindfarm-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Running ‘testthat.R’ [26s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optimus)
  This is optimus 0.1.0, roll out!
  > 
  > test_check("optimus")
  ── 1. Error: find_optimal() stops with wrong data or arguments (@test-find_optim
  argument "quo" is missing, with no default
  1: expect_error(expr = optimus::find_optimal(data = mixed, clustering = counts_cutree, 
         family = "poisson"), message = "some.*") at testthat/test-find_optimal.R:38
  2: quasi_capture(enquo(object), capture_error, label = label)
  3: label %||% quo_label(quo)
  4: quo_label(quo)
  5: expr_label(quo_expr(quo))
  6: quo_expr(quo)
  7: quo_splice(duplicate(quo), warn = warn)
  8: switch_expr(x, language = {
         if (is_quosure(x)) {
             if (!is_false(warn)) {
                 if (is_string(warn)) {
                     msg <- warn
                 }
                 else {
                     msg <- "Collapsing inner quosure"
                 }
                 warn(msg)
                 warn <- FALSE
             }
             while (is_quosure(x)) {
                 x <- f_rhs(x)
             }
             if (!is_null(parent)) {
                 mut_node_car(parent, x)
             }
             quo_splice(x, parent, warn = warn)
         }
         else {
             quo_splice(node_cdr(x), warn = warn)
         }
     }, pairlist = {
         while (!is_null(x)) {
             quo_splice(node_car(x), x, warn = warn)
             x <- node_cdr(x)
         }
     })
  9: expr_type_of(.x)
  10: typeof(x)
  11: duplicate(quo)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Error: find_optimal() stops with wrong data or arguments (@test-find_optimal.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.1Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optrdd)
  > 
  > test_check("optrdd")
  ── 1. Error: (unknown) (@test_all.R#52)  ───────────────────────────────────────
  invalid argument to unary operator
  1: optrdd(X = X, Y = Y, W = W, max.second.derivative = max.second.derivative, optimizer = "mosek", 
         verbose = FALSE) at testthat/test_all.R:52
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 8 SKIPPED: 1 FAILED: 1
  1. Error: (unknown) (@test_all.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/osc.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   4.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.0Mb
[,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'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error in loadVignetteBuilder(vigns$pkgdir) : 
  vignette builder 'knitr' not found
Calls: buildVignettes -> loadVignetteBuilder
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
Found the following significant warnings:
  export_blacs/pkg_tools.c:32:26: warning: incompatible pointer types assigning to 'BLACSCONTEXT *' (aka 'struct bLaCsCoNtExT *') from 'BLACSCONTEXT **' (aka 'struct bLaCsCoNtExT **'); dereference with * [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-clang/pbdBASE.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    lib   9.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   6.4Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Peaks.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devtools’ ‘ggplot2’ ‘haven’ ‘tidyverse’
  All declared Imports should be used.
Running examples in ‘PerformanceAnalytics-Ex.R’ failed
The error most likely occurred in:

> ### Name: Omega
> ### Title: calculate Omega for a return series
> ### Aliases: Omega
> 
> ### ** Examples
> 
> data(edhec)
>     Omega(edhec)
               Convertible Arbitrage CTA Global Distressed Securities
Omega (L = 0%)              2.602138   1.936841              3.230443
               Emerging Markets Equity Market Neutral Event Driven
Omega (L = 0%)         1.765435              6.213714     2.999655
               Fixed Income Arbitrage Global Macro Long/Short Equity
Omega (L = 0%)               2.585943     3.516616          2.438064
               Merger Arbitrage Relative Value Short Selling Funds of Funds
Omega (L = 0%)         4.595886       3.815368      1.228785       2.460153
>     Omega(edhec[,13],method="interp",output="point")
Error: 'Ecdf.default' is not an exported object from 'namespace:Hmisc'
Execution halted
Namespace in Imports field not imported from: ‘goft’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Found the following significant warnings:
  calc.c:741:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/PET.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘cluster’ ‘graph’
  All declared Imports should be used.
File ‘pgam/R/zzz.r’:
  .onLoad calls:
    require("stats", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    require("utils", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    cat("This is pgam library version", ver, "\n", sep = " ")

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

This is pgam library version 0.4.12 
pgam: warning in assign("loglik", NULL, env = pgam.env): partial
  argument match of 'env' to 'envir'
pgam: warning in get("loglik", env = pgam.env): partial argument match
  of 'env' to 'envir'
pgam.likelihood: warning in assign("loglik", loglik, env = env):
  partial argument match of 'env' to 'envir'
envelope.pgam: no visible global function definition for ‘par’
periodogram: no visible global function definition for ‘axis’
periodogram: no visible global function definition for ‘title’
periodogram: no visible global function definition for ‘lines’
plot.pgam: no visible global function definition for ‘plot’
Undefined global functions or variables:
  axis lines par plot title
Consider adding
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/PGICA.Rcheck/Sim’, resetting
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PhaseType.Rcheck/00install.out’ for details.
Found the following significant warnings:
  phreeqcpp/cvode.cpp:3783:8: warning: explicitly assigning value of variable of type 'realtype' (aka 'double') to itself [-Wself-assign]
  phreeqcpp/model.cpp:3047:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/model.cpp:3048:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:142:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:155:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:167:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:179:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:193:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:205:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/transport.cpp:630:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ReportingTools’
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Found the following significant warnings:
  hcubature.c:917:15: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/planar.Rcheck/00install.out’ for details.
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.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Found the following significant warnings:
  heftall.c:1389:2: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lsdall.c:2077:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:505:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:999:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:1078:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2199:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2208:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2218:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2224:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/polspline.Rcheck/00install.out’ for details.
Found the following significant warnings:
  whopgenome/rdnapp_MAF.h:243:12: warning: explicitly assigning value of variable of type 'unsigned int' to itself [-Wself-assign]
  whopgenome/rdnapp_MAF.h:409:45: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  whopgenome/whopgen_vcf.cpp:263:28: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  whopgenome/whoptbi_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:152:44: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  whopgenome/whoptbi_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PopGenome.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Found the following significant warnings:
  powell.c:398:17: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  powell.c:499:17: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/powell.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ppcc.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following significant warnings:
  ./shared.h:56:9: warning: comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/praznik.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computeA.c:62:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/prc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:52: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:60: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/PreciseSums.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.5Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 139-146 (architect.Rmd) 
Error: processing vignette 'architect.Rmd' failed with diagnostics:
there is no package called 'KernSmooth'
Execution halted
Namespaces in Imports field not imported from:
  ‘graphics’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘utils’
  All declared Imports should be used.
Packages suggested but not available for checking: ‘gurobi’ ‘lpsymphony’
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   6.4Mb
    libs      5.5Mb
Package suggested but not available for checking: ‘qtbase’
Namespaces in Imports field not imported from:
  ‘distcrete’ ‘incidence’
  All declared Imports should be used.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
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.
Found the following significant warnings:
  gaussianProcesses/GaussianProcess.cpp:5:21: warning: field 'Observations' will be initialized after field 'covFunc' [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:5:42: warning: field 'covFunc' will be initialized after base 'ForwardModel' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/psgp.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   2.4Mb
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ptinpoly.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc        3.8Mb
    examples   2.3Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Compilation used the following non-portable flag(s):
  ‘-Werror=format-security’ ‘-Wp,-D_FORTIFY_SOURCE=2’
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/QPot.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    contrib   3.8Mb
    doc       2.9Mb
    libs      1.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.7Mb
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      2.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/r2lh.Rcheck/tmp’, resetting
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘psych’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dtplyr’
  All declared Imports should be used.
Found the following significant warnings:
  randtoolbox.c:271:37: warning: incompatible pointer types passing 'unsigned long long *' to parameter of type 'uint64_t *' (aka 'unsigned long *') [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-clang/randtoolbox.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.0Mb
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    libs  27.2Mb
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   6.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Package suggested but not available for checking: ‘ROpenOffice’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      1.3Mb
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    include  25.5Mb
    libs      1.8Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs     23.4Mb
Error in re-building vignettes:
  ...
Latexmk: This is Latexmk, John Collins, 12 Dec. 2017, version: 4.54c.
Loading required package: RcppGSL
installed size is 51.4Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      38.2Mb
    libs     11.1Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      6.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Error in re-building vignettes:
  ...
Quitting from lines 148-189 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.0Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.4Mb
    libs      3.9Mb
installed size is 150.3Mb
  sub-directories of 1Mb or more:
    include    4.6Mb
    lib      110.2Mb
    libs      35.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following significant warnings:
  cwb/cqp/corpmanag.c:1832:12: warning: comparison of function 'split_subcorpus_name' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/rcqp.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rcompression’
Namespaces in Imports field not imported from:
  ‘DT’ ‘shiny’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  ── 1. Error: dmoz cat (@test-dmoz-cat.R#5)  ────────────────────────────────────
  HTTP error 404.
  1: get_dmoz_data() at testthat/test-dmoz-cat.R:5
  2: curl_download("https://github.com/soodoku/domain_classifier/blob/master/rdomains/data-raw/dmoz/dmoz_domain_category.zip?raw=true", 
         tmp)
  
  ── 2. Error: shallalist cat (@test-shalla-cat.R#5)  ────────────────────────────
  Timeout was reached: Resolving timed out after 10000 milliseconds
  1: get_shalla_data() at testthat/test-shalla-cat.R:5
  2: curl_download("http://www.shallalist.de/Downloads/shallalist.tar.gz", tmp)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Error: dmoz cat (@test-dmoz-cat.R#5) 
  2. Error: shallalist cat (@test-shalla-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
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.
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.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.5Mb
Found the following apparent object files/libraries:
  inst/obj/cube.obj inst/obj/cube_badmtl.obj
Object files/libraries should not be included in a source package.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
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)
Error in re-building vignettes:
  ...
Loading required package: REBayes
Loading required package: Matrix
Loading required package: splines
Quitting from lines 212-310 (Bdecon.Rnw) 
Timing stopped at: 0.102 0.013 0.116
Error: processing vignette 'Bdecon.Rnw' failed with diagnostics:
Mosek error:  MSK_RES_ERR_SIZE_LICENSE_CON: The problem has too many constraints.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/redcapAPI.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.3Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.2Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘Rcplex’
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
Namespaces in Imports field not imported from:
  ‘compiler’ ‘data.table’
  All declared Imports should be used.
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/repeated.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
installed size is 54.4Mb
  sub-directories of 1Mb or more:
    libs  53.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc     3.1Mb
    fonts   1.5Mb
    libs    2.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.5Mb
    libs   8.0Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RHRV.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computePvals.c:488:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ridge.Rcheck/00install.out’ for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
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.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONGlobals.h:44:49: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONValidator.cpp:394:105: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:397:104: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/RJSONIO.Rcheck/00install.out’ for details.
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  8.7Mb
  sub-directories of 1Mb or more:
    datasets   8.6Mb
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    exe  45.0Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    rmd   6.1Mb
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’
File ‘RMC/libs/RMC.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  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  Clustering/ClusteringInput.cpp:132:12: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  Kernel/IO/Input.cpp:212:12: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rmixmod.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
mosek: no visible global function definition for ‘help’
mosek_lptoprob: no visible global function definition for ‘is’
mosek_lptoprob: no visible global function definition for ‘as’
mosek_qptoprob: no visible global function definition for ‘is’
mosek_qptoprob: no visible global function definition for ‘as’
mosek_read: no visible global function definition for ‘help’
mosek_write: no visible global function definition for ‘help’
obtain_sparsematrix: no visible global function definition for ‘is’
obtain_sparsematrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as help is
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "help")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘Rmosek/libs/Rmosek.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 the following significant warnings:
  ./Rmpfr_utils.h:89:13: warning: comparison of constant 9223372036854775807 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rmpfr.Rcheck/00install.out’ for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:172:13: warning: variable length arrays are a C99 feature [-Wvla-extension]
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:220:16: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/data/gannet/ripley/R/packages/tests-clang/rncl.Rcheck/00install.out’ for details.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
installed size is 96.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     94.5Mb
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘microbenchmark’ ‘reshape2’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R   9.7Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/robfilter.Rcheck/00install.out’ for details.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for ‘prediction’
o.rocc: no visible global function definition for ‘performance’
o.rocc: no visible global function definition for ‘binom.test’
tr.rocc: no visible global function definition for ‘prediction’
tr.rocc: no visible global function definition for ‘performance’
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.0Mb
Namespace in Imports field not imported from: ‘vegan’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpOiB0S1’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpOiB0S1’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpOiB0S1’, resetting
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  Rserv.c:2976:16: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/00install.out’ for details.
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.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 50.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.4Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespace in Imports field not imported from: ‘pkgconfig’
  All declared Imports should be used.
installed size is 154.5Mb
  sub-directories of 1Mb or more:
    doc     2.4Mb
    libs  150.6Mb
installed size is 292.6Mb
  sub-directories of 1Mb or more:
    libs  290.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.5Mb
    projects   2.3Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Running examples in ‘RunuranGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: unuran.gui
> ### Title: A GUI for the UNU.RAN random variate generators.
> ### Aliases: unuran.gui
> ### Keywords: distribution datagen
> 
> ### ** Examples
> 
> ## start GUI to Runuran random number generator
> unuran.gui()
Error in unclass(x) : cannot unclass an external pointer
Calls: unuran.gui ... .delete -> .delete -> .delete -> ==.RGtkObject -> identical
Execution halted
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    libs  49.9Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
    test  19.6Mb
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  call_dvode.c:746:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lincmt.c:110:11: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:45: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:53: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxODE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  yacas/src/obmalloc.cpp:584:23: warning: comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Ryacas.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs    7.4Mb
    yacas   1.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘subplex’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
Running examples in ‘SAGA-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot
> ### Title: provides a custom plot of a genarch object
> ### Aliases: plot.genarch
> 
> ### ** Examples
> 
> data(PH)
> results <- AnalyzeCrossesMM(PH)
The following composite effects cannot be estimated with the line 
means available because they estimate identical quantities to 
lower order effects: 
CaAd

The composite genetic effects that will be tested are: 
 Aa, Ad, Ca, Mea, Med, AaAa, AaAd, AdAd, CaAa 

Generating Models....
 50
 100
 150
 200
 250
26 models were removed due to high covariances 
or linear relationships between predictor variables.  
The remaining 229 models have been evaluated.


AICc weights were used to select the minimum number of models whose weights sum 
to greater than 95% this model set includes 12 model(s)
> plot(results)
Error in if (maxval < 0) maxval <- 0 : 
  missing value where TRUE/FALSE needed
Calls: plot -> plot.genarch
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 267-270 (model-averaged-analysis.Rmd) 
Error: processing vignette 'model-averaged-analysis.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/SASxport.Rcheck/00install.out’ for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Found the following significant warnings:
  ./BGPscan.h:114:5: warning: field 'm_beta_alt' will be initialized after field 'm_inc_idx' [-Wreorder]
  ./USTscan.h:66:5: warning: field 'm_counts' will be initialized after field 'm_num_locs' [-Wreorder]
  ./USTscan.h:71:5: warning: field 'm_zone_lengths' will be initialized after field 'm_store_everything' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/scanstatistics.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: sp
sdm 1.0-41 (2017-07-26)
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-6 
Loading required package: dismo
Loading required package: mgcv
Quitting from lines 45-52 (quick_sdm.Rmd) 
Error: processing vignette 'quick_sdm.Rmd' failed with diagnostics:
fitFunction cannot be identified!
Execution halted
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SDMTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
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’
plot.SEL: no visible global function definition for ‘plot’
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 plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘XML’ ‘mgcv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘datasets’ ‘dbplyr’
  All declared Imports should be used.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs  12.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
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.
Package suggested but not available for checking: ‘MAST’
Found the following significant warnings:
  Warning: namespace ‘Biobase’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-clang/Seurat.Rcheck/00install.out’ for details.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc     10.1Mb
    libs     4.5Mb
    sqlite   1.5Mb
Found the following significant warnings:
  ./data/data_set.h:24:31: warning: field 'xpMat_' will be initialized after field 'Y' [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:19:5: warning: field 'scale_' will be initialized after field 'gamma_' [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:26:34: warning: field 'eta_' will be initialized after field 'a_' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/sgd.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    www   9.7Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’ ‘plotly’
  ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  ‘tools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinyBS’ ‘shinythemes’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   6.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    semantic   5.7Mb
Error in re-building vignettes:
  ...
Loading required package: sysfonts
Loading required package: showtextdb
Quitting from lines 42-58 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'curl'
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pwr’
  All declared Imports should be used.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.6Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
File ‘simpleboot/R/zzz.R’:
  .onLoad calls:
    require(boot)

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

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of 'rep' to 'replace'
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of 'rep' to 'replace'
Found the following significant warnings:
  expression.cpp:273:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:278:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:283:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:287:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:322:3: warning: field 'depexponent' will be initialized after field 'dependency' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/simplr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘mcmc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prediction’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SMCP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  SME.c:70:21: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  SME.c:71:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  SME.c:477:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  SME.c:478:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/sme.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘nlme’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CircStats’ ‘RandomFields’ ‘grDevices’ ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SpaDES.addins’ ‘SpaDES.core’ ‘SpaDES.tools’ ‘quickPlot’
  ‘reproducible’
  All declared Imports should be used.
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: sp
loading reproducible     0.1.3
loading quickPlot        0.1.2
loading SpaDES.core      0.1.0
loading SpaDES.tools     0.1.0
loading SpaDES.addins    0.1.0

Default paths for SpaDES directories set to:
  cachePath:  /tmp/Rtmpmw4qnn/SpaDES/cache
  inputPath:  /tmp/Rtmpmw4qnn/SpaDES/inputs
  modulePath: /tmp/Rtmpmw4qnn/SpaDES/modules
  outputPath: /tmp/Rtmpmw4qnn/SpaDES/outputs
These can be changed using 'setPaths()'. See '?setPaths'.
Quitting from lines 48-61 (iii-cache.Rmd) 
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
Some packages required for the simulation are not installed:
    tkrplot
Execution halted
Namespace in Imports field not imported from: ‘fastdigest’
  All declared Imports should be used.
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RCy3’
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
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.
Namespaces in Imports field not imported from:
  ‘moments’ ‘poweRlaw’
  All declared Imports should be used.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    doc    4.7Mb
    help   4.9Mb
    libs   1.7Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  23.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
Running examples in ‘specmine-Ex.R’ failed
The error most likely occurred in:

> ### Name: impute_nas_linapprox
> ### Title: Impute missing values with linear approximation
> ### Aliases: impute_nas_linapprox
> ### Keywords: missing values
> 
> ### ** Examples
> 
>   ## Example of NA imputation with linear approximation
>   data(propolis)
>   dataset = impute_nas_linapprox(propolis)
Error: 'spc.NA.linapprox' is not an exported object from 'namespace:hyperSpec'
Execution halted
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.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   7.3Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.9Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘geoR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 37-40 (SSDM.Rmd) 
Error: processing vignette 'SSDM.Rmd' failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpSnaHaw’, resetting
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.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   9.1Mb
    lib       1.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StatCharrms.tex' failed.
LaTeX errors:
! Too many }'s.
l.351 ...tion}{Other Endpoints Specification Tab}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! Too many }'s.
l.455 ...oc}{subsection}{Other Endpoints Results}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.##
                   ##..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.####
                     ..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter character
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringr’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Namespaces in Imports field not imported from:
  ‘lattice’ ‘xtable’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp45BYaI’, resetting
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
Running ‘testthat.R’ [9s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-clang/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  RMcrt.cpp:20:83: warning: field 'gdt' will be initialized after field 'unreliable' [-Wreorder]
  RVcrt.cpp:37:97: warning: field 'e' will be initialized after field 'unreliable' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/subselect.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SuppDists.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘matrixStats’ ‘nloptr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘curatedOvarianData’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.5Mb
installed size is 68.9Mb
  sub-directories of 1Mb or more:
    libs  68.1Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘broom’ ‘data.table’ ‘magrittr’ ‘pander’ ‘png’ ‘readr’
  ‘survsim’ ‘testthat’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
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
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/svd.Rcheck/00install.out’ for details.
Running examples in ‘svMisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: toRjson
> ### Title: Convert R object to and from RJSON specification
> ### Aliases: toRjson evalRjson listToJson
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## A complex R object
> Robj <- structure(list(
+ 	a = as.double(c(1:5, 6)),
+ 	LETTERS,
+ 	c = c(c1 = 4.5, c2 = 7.8, c3 = Inf, c4 = -Inf, NA, c6 = NaN),
+ 	c(TRUE, FALSE, NA),
+ 	e = factor(c("a", "b", "a")),
+ 	f = "this is a \"string\"\nwith\tspecial chars",
+ 	g = matrix(rnorm(4), ncol = 2),
+ 	`h&'$@` = data.frame(x = 1:3, y = rnorm(3),
+ 		fact = factor(c("b", "a", "b"))),
+ 	i = Sys.Date(),
+     j = list(1:5, y = "another item")),
+     comment = "My comment\n\"",
+     anAttrib = 1:10,
+     anotherAttrib = list(TRUE, y = 1:4))
> 
> ## Convert to simplest RJSON, without attributes
> Rjson1 <- toRjson(Robj)
> Rjson1
[1] list(c(1., 2., 3., 4., 5., 6.), c("A", "B", "C", "D", "E", "F",                              
[2] "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S",                             
[3] "T", "U", "V", "W", "X", "Y", "Z"), c(4.5, 7.8, Inf, -Inf, NA,                               
[4] NaN), c(TRUE, FALSE, NA), c("a", "b", "a"), "this is a \\"string\\"\\nwith\\tspecial chars", 
[5]     c(-0.626453810742332, 0.183643324222082, -0.835628612410047,                             
[6]     1.59528080213779), list(seq(1, 3), c(0.329507771815361, -0.820468384118015,              
[7]     0.487429052428485), c("b", "a", "b")), "2018-01-08", list(                               
[8]         seq(1, 5), "another item"))                                                          
> evalRjson(Rjson1)
Error in .getClassesFromCache(Class) : 
  class should be either a character-string name or a class definition
Calls: evalRjson ... new -> getClass -> getClassDef -> .getClassesFromCache
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘graphics’ ‘methods’ ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘kernlab’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/SWATmodel.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(swirlify)
  > library(swirl)
  
  | Hi! Type swirl() when you are ready to begin.
  
  
  Attaching package: 'swirl'
  
  The following object is masked from 'package:testthat':
  
      skip
  
  > 
  > test_check("swirlify")
  ── 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R
  all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    extdata   3.1Mb
Namespaces in Imports field not imported from:
  ‘crayon’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    sql   8.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    apps   2.6Mb
    libs   1.5Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘datasets’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘nlme’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   5.2Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    3.8Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘curl’ ‘devtools’ ‘rvest’ ‘timeSeries’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘reprex’ ‘rlang’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Found the following significant warnings:
  common.c:121:16: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/tiff.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 675-675 (tikzDevice.Rnw) 
Error: processing vignette 'tikzDevice.Rnw' failed with diagnostics:
there is no package called 'formatR'
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpofPD2z’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpofPD2z’, resetting
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/TimeMachine.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘forecast’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    examples  13.9Mb
    include    3.0Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
Found the following significant warnings:
  river.c:33:9: warning: incompatible pointer types assigning to 'int *' from 'double *' [-Wincompatible-pointer-types]
  river.c:34:9: warning: incompatible pointer types assigning to 'int *' from 'double *' [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-clang/topmodel.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 48-52 (Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd) 
Error: processing vignette 'Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd' failed with diagnostics:
'roxygen2' >= 5.0.0 must be installed for this functionality.
Execution halted
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.2Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  36.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/trib.Rcheck/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/trib.Rcheck/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/trib.Rcheck/trib/exdata/profile’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/trib.Rcheck/trib/exdata/profile’, resetting
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Found the following significant warnings:
  ./tsBSS.h:10:22: warning: 'varExx_k' has C-linkage specified, but returns user-defined type 'arma::mat' (aka 'Mat<double>') which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/data/gannet/ripley/R/packages/tests-clang/tsBSS.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘gsDesign’
  All declared Imports should be used.
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.
Found the following significant warnings:
  frame.c:147:21: warning: comparison of constant 4 with expression of type 'enum mad_layer' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/tuneR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpcJtNDY/treePos/2018_01_08/run’, resetting
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    dummydata   1.4Mb
    libs       21.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.6Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
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'
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   2.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc           4.8Mb
    htmlwidgets   3.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    extdata  10.8Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
installed size is 52.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  49.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘shinyjs’ ‘shinythemes’ ‘spThin’
  ‘spocc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Namespaces in Imports field not imported from:
  ‘monitoR’ ‘proxy’ ‘signal’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp1oaflp’, resetting
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/WhopGenome.Rcheck/00install.out’ for details.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Namespace in Imports field not imported from: ‘RandomFields’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
Error in re-building vignettes:
  ...
Quitting from lines 57-82 (wrswoR.Rmd) 
Error: processing vignette 'wrswoR.Rmd' failed with diagnostics:
there is no package called 'cluster'
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘seplyr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    java   9.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
Running examples in ‘xml2-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_xml
> ### Title: Read HTML or XML.
> ### Aliases: read_xml read_html read_xml.character read_xml.raw
> ###   read_xml.connection
> 
> ### ** Examples
> 
> # Literal xml/html is useful for small examples
> read_xml("<foo><bar /></foo>")
{xml_document}
<foo>
[1] <bar/>
> read_html("<html><title>Hi<title></html>")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> read_html("<html><title>Hi")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> 
> # From a local path
> read_html(system.file("extdata", "r-project.html", package = "xml2"))
{xml_document}
<html lang="en">
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
[2] <body>\n    <div class="container page">\n      <div class="row">\n       ...
> 
> # From a url
> cd <- read_xml("http://www.xmlfiles.com/examples/cd_catalog.xml")
Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html,  : 
  Specification mandate value for attribute async [41]
Calls: read_xml ... read_xml.connection -> read_xml.raw -> doc_parse_raw -> .Call
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp9vCssg/filematrices’, resetting
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R  14.6Mb
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   3.7Mb
installed size is 154.3Mb
  sub-directories of 1Mb or more:
    libs  153.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   5.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running examples in ‘bayesCL-Ex.R’ failed
The error most likely occurred in:

> ### Name: lasso
> ### Title: Bayesian Lasso
> ### Aliases: lasso
> ### Keywords: regression
> 
> ### ** Examples
> 
> 
> set.seed(0)
> n_samples  <- 500
> n_features <- 40
> X <- matrix(rnorm(n_features * n_samples), nrow = n_samples)
> y <- 2 * X[,1] - 3 * X[,2] + rnorm(n_samples) # only features 1 & 2 are relevant
> 
> X_train <- X[1:400,]
> y_train <- y[1:400]
> X_test  <- X[401:500,]
> y_test  <- y[401:500]
> 
> 
> # START ------------------------------------------------------------------------
> 
> # first, standardize data !!!
> X_train <- scale(X_train)
> 
> tmp00 <- bayesCL::lasso(X = X_train, 
+                           y = y_train, 
+                           T = 500,  # number of Gibbs sampling iterations
+                           icept = T,
+                           device=0  ) # use constant term (intercept), we do
------------------------------
Platform and device selection

 *** caught segfault ***
address 0x7481890, cause 'memory not mapped'

Traceback:
 1: .Call("prepareCL", as.integer(platf), as.integer(device_id),     as.character(paste(.libPaths()[1], "/bayesCL", .Platform$file.sep,         "polyaGammaf.cl", sep = "")), as.character(paste(.libPaths()[1],         "/bayesCL", .Platform$file.sep, "polyaGammaf-", platf,         "-", device_id, ".bin", sep = "")), as.integer(params))
 2: prepare(precision = 0, device = device, parameters = parameters)
 3: bayesCL::lasso(X = X_train, y = y_train, T = 500, icept = T,     device = 0)
An irrecoverable exception occurred. R is aborting now ...
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  17.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 52.4Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/bayesMCClust.Rcheck/bayesMCClust-wd’, resetting
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  29.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    libs  76.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  bcrypt/bcrypt.c:144:24: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
  bcrypt/bcrypt.c:254:29: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/bcrypt.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 48.2Mb
  sub-directories of 1Mb or more:
    libs  46.8Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.0Mb
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      9.2Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/biorxivr.Rcheck/vign_test/biorxivr") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/index.Rmd’
(Is a VignetteBuilder field missing?)
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 17-20 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
failed to load external entity "http://www.biorxiv.org/search/Ecology?page=0"
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
blighty: no visible global function definition for ‘par’
blighty: no visible global function definition for ‘polygon’
blighty: no visible global function definition for ‘points’
blighty: no visible global function definition for ‘box’
blighty: no visible global function definition for ‘axis’
blighty: no visible global function definition for ‘abline’
map.scale: no visible global function definition for ‘locator’
map.scale: no visible global function definition for ‘segments’
map.scale: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘locator’
north.pointer: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘arrows’
north.pointer: no visible global function definition for ‘segments’
sqlimits: no visible global function definition for ‘frame’
sqlimits: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
installed size is 417.2Mb
  sub-directories of 1Mb or more:
    include    2.9Mb
    lib      414.1Mb
installed size is 80.0Mb
  sub-directories of 1Mb or more:
    libs  79.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    bin    2.2Mb
    doc    1.2Mb
    libs   2.2Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
installed size is 88.3Mb
  sub-directories of 1Mb or more:
    libs  87.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/cda.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Found the following significant warnings:
  BlockCEM.h:52:44: warning: ‘BlockCEM<double>::Y’ will be initialized after [-Wreorder]
  BlockCEM.h:51:44: warning:   ‘FortranLinalg::DenseMatrix<double> BlockCEM<double>::X’ [-Wreorder]
  BlockCEM.h:152:5: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/cems.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel’, resetting
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Found the following significant warnings:
  bdsmatrix_stub.h:41:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:44:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:50:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:53:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:97:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:100:12: warning: return from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/coxme.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   6.1Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
Found the following significant warnings:
  BIC_comp_dposv.c:1813:44: warning: passing argument 4 of ‘qsort’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/dagbag.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/DatABEL.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 53.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  50.8Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Running examples in ‘ddeploy-Ex.R’ failed
The error most likely occurred in:

> ### Name: duke_predict
> ### Title: Predict using deployed model using REST API.
> ### Aliases: duke_predict
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> duke_predict(auth_details=duke_auth,model_name="example_fit",example_data)
Error: lexical error: invalid char in json text.
                                       <html>   <head>     <title>Inte
                     (right here) ------^
Execution halted
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.3Mb
    libs   1.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      3.4Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  42.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  25.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Found the following significant warnings:
  dcm2niix/nii_dicom.cpp:577:5: warning: ‘%s’ directive output may be truncated writing up to 63 bytes into a region of size 24 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/divest.Rcheck/00install.out’ for details.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    include  19.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   6.3Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
Found the following significant warnings:
  DPPmcmc.h:91:16: warning: ‘DPPmcmc::model’ will be initialized after [-Wreorder]
  DPPmcmc.h:82:12: warning:   ‘Rcpp::Function DPPmcmc::effectiveSizeFunction’ [-Wreorder]
  DPPmcmc.cpp:11:1: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/DPP.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   9.1Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  19.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    models   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpyweYAl’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpyweYAl’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpyweYAl’, resetting
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Quitting from lines 172-181 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Package `maps` required for `map_data`.
Please install and try again.
Execution halted
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
Found the following significant warnings:
  Matrix.h:42:7: warning: ‘myMatrix::numrow’ will be initialized after [-Wreorder]
  Matrix.h:41:7: warning:   ‘int myMatrix::numcol’ [-Wreorder]
  Matrix.h:8:12: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/Emcdf.Rcheck/00install.out’ for details.
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  27.4Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/EmiStatR.Rcheck/EmiStatR/shiny/EmiStatR_output’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/EmiStatR.Rcheck/EmiStatR/shiny/EmiStatR_output’, resetting
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    xsd   5.4Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/data/gannet/ripley/R/packages/tests-devel/expoRkit.Rcheck/00install.out’ for details.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Running ‘testthat.R’ [135s/164s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eyetrackingR)
  > 
  > test_check("eyetrackingR")
  Test Type:	 lmer 
  Predictor:	 (Intercept) 
  Formula:	 Prop ~ AOI + (1 | Trial) 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15500 - 21000 Test Type:	 boot_splines 
  Predictor:	 Target 
  Formula:	 Prop ~ Target 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15900 - 21000 ── 1. Error: (unknown) (@test_cluster_analysis.R#143)  ─────────────────────────
  no applicable method for 'make_time_cluster_data' applied to an object of class "data.frame"
  1: make_time_cluster_data(response_time_by_ppt, predictor_column = "Sex", test = "boot_splines", 
         within_subj = FALSE, smoother = "smooth.spline", alpha = 0.05) at testthat/test_cluster_analysis.R:143
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_cluster_analysis.R#143) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs  11.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Running ‘boot.R’
  Running ‘disttests.R’
  Running ‘grouping.R’
  Running ‘plots.R’
  Running ‘weights.R’
Running the tests in ‘tests/disttests.R’ failed.
Complete output:
  > library(flexclust)
  Loading required package: grid
  Loading required package: lattice
  Loading required package: modeltools
  Loading required package: stats4
  > 
  > ## create a random matrix
  > x <- matrix(rnorm(1000), ncol=4)
  > rownames(x) <- 1:nrow(x)
  > 
  > ## test canberra at margin
  > x[1:10,1] <- 0
  > x[1:20,2] <- 0
  > x[1:30,3] <- 0
  > 
  > stopifnot(all.equal(dist2(x,x,"eucl"), as.matrix(dist(x, "eucl"))))
  > stopifnot(all.equal(dist2(x,x,"man"), as.matrix(dist(x, "man"))))
  > stopifnot(all.equal(dist2(x,x,"max"), as.matrix(dist(x, "max"))))
  > stopifnot(all.equal(dist2(x,x,"bin"), as.matrix(dist(x, "bin"))))
  > stopifnot(all.equal(dist2(x,x,"can"), as.matrix(dist(x, "can"))))
  Error: dist2(x, x, "can") and as.matrix(dist(x, "can")) are not equal:
    Mean relative difference: 0.8985417
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Running ‘testthat.R’ [58s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  ── 1. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id1 not equal to c(1, 1, 2, 2, 3).
  Lengths differ: 6 is not 5
  
  ── 2. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id2 not equal to c(1, 2, 1, 2, 3).
  Lengths differ: 6 is not 5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 224 SKIPPED: 0 FAILED: 2
  1. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#50) 
  2. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  12.8Mb
installed size is 58.6Mb
  sub-directories of 1Mb or more:
    libs  58.2Mb
Found the following significant warnings:
  m4_prod2_ms.cpp:19:12: warning: ‘paraPro2::v’ will be initialized after [-Wreorder]
  m4_prod2_ms.cpp:18:16: warning:   ‘const size_t paraPro2::r’ [-Wreorder]
  m4_prod2_ms.cpp:24:3: warning:   when initialized here [-Wreorder]
  m4_prod2_ms.cpp:30:3: warning:   when initialized here [-Wreorder]
  m4_prod2_p.cpp:18:12: warning: ‘paraPro2_p::v’ will be initialized after [-Wreorder]
  m4_prod2_p.cpp:17:16: warning:   ‘const size_t paraPro2_p::r’ [-Wreorder]
  m4_prod2_p.cpp:23:3: warning:   when initialized here [-Wreorder]
  m4_prod2_p.cpp:30:3: warning:   when initialized here [-Wreorder]
  m4_prod_ms.cpp:19:18: warning: ‘paraPro_ms::v’ will be initialized after [-Wreorder]
  m4_prod_ms.cpp:18:16: warning:   ‘const size_t paraPro_ms::r’ [-Wreorder]
  m4_prod_ms.cpp:25:3: warning:   when initialized here [-Wreorder]
  m4_prod_p.cpp:18:18: warning: ‘paraPro_p::v’ will be initialized after [-Wreorder]
  m4_prod_p.cpp:17:16: warning:   ‘const size_t paraPro_p::r’ [-Wreorder]
  m4_prod_p.cpp:24:3: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/gaston.Rcheck/00install.out’ for details.
installed size is 75.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     72.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  17.7Mb
Found the following significant warnings:
  Gdmlib.cpp:1665:9: warning: specified bound 256 equals the size of the destination [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/GenABEL.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.2Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  13.2Mb
.ldots.set: no visible global function definition for ‘getS3method’
grf: no visible global function definition for ‘chull’
image.grf: no visible global function definition for ‘heat.colors’
image.krige.bayes: no visible global function definition for
  ‘heat.colors’
legend.krige: no visible global function definition for ‘heat.colors’
points.geodata: no visible global function definition for
  ‘terrain.colors’
points.geodata: no visible global function definition for ‘gray’
read.geodata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  chull getS3method gray heat.colors read.table terrain.colors
Consider adding
  importFrom("grDevices", "chull", "gray", "heat.colors",
             "terrain.colors")
  importFrom("utils", "getS3method", "read.table")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Running examples in ‘ggfortify-Ex.R’ failed
The error most likely occurred in:

> ### Name: autoplot.ts
> ### Title: Autoplot time-series-like
> ### Aliases: autoplot.ts autoplot.xts autoplot.timeSeries autoplot.irts
> ###   autoplot.stl autoplot.decomposed.ts
> 
> ### ** Examples
> 
> data(Canada, package = 'vars')
> autoplot(AirPassengers)
> autoplot(UKgas, ts.geom = 'bar')
> autoplot(Canada)
> autoplot(Canada, facets = FALSE)
> 
> library(zoo)

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

> autoplot(xts::as.xts(AirPassengers))
Error in data.frame(index(model), ...) : 
  arguments imply differing number of rows: 144, 1, 0
Calls: autoplot ... autoplot.xts -> <Anonymous> -> fortify.zoo -> cbind -> data.frame
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Loading required package: MASS
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: urca
Loading required package: lmtest
Quitting from lines 169-174 (intro_Chinese.Rmd) 
Error: processing vignette 'intro_Chinese.Rmd' failed with diagnostics:
arguments imply differing number of rows: 144, 1, 0
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 51.7Mb
  sub-directories of 1Mb or more:
    libs  51.0Mb
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Error in re-building vignettes:
  ...
trying URL 'https://hughparsonage.github.io/drat/src/contrib/taxstats_0.0.4.1314.tar.gz'
Content type 'application/gzip' length 52654612 bytes (50.2 MB)
==================================================
downloaded 50.2 MB

* installing *source* package ‘taxstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (taxstats)

The downloaded source packages are in
	'/tmp/RtmptvD0Xj/downloaded_packages'
Quitting from lines 437-441 (companion-to-sample-file-1314.Rmd) 
Error: processing vignette 'companion-to-sample-file-1314.Rmd' failed with diagnostics:
there is no package called 'mgcv'
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Found the following significant warnings:
  readstat/sas/readstat_xport_write.c:339:13: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
  readstat/sas/readstat_xport_write.c:306:13: warning: ‘%-40s’ directive output may be truncated writing between 40 and 99 bytes into a region of size 49 [-Wformat-truncation=]
  readstat/sas/readstat_sas.c:304:14: warning: ‘%1ld’ directive output may be truncated writing between 1 and 16 bytes into a region of size 8 [-Wformat-truncation=]
  readstat/sas/readstat_sas7bdat_read.c:517:101: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size between 435 and 954 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:610:52: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:638:56: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:697:51: warning: ‘%05d’ directive output may be truncated writing between 5 and 11 bytes into a region of size between 1 and 10 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:716:51: warning: ‘%05d’ directive output may be truncated writing between 5 and 11 bytes into a region of size between 1 and 10 [-Wformat-truncation=]
  readstat/spss/readstat_spss.c:139:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/haven.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lassoModels/IPenalizedSolver.h:221:28: warning: ‘HD::IPenalizedSolver::p_y_’ will be initialized after [-Wreorder]
  lassoModels/IPenalizedSolver.h:217:18: warning:   ‘STK::Real HD::IPenalizedSolver::threshold_’ [-Wreorder]
  lassoModels/IPenalizedSolver.h:112:7: warning:   when initialized here [-Wreorder]
  lassoModels/IPenalizedSolver.h:126:7: warning:   when initialized here [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.h:154:21: warning: ‘HD::LogisticFusedLassoSolver::cginit_’ will be initialized after [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.h:147:26: warning:   ‘HD::FusedLassoPenalty* HD::LogisticFusedLassoSolver::p_penalty_’ [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.cpp:51:3: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/HDPenReg.Rcheck/00install.out’ for details.
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  28.0Mb
print.tsum: warning in print.default(x$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: no visible global function definition for ‘quantile’
print.tsum: no visible global function definition for ‘printCoefmat’
print.tsum: no visible global function definition for ‘symnum’
tlm: no visible global function definition for ‘formula’
tlm: no visible binding for global variable ‘na.fail’
tlm: no visible global function definition for ‘model.matrix’
tlm: no visible global function definition for ‘model.extract’
tlm: no visible binding for global variable ‘response’
tlm: no visible global function definition for ‘lm.fit’
tlm: no visible global function definition for ‘coef’
tlm: no visible global function definition for ‘resid’
tlm: no visible global function definition for ‘Gamma’
tlm: no visible binding for global variable ‘dofse’
tlm: no visible binding for global variable ‘logLik’
tscore: no visible global function definition for ‘model.extract’
tscore: no visible binding for global variable ‘response’
tscore : <anonymous>: no visible global function definition for
  ‘model.matrix’
tscore: no visible global function definition for ‘resid’
tscore: no visible global function definition for ‘pchisq’
tscore: no visible global function definition for ‘printCoefmat’
tsum: no visible global function definition for ‘pnorm’
tsum: no visible global function definition for ‘pt’
tsum: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  Gamma coef dofse formula lm.fit logLik model.extract model.matrix
  na.fail pchisq pnorm printCoefmat pt quantile resid residuals
  response symnum
Consider adding
  importFrom("stats", "Gamma", "coef", "formula", "lm.fit", "logLik",
             "model.extract", "model.matrix", "na.fail", "pchisq",
             "pnorm", "printCoefmat", "pt", "quantile", "resid",
             "residuals", "symnum")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        6.8Mb
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpsPfve8’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpsPfve8’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpsPfve8’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpsPfve8’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpsPfve8’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpsPfve8’, resetting
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   5.4Mb
Running ‘testthat.R’ [42s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(huxtable)
  
  Attaching package: 'huxtable'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > 
  > we_are_in_R_CMD_check <- TRUE
  > test_check("huxtable")
  ── 1. Failure: Quick output functions work (@test-output.R#135)  ───────────────
  `quick_pdf(m, dfr, ht, file = tf)` threw an error.
  Message: Could not move pdf file to /tmp/RtmpndnSjU/file839e6382b562. The pdf file remains at "file839e64456f85.pdf" in the current working directory.
  Class:   simpleError/error/condition
  
  ── 2. Failure: Quick output functions work (@test-output.R#136)  ───────────────
  file.exists(tf) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 301 SKIPPED: 48 FAILED: 2
  1. Failure: Quick output functions work (@test-output.R#135) 
  2. Failure: Quick output functions work (@test-output.R#136) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   8.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.3Mb
    doc    2.2Mb
    libs   1.1Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.4Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  25.4Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  17.4Mb
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     32.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.7Mb
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 significant warnings:
  s_hull_pro.h:75:9: warning: ‘Shx::ro’ will be initialized after [-Wreorder]
  s_hull_pro.h:74:14: warning:   ‘float Shx::tr’ [-Wreorder]
  s_hull_pro.h:77:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:74:17: warning: ‘Shx::tc’ will be initialized after [-Wreorder]
  s_hull_pro.h:73:7: warning:   ‘int Shx::id’ [-Wreorder]
  s_hull_pro.h:78:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:112:11: warning: ‘Dupex::c’ will be initialized after [-Wreorder]
  s_hull_pro.h:111:7: warning:   ‘int Dupex::id’ [-Wreorder]
  s_hull_pro.h:115:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:116:3: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/interp.Rcheck/00install.out’ for details.
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Found the following significant warnings:
  as_output.c:323:24: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/iotools.Rcheck/00install.out’ for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   8.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.9Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/KATforDCEMRI.Rcheck/KATforDCEMRI_benchmark_test’, resetting
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
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.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.8Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   7.3Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs          15.0Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/lazyWeave.Rcheck/00install.out’ for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs      22.0Mb
    testdata   1.5Mb
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/localdepth.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cvrout.c:286:32: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/LogicOpt.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  42.8Mb
Running ‘testthat.R’ [32s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  ── 1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ── 2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2456 SKIPPED: 36 FAILED: 2
  1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88) 
  2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   6.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/markmyassignment.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   8.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   6.3Mb
plot.mathgraph: no visible global function definition for ‘plot’
plot.mathgraph: no visible global function definition for ‘box’
plot.mathgraph: no visible global function definition for ‘segments’
plot.mathgraph: no visible global function definition for ‘arrows’
plot.mathgraph: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows box plot segments text
Consider adding
  importFrom("graphics", "arrows", "box", "plot", "segments", "text")
to your NAMESPACE file.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  17.0Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
    libs      1.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   9.2Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp6lVDyh’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp6lVDyh’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp6lVDyh’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp6lVDyh’, resetting
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  16.6Mb
    misc   1.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   6.8Mb
Found the following significant warnings:
  ../inst/projects/MixAll/ILauncher.h:103:27: warning: ‘STK::ILauncher::v_models_’ will be initialized after [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:99:18: warning:   ‘STK::RDataHandler STK::ILauncher::handler_’ [-Wreorder]
  ILauncher.cpp:47:1: warning:   when initialized here [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:99:18: warning: ‘STK::ILauncher::handler_’ will be initialized after [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:88:46: warning:   ‘STK::DiagGaussianMixtureManager<STK::RDataHandler> STK::ILauncher::diagGaussianManager_’ [-Wreorder]
  ILauncher.cpp:63:1: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/MixAll.Rcheck/00install.out’ for details.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Found the following significant warnings:
  nelder_mead_min.c:180:21: warning: ‘%5d’ directive writing between 5 and 10 bytes into a region of size 6 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/mlegp.Rcheck/00install.out’ for details.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    chunks   3.4Mb
    libs    38.8Mb
Running examples in ‘mlmm-Ex.R’ failed
The error most likely occurred in:

> ### Name: mlmc
> ### Title: mlmc for missing and censored response in multilevel model.
> ### Aliases: mlmc
> 
> ### ** Examples
> 
> ## Don't show: 
> testfun=function()
+ {set.seed(100)
+  var2=abs(rnorm(50,0,1))
+  var1=(1/0.85)*var2;
+  geneid=rep(c(1:10),5);sid=c(rep(c(1:25),2),rep(c(26:50),2));
+  censor=rep(0,50)
+  pidname="geneid";sidname="sid";
+  miss_logit=var2*(-0.9);
+  miss=rbinom(50,1,exp(miss_logit)/(exp(miss_logit)+1));
+  censor=rep(0,50)
+  for (i in 1:50) {if (var1[i]<0.05) censor[i]=1}
+  for ( i in 1:50) {if ((miss[i]==1) & (censor[i]==1)) miss[i]=0};
+  for ( i in 1:50) {if (miss[i]==1) var1[i]=NA;
+  if (censor[i]==1) var1[i]=0.05}
+  pdata=data.frame(var1,var2,miss,censor,geneid,sid)
+  pathdir=getwd()
+  if (R.Version()$arch=="i386") fp=system.file("chunks","mlmc_i32.rds",package="mlmm")
+  if (R.Version()$arch=="x86_64") fp=system.file("chunks","mlmc_i64.rds",package="mlmm")
+  mcfit=readRDS(fp)
+  model1=mlmc(formula_completed=var1~var2,formula_missing=miss~var2,
+              formula_censor=censor~1,formula_subject=~var2,pdata=pdata,response_censorlim=0.05,
+              respond_dep_missing=TRUE,pidname="geneid",sidname="sid",pathname=pathdir,
+              iterno=10,chains=2,savefile=FALSE,usefit=TRUE,stanfit=mcfit)
+  }
> system.time(testfun())
Error in prep_call_sampler(object) : 
  the compiled object from C++ code for this model is invalid, possible reasons:
  - compiled with save_dso=FALSE;
  - compiled on a different platform;
  - does not exist (created from reading csv files).
Calls: system.time ... sampling -> .local -> <Anonymous> -> prep_call_sampler
Timing stopped at: 0.209 0.002 0.213
Execution halted
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Running ‘testthat.R’ [21s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modmarg)
  > 
  > test_check("modmarg")
  ── 1. Error: Collinear cols treated right (@test_glm.R#288)  ───────────────────
  non-conformable arguments
  1: marg(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 30, 
         5))) at testthat/test_glm.R:288
  2: marg.glm(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 
         30, 5)))
  3: .marg(mod = mod, var_interest = var_interest, data = data, weights = weights, ...)
  4: lapply(data, function(x) {
         df_levels <- at_transforms(model_df = x, at_list = gen_at_list(df = x, var_interest = var_interest, 
             at_var_interest = at_var_interest))
         pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
             weights = weights, link_func = NULL, deriv_func = NULL)
     })
  5: FUN(X[[i]], ...)
  6: pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  7: pred_se.glm(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  8: .pred_se(model = model, deriv_func = model$family$mu.eta, link_func = model$family$linkinv, 
         ...)
  9: calc_pred_se(vcov_mat, jacobs)
  10: diag(jac %*% vcov_model %*% t(jac))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 303 SKIPPED: 0 FAILED: 1
  1. Error: Collinear cols treated right (@test_glm.R#288) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.6Mb
    libs   3.4Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  10.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    libs  67.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   7.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   7.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    R              3.4Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.2Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.1Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  15.3Mb
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/ODMconverter.Rcheck/ODMconverter/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/ODMconverter.Rcheck/ODMconverter/extdata’, resetting
installed size is 87.6Mb
  sub-directories of 1Mb or more:
    libs  87.2Mb
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/opefimor.Rcheck/opefimor/book’, resetting
installed size is 153.5Mb
  sub-directories of 1Mb or more:
    R         2.3Mb
    libs    143.7Mb
    models    4.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Running ‘testthat.R’ [25s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      5.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   5.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   3.4Mb
Found the following significant warnings:
  pads_circle_pack.cpp:233:6: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/packcircles.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  export_blacs/pkg_tools.c:32:26: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/pbdBASE.Rcheck/00install.out’ for details.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    lib  12.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.6Mb
    libs      1.4Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  sparse.c:926:16: warning: self-comparison always evaluates to false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-devel/PET.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/PGICA.Rcheck/Sim’, resetting
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   1.7Mb
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   7.0Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   6.4Mb
    libs      6.0Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   3.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.4Mb
Found the following significant warnings:
  gaussianProcesses/GaussianProcess.h:66:7: warning: ‘GaussianProcess::Observations’ will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning:   ‘CovarianceFunction& GaussianProcess::covFunc’ [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:3:1: warning:   when initialized here [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning: ‘GaussianProcess::covFunc’ will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:6:12: warning:   base ‘ForwardModel’ [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/psgp.Rcheck/00install.out’ for details.
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is 66.8Mb
  sub-directories of 1Mb or more:
    libs   56.6Mb
    local   9.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    contrib   3.8Mb
    doc       2.9Mb
    libs      1.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   6.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      2.9Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/r2lh.Rcheck/tmp’, resetting
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   4.7Mb
.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 significant warnings:
  randtoolbox.c:271:37: warning: passing argument 1 of ‘get_seed_congruRand’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/randtoolbox.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   3.4Mb
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   9.1Mb
Found the following significant warnings:
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 41 [-Wformat-overflow=]
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 42 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RCALI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      1.9Mb
Error in re-building vignettes:
  ...
Latexmk: This is Latexmk, John Collins, 12 Dec. 2017, version: 4.54c.
Error in rmultinom(n, size, prob) : NA in probability vector
Error in rmultinomC(n, size, prob) : NAs not allowed in probability
Error in rmultinom(n, size, prob) : no positive probabilities
Error in rmultinomC(n, size, prob) : Not enough positive probabilities
Error : Only CSC, COO and CSR matrices from SciPy are supported.
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘slam’
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(lm) : lgCMatrix is not supported.
Error in asSpMat(L) : lgTMatrix is not supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(nm) : ngCMatrix is not supported.
Error in asSpMat(ngt) : ngTMatrix is not supported.
Error in asSpMat(nM) : ntTMatrix is not supported.
Error in asSpMat(nsc) : nsCMatrix is not supported.
Error in asSpMat(ldi) : ldiMatrix is not supported.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppArmadillo-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \setmargrb
              {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    include  25.5Mb
    libs      2.3Mb
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs     23.8Mb
installed size is 81.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      62.5Mb
    libs     16.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      6.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.1Mb
installed size is 57.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     48.3Mb
installed size is 170.6Mb
  sub-directories of 1Mb or more:
    include    4.6Mb
    lib      129.6Mb
    libs      36.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  11.0Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
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.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.6Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/redcapAPI.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   5.9Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.3Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 84.7Mb
  sub-directories of 1Mb or more:
    libs  83.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      2.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc     3.1Mb
    fonts   1.5Mb
    libs    2.6Mb
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/RGtk2.Rcheck/00install.out’ for details.
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    help  10.5Mb
    libs  10.8Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/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.
Found the following significant warnings:
  readPEDfile.c:321:74: warning: ‘%s’ directive output may be truncated writing up to 63 bytes into a region of size between 46 and 109 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rJPSGCS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  LASlib/laswriter_las.cpp:126:6: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  LASzip/laszip.cpp:275:6: warning: ‘ bytes’ directive writing 6 bytes into a region of size between 5 and 18 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rlas.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rmixmod.Rcheck/00install.out’ for details.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is 97.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.6Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Found the following significant warnings:
  rph_tfbs.c:811:26: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rphast.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.1Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpizpg3l’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpizpg3l’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmpizpg3l’, resetting
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/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.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.7Mb
installed size is 150.7Mb
  sub-directories of 1Mb or more:
    doc     2.4Mb
    libs  146.7Mb
installed size is 251.8Mb
  sub-directories of 1Mb or more:
    libs  249.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
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 significant warnings:
  rph_tfbs.c:811:26: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rtfbs.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.7Mb
    projects   2.3Mb
installed size is 45.0Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
    test  19.6Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.0Mb
    yacas   1.5Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/SASxport.Rcheck/00install.out’ for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Found the following significant warnings:
  BGPscan.h:63:10: warning: ‘BGPscan::m_beta_alt’ will be initialized after [-Wreorder]
  BGPscan.h:49:15: warning:   ‘arma::uword BGPscan::m_inc_idx’ [-Wreorder]
  BGPscan.h:96:8: warning:   when initialized here [-Wreorder]
  USTscan.h:28:15: warning: ‘USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_counts’ will be initialized after [-Wreorder]
  USTscan.h:23:15: warning:   ‘arma::uword USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_num_locs’ [-Wreorder]
  USTscan.h:62:8: warning:   when initialized here [-Wreorder]
  USTscan.h:30:15: warning: ‘USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_zone_lengths’ will be initialized after [-Wreorder]
  USTscan.h:26:15: warning:   ‘bool USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_store_everything’ [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/scanstatistics.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs  16.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Found the following significant warnings:
  Warning: namespace ‘Biobase’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/Seurat.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc     10.1Mb
    libs     6.2Mb
    sqlite   1.5Mb
Found the following significant warnings:
  data/data_set.h:79:25: warning: ‘data_set::xpMat_’ will be initialized after [-Wreorder]
  data/data_set.h:64:7: warning:   ‘arma::mat data_set::Y’ [-Wreorder]
  data/data_set.h:23:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:30:10: warning: ‘onedim_learn_rate::scale_’ will be initialized after [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:27:10: warning:   ‘double onedim_learn_rate::gamma_’ [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:18:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:51:10: warning: ‘ddim_learn_rate::eta_’ will be initialized after [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:48:10: warning:   ‘double ddim_learn_rate::a_’ [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:24:3: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/sgd.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.7Mb
Found the following significant warnings:
  expression.h:80:10: warning: ‘ev3::Operand::exponent’ will be initialized after [-Wreorder]
  expression.h:58:7: warning:   ‘int ev3::Operand::dependency’ [-Wreorder]
  expression.cpp:271:1: warning:   when initialized here [-Wreorder]
  expression.cpp:276:1: warning:   when initialized here [-Wreorder]
  expression.cpp:281:1: warning:   when initialized here [-Wreorder]
  expression.cpp:286:1: warning:   when initialized here [-Wreorder]
  expression.h:83:11: warning: ‘ev3::Operand::depexponent’ will be initialized after [-Wreorder]
  expression.cpp:317:1: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/simplr.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Found the following significant warnings:
  NelderMead.c:140:24: warning: ‘%5d’ directive writing between 5 and 10 bytes into a region of size 6 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/sme.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.3Mb
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: sp
loading reproducible     0.1.3
loading quickPlot        0.1.2
loading SpaDES.core      0.1.0
loading SpaDES.tools     0.1.0
loading SpaDES.addins    0.1.0

Default paths for SpaDES directories set to:
  cachePath:  /tmp/Rtmpy89WqF/SpaDES/cache
  inputPath:  /tmp/Rtmpy89WqF/SpaDES/inputs
  modulePath: /tmp/Rtmpy89WqF/SpaDES/modules
  outputPath: /tmp/Rtmpy89WqF/SpaDES/outputs
These can be changed using 'setPaths()'. See '?setPaths'.
Quitting from lines 48-61 (iii-cache.Rmd) 
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
Some packages required for the simulation are not installed:
    tkrplot
Execution halted
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    doc    4.7Mb
    help   4.9Mb
    libs   2.2Mb
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  27.7Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   9.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  13.4Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp8DoLbZ’, resetting
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    include   9.1Mb
    lib       1.7Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpx920ma’, resetting
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Running ‘testthat.R’ [9s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-devel/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  RMcrt.h:80:13: warning: ‘extendedleaps::rmdata::gdt’ will be initialized after [-Wreorder]
  RMcrt.h:76:10: warning:   ‘bool extendedleaps::rmdata::unreliable’ [-Wreorder]
  RMcrt.cpp:19:1: warning:   when initialized here [-Wreorder]
  RVcrt.h:101:18: warning: ‘extendedleaps::rvdata::e’ will be initialized after [-Wreorder]
  RVcrt.h:99:10: warning:   ‘bool extendedleaps::rvdata::unreliable’ [-Wreorder]
  RVcrt.cpp:36:1: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/subselect.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.7Mb
installed size is 60.5Mb
  sub-directories of 1Mb or more:
    libs  59.7Mb
Running examples in ‘svMisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: toRjson
> ### Title: Convert R object to and from RJSON specification
> ### Aliases: toRjson evalRjson listToJson
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## A complex R object
> Robj <- structure(list(
+ 	a = as.double(c(1:5, 6)),
+ 	LETTERS,
+ 	c = c(c1 = 4.5, c2 = 7.8, c3 = Inf, c4 = -Inf, NA, c6 = NaN),
+ 	c(TRUE, FALSE, NA),
+ 	e = factor(c("a", "b", "a")),
+ 	f = "this is a \"string\"\nwith\tspecial chars",
+ 	g = matrix(rnorm(4), ncol = 2),
+ 	`h&'$@` = data.frame(x = 1:3, y = rnorm(3),
+ 		fact = factor(c("b", "a", "b"))),
+ 	i = Sys.Date(),
+     j = list(1:5, y = "another item")),
+     comment = "My comment\n\"",
+     anAttrib = 1:10,
+     anotherAttrib = list(TRUE, y = 1:4))
> 
> ## Convert to simplest RJSON, without attributes
> Rjson1 <- toRjson(Robj)
> Rjson1
[1] list(c(1., 2., 3., 4., 5., 6.), c("A", "B", "C", "D", "E", "F",                              
[2] "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S",                             
[3] "T", "U", "V", "W", "X", "Y", "Z"), c(4.5, 7.8, Inf, -Inf, NA,                               
[4] NaN), c(TRUE, FALSE, NA), c("a", "b", "a"), "this is a \\"string\\"\\nwith\\tspecial chars", 
[5]     c(-0.626453810742332, 0.183643324222082, -0.835628612410047,                             
[6]     1.59528080213779), list(seq(1, 3), c(0.329507771815361, -0.820468384118015,              
[7]     0.487429052428485), c("b", "a", "b")), "2018-01-09", list(                               
[8]         seq(1, 5), "another item"))                                                          
> evalRjson(Rjson1)
Error in .getClassesFromCache(Class) : 
  class should be either a character-string name or a class definition
Calls: evalRjson ... new -> getClass -> getClassDef -> .getClassesFromCache
Execution halted
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SWATmodel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  sybilSBML.c:2236:32: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
  sybilSBML.c:2247:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/sybilSBML.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.2Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  31.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    apps   2.6Mb
    libs   2.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   6.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpWaotvi’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpWaotvi’, resetting
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    examples  13.4Mb
    include    3.0Mb
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
Found the following significant warnings:
  river.c:33:9: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  river.c:34:9: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/topmodel.Rcheck/00install.out’ for details.
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/trib.Rcheck/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/trib.Rcheck/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/trib.Rcheck/trib/exdata/profile’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/trib.Rcheck/trib/exdata/profile’, resetting
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmptAe5Gr/treePos/2018_01_09/run’, resetting
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    dummydata   1.4Mb
    libs       20.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.0Mb
Found the following significant warnings:
  libunrtf/convert.c:1397:21: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/unrtf.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/VariABEL.Rcheck/00install.out’ for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Found the following significant warnings:
  EM.c:386:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
  EM.c:391:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/VBmix.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  47.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprR1R22’, resetting
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Packages in Depends field not imported from:
  'Rglpk' 'corrplot' 'lattice' 'rgl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
multiplot: no visible global function definition for 'rainbow'
multiplot: no visible global function definition for 'plot'
multiplot: no visible global function definition for 'text'
multiplot: no visible global function definition for 'lines'
multiplot: no visible global function definition for 'par'
plot.abf2: no visible global function definition for 'plot'
plot.abf2: no visible global function definition for 'abline'
plot.abf2: no visible global function definition for 'text'
plot.abf2split: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rgraphviz'
fillCSVData: no visible global function definition for 'read.table'
fillData: no visible global function definition for 'edit'
plotGraphs: no visible global function definition for 'par'
plotGraphs: no visible global function definition for 'plot'
plotGraphs: no visible global function definition for 'lines'
plotGraphs: no visible global function definition for 'legend'
plotGraphs: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new edit legend lines par plot read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
print.funlinWLS: no visible global function definition for 'pchisq'
print.linML: no visible global function definition for 'pchisq'
print.loglinML: no visible global function definition for 'pchisq'
print.satMarML: no visible global function definition for 'pchisq'
print.satMcarWLS: no visible global function definition for 'pchisq'
summary.funlinWLS: no visible global function definition for 'pchisq'
summary.linML: no visible global function definition for 'pchisq'
summary.loglinML: no visible global function definition for 'pchisq'
summary.satMarML: no visible global function definition for 'pchisq'
summary.satMcarWLS: no visible global function definition for 'pchisq'
summary.waldTest: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
acm: no visible global function definition for 'read.table'
clusters: no visible global function definition for 'write.matrix'
clusters: no visible global function definition for 'dev.new'
clusters: no visible global function definition for 'par'
clusters: no visible global function definition for 'hist'
clusters: no visible global function definition for 'legend'
clusters: no visible global function definition for 'pdf'
clusters: no visible global function definition for 'dev.off'
erra: no visible global function definition for 'read.table'
erra: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  dev.new dev.off hist legend par pbeta pdf read.table write.matrix
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "pbeta")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/RtmpCCovbc/filematrices', resetting
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/Rtmp4wDxuc/filematrices', resetting
'library' or 'require' call to 'mvtnorm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Aggregate: no visible global function definition for 'aggregate'
Aggregate: no visible binding for global variable 'tail'
Aggregate: no visible binding for global variable 'var'
cocktailEnsemble: no visible global function definition for 'glm'
cocktailEnsemble: no visible global function definition for 'binomial'
cocktailEnsemble: no visible global function definition for 'step'
cocktailEnsemble: no visible binding for global variable 'na.omit'
imputeMissings : <anonymous>: no visible global function definition for
  'median'
predict.cocktailEnsemble: no visible global function definition for
  'predict'
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
.amdai.initparam: no visible global function definition for 'cov'
.amdat.initiparam: no visible global function definition for 'cov'
amdai: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'SemiPar' 'nlme'
  Please remove these calls from your code.
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'Matrix'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Rcpp'
  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:
  'Matrix' 'coda' 'mvtnorm' 'MCMCpack' 'spatstat' 'parallel'
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:
  'MCMCpack' 'Matrix' 'coda' 'mvtnorm' 'parallel' 'spatstat'
  Please remove these calls from your code.
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.
critical.values: no visible global function definition for 'rnorm'
critical.values: no visible global function definition for 'quantile'
mandel.test: no visible global function definition for 'qf'
mtukey.test : p.test: no visible global function definition for 'qf'
mtukey.test: no visible binding for global variable 'quantile'
mtukey.test: no visible global function definition for 'rnorm'
tukey.test: no visible global function definition for 'qf'
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data       2.7Mb
    pictures   2.1Mb
ADM3: no visible global function definition for 'read.table'
ADM3: no visible global function definition for 'write.table'
dLRs: no visible global function definition for 'IQR'
dLRs: no visible global function definition for 'na.omit'
dLRs: no visible global function definition for 'qnorm'
plotADM3: no visible global function definition for 'plot'
plotADM3: no visible global function definition for 'abline'
plotADM3: no visible global function definition for 'segments'
Undefined global functions or variables:
  IQR abline na.omit plot qnorm read.table segments write.table
Consider adding
  importFrom("graphics", "abline", "plot", "segments")
  importFrom("stats", "IQR", "na.omit", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
bayescan: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
aftgee: no visible global function definition for 'model.extract'
aftgee: no visible global function definition for 'model.matrix'
aftgee: no visible global function definition for 'lm'
aftgee: no visible global function definition for 'vcov'
aftgee.fit: no visible global function definition for 'lm'
aftgee.fit: no visible global function definition for 'rexp'
aftgee.fit: no visible global function definition for 'var'
aftsrr: no visible global function definition for 'model.extract'
aftsrr: no visible global function definition for 'model.matrix'
aftsrr.fit: no visible global function definition for 'lm'
aftsrr.fit: no visible global function definition for 'rexp'
aftsrr.fit: no visible global function definition for 'var'
getSmoothSuv: no visible global function definition for 'pnorm'
print.summary.aftgee: no visible global function definition for
  'printCoefmat'
print.summary.aftsrr: no visible global function definition for
  'printCoefmat'
solveGehan: no visible global function definition for 'nlm'
summary.aftgee: no visible global function definition for 'pnorm'
summary.aftsrr: no visible global function definition for 'pnorm'
viEmp: no visible global function definition for 'rexp'
viEmp: no visible global function definition for 'rnorm'
viEmp: no visible global function definition for 'var'
zlFun: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm model.extract model.matrix nlm pnorm printCoefmat rexp rnorm var
  vcov
Consider adding
  importFrom("stats", "lm", "model.extract", "model.matrix", "nlm",
             "pnorm", "printCoefmat", "rexp", "rnorm", "var", "vcov")
to your NAMESPACE file.
closure_total_fair: no visible global function definition for 'is'
closure_transitive: no visible global function definition for 'is'
de_transitive: no visible global function definition for 'is'
get_equivalence_classes: no visible global function definition for 'is'
get_incomparable_pairs: no visible global function definition for 'is'
get_independent_sets: no visible global function definition for 'is'
is_reflexive: no visible global function definition for 'is'
is_total: no visible global function definition for 'is'
is_transitive: no visible global function definition for 'is'
pareto2_estimate_mle: no visible global function definition for
  'uniroot'
pareto2_test_f: no visible global function definition for 'qf'
pareto2_test_f: no visible global function definition for 'pf'
plot.citfun: no visible global function definition for 'plot'
plot.citfun: no visible global function definition for 'par'
plot.citfun: no visible global function definition for 'segments'
plot.citfun: no visible global function definition for 'points'
plot_producer: no visible global function definition for 'plot'
plot_producer: no visible global function definition for 'par'
plot_producer: no visible global function definition for 'segments'
plot_producer: no visible global function definition for 'points'
rpareto2: no visible global function definition for 'runif'
Undefined global functions or variables:
  is par pf plot points qf runif segments uniroot
Consider adding
  importFrom("graphics", "par", "plot", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "pf", "qf", "runif", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
IIR: no visible global function definition for 'qnorm'
TIR: no visible global function definition for 'qnorm'
agreement: no visible global function definition for 'var'
agreement: no visible global function definition for 'pchisq'
agreement: no visible global function definition for 'dnorm'
agreement: no visible global function definition for 'qnorm'
html.report: no visible global function definition for 'plot'
plot.report: no visible global function definition for 'plot'
plot.report: no visible global function definition for 'axis'
plot.report: no visible global function definition for 'points'
unified.agreement: no visible global function definition for 'lm'
unified.agreement: no visible global function definition for 'qnorm'
unified.agreement: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  axis dnorm lm pchisq plot pnorm points qnorm var
Consider adding
  importFrom("graphics", "axis", "plot", "points")
  importFrom("stats", "dnorm", "lm", "pchisq", "pnorm", "qnorm", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace with empty importFrom: 'survival'
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'survival'
A package should be listed in only one of these fields.
backfit.cox.interaction: no visible global function definition for
  'coxph'
backfit.lm.interaction: no visible global function definition for 'lm'
backfit.logistic.interaction: no visible global function definition for
  'glm'
backfit.logistic.main: no visible global function definition for 'glm'
cox.interaction: no visible global function definition for 'coxph'
cv.cox.interaction: no visible global function definition for 'coxph'
cv.cox.main: no visible global function definition for 'coxph'
cv.lm.interaction: no visible global function definition for 'lm'
cv.lm.main: no visible global function definition for 'lm'
cv.logistic.interaction: no visible global function definition for
  'glm'
cv.logistic.main: no visible global function definition for 'glm'
lm.interaction: no visible global function definition for 'lm'
logistic.interaction: no visible global function definition for 'glm'
logistic.main: no visible global function definition for 'glm'
Undefined global functions or variables:
  coxph glm lm
Consider adding
  importFrom("stats", "glm", "lm")
to your NAMESPACE file.
dke.fun.default: no visible global function definition for 'hist'
kef: no visible global function definition for 'dbinom'
kef: no visible global function definition for 'dgamma'
kef: no visible global function definition for 'dlnorm'
plot.dke.fun: no visible global function definition for 'hist'
plot.dke.fun: no visible global function definition for 'lines'
plot.hcvc.fun1d: no visible global function definition for
  'plot.default'
plot.hcvd.fun1d: no visible global function definition for
  'plot.default'
plot.kern.fun1d: no visible global function definition for
  'plot.default'
plot.kpmfe.fun1d: no visible global function definition for
  'plot.default'
plot.reg.fun1d: no visible global function definition for
  'plot.default'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
adpbar: no visible global function definition for 'optim'
alabama: no visible global function definition for 'optim'
auglag: no visible global function definition for 'modifyList'
auglag1: no visible global function definition for 'optim'
auglag1: no visible global function definition for 'nlminb'
auglag2: no visible global function definition for 'optim'
auglag2: no visible global function definition for 'nlminb'
auglag3: no visible global function definition for 'optim'
auglag3: no visible global function definition for 'nlminb'
augpen: no visible global function definition for 'optim'
constrOptim.nl: no visible global function definition for 'modifyList'
Undefined global functions or variables:
  modifyList nlminb optim
Consider adding
  importFrom("stats", "nlminb", "optim")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
eval.blockdesign: no visible global function definition for
  'model.matrix'
eval.design: no visible global function definition for 'model.matrix'
expand.formula: no visible global function definition for 'as.formula'
model.matrix.formula: no visible global function definition for
  'model.matrix.default'
model.matrix.terms: no visible global function definition for
  'model.matrix.default'
optBlock : set.factors: no visible global function definition for 'C'
optBlock : remove.nesting: no visible global function definition for
  'as.formula'
optBlock: no visible global function definition for 'formula'
optBlock: no visible global function definition for 'model.matrix'
optFederov: no visible global function definition for 'formula'
optFederov: no visible global function definition for 'model.matrix'
optMonteCarlo : RandomLevels: no visible global function definition for
  'runif'
optMonteCarlo : RandomMixture: no visible global function definition
  for 'rexp'
optMonteCarlo : expand: no visible global function definition for
  'model.matrix'
optMonteCarlo: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  C as.formula formula model.matrix model.matrix.default rexp runif
Consider adding
  importFrom("stats", "C", "as.formula", "formula", "model.matrix",
             "model.matrix.default", "rexp", "runif")
to your NAMESPACE file.
hierarchical: no visible global function definition for 'terms'
hierarchical: no visible global function definition for 'loglin'
hierarchical: no visible global function definition for 'dmultinom'
markov: no visible global function definition for 'download.file'
metropolis: no visible global function definition for 'runif'
mpolyListToMat : <anonymous>: no visible global function definition for
  'runif'
polyOptim: no visible global function definition for 'deriv'
print.hierarchical: no visible binding for global variable 'sd'
spectral : summarize: no visible global function definition for 'sd'
subsets : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  combn deriv dmultinom download.file loglin runif sd terms
Consider adding
  importFrom("stats", "deriv", "dmultinom", "loglin", "runif", "sd",
             "terms")
  importFrom("utils", "combn", "download.file")
to your NAMESPACE file.
gascuel: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
allanVarSelect: no visible global function definition for 'read.csv'
fitvbiglm: no visible global function definition for 'read.csv'
fitvbiglm: no visible global function definition for 'update'
getbestchunksize: no visible global function definition for 'read.csv'
getbestchunksize: no visible global function definition for
  'object.size'
predictvbiglm: no visible global function definition for 'read.csv'
predictvbiglm: no visible global function definition for 'predict'
predictvbiglm: no visible global function definition for
  'weighted.mean'
readinbigdata : <anonymous>: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  object.size predict read.csv update weighted.mean
Consider adding
  importFrom("stats", "predict", "update", "weighted.mean")
  importFrom("utils", "object.size", "read.csv")
to your NAMESPACE file.
amCSV.amCluster: no visible global function definition for 'write.csv'
amCSV.amPairwise: no visible global function definition for 'write.csv'
amCSV.amUnique: no visible global function definition for 'write.csv'
amCluster: no visible global function definition for 'hclust'
amCluster: no visible global function definition for 'as.dist'
amHTML.amCluster: no visible global function definition for 'browseURL'
amHTML.amPairwise: no visible global function definition for
  'browseURL'
amHTML.amUnique: no visible global function definition for 'browseURL'
amUniqueProfile: no visible global function definition for 'layout'
amUniqueProfile: no visible global function definition for 'par'
amUniqueProfile: no visible global function definition for
  'plot.default'
amUniqueProfile: no visible global function definition for 'points'
amUniqueProfile: no visible global function definition for 'lines'
amUniqueProfile: no visible global function definition for 'arrows'
amUniqueProfile: no visible global function definition for 'text'
amUniqueProfile: no visible global function definition for 'legend'
Undefined global functions or variables:
  arrows as.dist browseURL hclust layout legend lines par plot.default
  points text write.csv
Consider adding
  importFrom("graphics", "arrows", "layout", "legend", "lines", "par",
             "plot.default", "points", "text")
  importFrom("stats", "as.dist", "hclust")
  importFrom("utils", "browseURL", "write.csv")
to your NAMESPACE file.
batch.possSpells.fnc: no visible binding for global variable 'words'
possSpells.fnc: no visible binding for global variable 'len.phons'
possSpells.fnc: no visible binding for global variable 'phon1'
possSpells.fnc: no visible binding for global variable 'len.total'
possSpells.fnc: no visible binding for global variable 'poss.spells'
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Package in Depends field not imported from: 'car'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'car:::bcPower' 'car:::bootCase' 'car:::deltaMethod'
  'car:::infIndexPlot' 'car:::invResPlot' 'car:::invTranEstimate'
  'car:::invTranPlot' 'car:::marginalModelPlot' 'car:::outlierTest'
  'car:::powerTransform' 'car:::residualPlot' 'car:::residualPlots'
  'car:::testTransform'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'car:::residCurvTest' 'car:::tukeyNonaddTest'
  See the note in ?`:::` about the use of this operator.
alr4Web: no visible global function definition for 'browseURL'
print.summary.lm: no visible binding for global variable 'quantile'
print.summary.lm: no visible global function definition for 'quantile'
print.summary.lm: no visible global function definition for
  'printCoefmat'
print.summary.lm: no visible global function definition for 'naprint'
print.summary.lm: no visible global function definition for 'pf'
print.summary.lm: no visible global function definition for 'symnum'
Undefined global functions or variables:
  browseURL naprint pf printCoefmat quantile symnum
Consider adding
  importFrom("stats", "naprint", "pf", "printCoefmat", "quantile",
             "symnum")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Package suggested but not available for checking: 'Biobase'
'library' or 'require' call to 'Biobase' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
EXP.step: no visible global function definition for 'rgamma'
EXP.step: no visible global function definition for 'rnorm'
MAX.step: no visible global function definition for 'uniroot'
Norm.GMedian: no visible binding for global variable 'median'
RNASeq.Data.Gene: no visible binding for global variable 'quantile'
decom.initial: no visible global function definition for 'kmeans'
decom.initial: no visible global function definition for 'quantile'
decom.initial: no visible global function definition for 'var'
dispersion.nb.QL: no visible binding for global variable 'quantile'
est.mu.nb.mle: no visible global function definition for 'runif'
est.v.nb.QL: no visible global function definition for 'runif'
pdf2grid: no visible global function definition for 'dnorm'
pdf2grid: no visible global function definition for 'dgamma'
prior.grid: no visible global function definition for 'sd'
prior.grid: no visible global function definition for 'dnorm'
test.AMAP: no visible global function definition for 'rgamma'
test.AMAP: no visible global function definition for 'rnorm'
test.AMAP: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Checking should be performed on sources prepared by 'R CMD build'.
amltest: no visible global function definition for 'var'
amltest: no visible global function definition for 'optim'
amltest: no visible global function definition for 'lm'
cleanclust: no visible global function definition for 'cor'
cleanclust: no visible global function definition for 'hclust'
cleanclust: no visible global function definition for 'as.dist'
cleanclust: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
AMOEBA : Classi: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
random.init.MLPneuron: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Analyz.loadSteps,Analyz: 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.
Packages in Depends field not imported from:
  'discretization' 'foreign' 'functional' 'stringr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aode: no visible global function definition for 'Compose'
mdl: no visible global function definition for 'cutPoints'
setVar: no visible global function definition for 'Compose'
Undefined global functions or variables:
  Compose cutPoints
andrews: no visible global function definition for 'plot.new'
andrews: no visible global function definition for 'plot.window'
andrews: no visible global function definition for 'title'
andrews: no visible global function definition for 'axis'
andrews: no visible global function definition for 'box'
andrews: no visible global function definition for 'lines'
andrews: no visible global function definition for 'rainbow'
andrews: no visible global function definition for 'hsv'
selectand: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
plot,ANFIS: no visible binding for global variable 'X'
plotMF,ANFIS : <anonymous>: no visible global function definition for
  'lines'
plotMFs,ANFIS: no visible global function definition for 'par'
Undefined global functions or variables:
  X lines par
Consider adding
  importFrom("graphics", "lines", "par")
to your NAMESPACE file.
GetTotalValues: no visible global function definition for 'rgamma'
GetTotalValues: no visible global function definition for 'runif'
MakeAnglers: no visible global function definition for 'runif'
MakeAnglers: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma runif
Consider adding
  importFrom("stats", "rgamma", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'anoint' 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.
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
aw_map: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to 'boot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
varbin: no visible global function definition for 'boot'
Undefined global functions or variables:
  boot
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'boot' 'lme4' 'methods'
  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 'tkrplot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
TSPM: no visible global function definition for 'glm'
TSPM: no visible binding for global variable 'poisson'
TSPM: no visible global function definition for 'hatvalues'
TSPM: no visible global function definition for 'residuals'
TSPM: no visible global function definition for 'deviance'
TSPM: no visible global function definition for 'qchisq'
TSPM: no visible global function definition for 'qf'
TSPM: no visible global function definition for 'pf'
TSPM: no visible global function definition for 'pchisq'
TSPM: no visible global function definition for 'p.adjust'
norm.inttable: no visible global function definition for 'median'
norm.inttable : <anonymous>: no visible global function definition for
  'quantile'
saint_permF: no visible global function definition for 'read.table'
saint_permF: no visible global function definition for 'write.table'
saint_permF: no visible global function definition for 'write.csv2'
tspm_apms: no visible global function definition for 'read.table'
varFilter : <anonymous>: no visible global function definition for
  'median'
varFilter: no visible global function definition for 'median'
varFilter: no visible global function definition for 'quantile'
Undefined global functions or variables:
  deviance glm hatvalues median p.adjust pchisq pf poisson qchisq qf
  quantile read.table residuals write.csv2 write.table
Consider adding
  importFrom("stats", "deviance", "glm", "hatvalues", "median",
             "p.adjust", "pchisq", "pf", "poisson", "qchisq", "qf",
             "quantile", "residuals")
  importFrom("utils", "read.table", "write.csv2", "write.table")
to your NAMESPACE file.
apple: no visible global function definition for 'ginv'
apple: no visible global function definition for 'runif'
deri: no visible global function definition for 'ginv'
logit: no visible global function definition for 'qlogis'
plot.apple: no visible global function definition for 'matplot'
plot.apple: no visible global function definition for 'lines'
y.app: no visible global function definition for 'ginv'
Undefined global functions or variables:
  ginv lines matplot qlogis runif
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "qlogis", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'ellipse' 'lattice'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bookTheme: no visible global function definition for 'trellis.par.set'
easyBoundaryFunc: no visible global function definition for 'runif'
getPackages: no visible global function definition for
  'install.packages'
permuteRelief: no visible binding for global variable 'sd'
quadBoundaryFunc: no visible global function definition for 'runif'
transparentTheme: no visible global function definition for 'rgb'
transparentTheme: no visible global function definition for
  'trellis.par.set'
upperp: no visible global function definition for 'ellipse'
upperp: no visible global function definition for 'panel.xyplot'
upperp: no visible global function definition for 'trellis.par.get'
Undefined global functions or variables:
  ellipse install.packages panel.xyplot rgb runif sd trellis.par.get
  trellis.par.set
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "runif", "sd")
  importFrom("utils", "install.packages")
to your NAMESPACE file.
Package in Depends field not imported from: 'emulator'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Afun: no visible global function definition for 'corr.matrix'
betahat.app.H: no visible global function definition for 'quad.form'
betahat.app.H: no visible global function definition for
  'quad.form.inv'
cdash.fun: no visible global function definition for 'quad.3form'
cdash.fun: no visible global function definition for 'quad.form'
generate.toy.observations : delta: no visible global function
  definition for 'rmvnorm'
generate.toy.observations : delta: no visible global function
  definition for 'corr.matrix'
object: no visible global function definition for 'quad.form'
opt.1: no visible global function definition for 'optim'
opt.gt.1: no visible global function definition for 'optim'
subsets.fun : select: no visible global function definition for
  'rbinom'
Undefined global functions or variables:
  corr.matrix optim quad.3form quad.form quad.form.inv rbinom rmvnorm
Consider adding
  importFrom("stats", "optim", "rbinom")
to your NAMESPACE file.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for 'write.table'
runAPSIM: no visible global function definition for 'read.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
kristen.colors: no visible global function definition for
  'colorRampPalette'
kristen.colors: no visible global function definition for 'grey'
plot3d.points: no visible global function definition for 'heat.colors'
plot3d.points: no visible global function definition for 'plot'
ragged.image: no visible global function definition for 'heat.colors'
ragged.image: no visible global function definition for 'image'
scatterplot.density: no visible global function definition for 'grey'
scatterplot.density: no visible global function definition for 'image'
scatterplot.density: no visible global function definition for 'abline'
scatterplot.density: no visible global function definition for 'lm'
scatterplot.density: no visible global function definition for 'legend'
vertical.image.legend: no visible global function definition for 'par'
vertical.image.legend: no visible global function definition for
  'image'
vertical.image.legend: no visible global function definition for 'axis'
vertical.image.legend: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box colorRampPalette grey heat.colors image legend lm par
  plot
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
aqDayOfWeekStat: no visible global function definition for 'index'
aqDropHour: no visible global function definition for 'index'
aqFilterOHLCSD: no visible binding for global variable 'sd'
aqHourIndex: no visible global function definition for 'index'
aqHourlyStat: no visible global function definition for 'index'
aqLoadOHLC: no visible global function definition for 'read.csv'
aqLoadSeriesField: no visible global function definition for 'read.csv'
aqLoadXtsFromCsv: no visible global function definition for 'read.csv2'
aqLoadYahooEOD: no visible global function definition for 'read.csv'
aqSaveXtsToCsv: no visible global function definition for 'write.csv2'
aqStoreSeriesField: no visible global function definition for 'index'
aqStoreSeriesField: no visible global function definition for
  'capture.output'
aqStoreSeriesField: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  capture.output index read.csv read.csv2 sd write.csv2 write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "capture.output", "read.csv", "read.csv2",
             "write.csv2", "write.table")
to your NAMESPACE file.
AR1seg_func: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'TSP'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for 'filter'
ardec.lm: no visible global function definition for 'ar'
ardec.lm: no visible global function definition for 'lm'
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
arfimaOLS: no visible global function definition for 'lm'
arfimaPrep: no visible global function definition for 'aggregate'
arfimaPrep: no visible global function definition for 'arima'
arfimaPrep: no visible global function definition for 'lm'
arfimaPrep: no visible global function definition for 'residuals'
Undefined global functions or variables:
  aggregate arima lm residuals
Consider adding
  importFrom("stats", "aggregate", "arima", "lm", "residuals")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'sfit' 'expectile' 'HaarSeg' 'mpcbs'
binarize.array: no visible binding for global variable 'sd'
mskmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans sd
Consider adding
  importFrom("stats", "kmeans", "sd")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'cacheSweave'
Warning: no function found corresponding to methods exports from 'ascii' 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 in package code:
  'cacheSweave' 'weaver'
  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.
':::' call which should be '::': 'utils:::RtangleSetup'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'survival:::survmean' 'utils:::.SweaveValidFilenameRegexp'
  'utils:::RtangleFinish' 'utils:::RtangleRuncode'
  'utils:::SweaveParseOptions'
  See the note in ?`:::` about the use of this operator.
Unavailable namespace imported from by a ':::' call: 'cacheSweave'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'cbind.ascii':
  'cbind.ascii'

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.
Packages which this enhances but not available for checking:
  'REBayes' 'Rmosek'
NeedsCompilation field should likely be 'yes'
'library' or 'require' calls to packages already attached by Depends:
  'Hmisc' 'splancs'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Hmisc' 'shapefiles' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ASP.Score: no visible global function definition for 'pnorm'
Graphs.Bayesian: no visible global function definition for 'dev.new'
colorhex: no visible global function definition for 'gray'
colorhex: no visible global function definition for 'rgb'
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'asreml'
':::' call which should be '::': 'assertive.base:::print_and_capture'
  See the note in ?`:::` about the use of this operator.
Running examples in 'assist-Ex.R' failed
The error most likely occurred in:

> ### Name: anova.ssr
> ### Title: Testing a Non-parametric Function Fitted via Smoothing Splines
> ### Aliases: anova.ssr
> ### Keywords: file
> 
> ### ** Examples
> 
> data(acid)
> 
> # fit a partial thin-plate spline
> temp <- ssr(ph~t1+x1+x2, rk=tp(t1), data=acid, spar="m")
At line 1992 of file rkpk1.f
Fortran runtime error: Index '2' of dimension 1 of array 'jpvt' above upper bound of 1
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.
CALPHA: no visible global function definition for 'dbinom'
CALPHA: no visible global function definition for 'pchisq'
CAST: no visible global function definition for 'fisher.test'
CAST: no visible global function definition for 'chisq.test'
CMC: no visible global function definition for 'pf'
MULTI: no visible global function definition for 'complete.cases'
RVT1: no visible global function definition for 'pchisq'
RVT2: no visible global function definition for 'pchisq'
RWAS: no visible global function definition for 'pnorm'
SKAT: no visible global function definition for 'dbeta'
SKAT: no visible global function definition for 'pchisq'
TTEST: no visible global function definition for 'complete.cases'
TTEST: no visible global function definition for 'pf'
WST: no visible global function definition for 'mvfft'
WST: no visible global function definition for 'pnorm'
my_cmc_method: no visible global function definition for
  'complete.cases'
my_getUV: no visible global function definition for 'complete.cases'
my_orwss_method: no visible global function definition for 'sd'
my_rarecov_method: no visible global function definition for
  'chisq.test'
my_rbt_method: no visible global function definition for 'ppois'
my_score_method: no visible global function definition for 'pchisq'
my_ssu_method: no visible global function definition for 'pchisq'
my_ssuw_method: no visible global function definition for 'pchisq'
my_sum_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pmvnorm'
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  'src/mlogl.c'
beamDiskOverlap: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for 'spline'
galage: no visible global function definition for 'integrate'
lumdist: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
VPC.graph : findQuantile: no visible global function definition for
  'quantile'
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for 'quantile'
asVPC.binW: no visible global function definition for 'median'
asVPC.binW : <anonymous>: no visible global function definition for
  'quantile'
asVPC.binW: no visible global function definition for 'quantile'
asVPC.distanceW: no visible global function definition for 'median'
asVPC.distanceW : <anonymous>: no visible global function definition
  for 'quantile'
asVPC.distanceW: no visible global function definition for 'quantile'
makeCOVbin: no visible global function definition for 'quantile'
makeCOVbin: no visible global function definition for 'median'
read_Simdata: no visible global function definition for 'read.table'
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
asymp.test.default: no visible global function definition for 'var'
asymp.test.default: no visible global function definition for 'pnorm'
asymp.test.default: no visible global function definition for 'qnorm'
asymp.test.formula: no visible global function definition for 'terms'
seDMean.default: no visible global function definition for 'var'
seDMeanG.default: no visible global function definition for 'var'
seDVar.default: no visible global function definition for 'var'
seMean.default: no visible global function definition for 'var'
seRMean.default: no visible global function definition for 'var'
seRVar.default: no visible global function definition for 'var'
seVar.default: no visible global function definition for 'var'
Undefined global functions or variables:
  pnorm qnorm terms var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "terms", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'cairoDevice' 'gWidgetsRGtk2' 'partitions' 'proto'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.est.ATT: no visible global function definition for 'tail'
get.est.MT: no visible global function definition for 'tail'
get.est.simple: no visible global function definition for 'tail'
newton.r: no visible global function definition for 'tail'
plot.ATE: no visible global function definition for 'par'
plot.ATE: no visible global function definition for 'plot'
plot.ATE: no visible global function definition for 'axis'
plot.ATE: no visible global function definition for 'abline'
plot.ATE: no visible global function definition for 'lines'
plot.ATE: no visible global function definition for 'legend'
plot.ATE: no visible global function definition for 'points'
print.summary.ATE: no visible global function definition for
  'printCoefmat'
summary.ATE: no visible global function definition for 'qnorm'
summary.ATE: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis legend lines par plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'runif'
atmcmc: no visible global function definition for 'par'
atmcmc: no visible global function definition for 'lm'
atmcmc: no visible global function definition for 'lines'
atmcmc: no visible global function definition for 'var'
atmcmc: no visible global function definition for 'cov'
atmcmc: no visible global function definition for 'quantile'
atmcmc: no visible global function definition for 'sd'
plotmcmc: no visible global function definition for 'pdf'
plotmcmc: no visible global function definition for 'par'
plotmcmc: no visible global function definition for 'dev.new'
plotmcmc: no visible global function definition for 'png'
plotmcmc: no visible global function definition for 'hist'
plotmcmc: no visible global function definition for 'dev.off'
plotmcmc: no visible global function definition for 'plot'
plotmcmc: no visible global function definition for 'lines'
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
LHSdesign: no visible global function definition for 'qnorm'
LHSdesign: no visible global function definition for 'qunif'
LHSdesign: no visible global function definition for 'qt'
MCdesign: no visible global function definition for 'rnorm'
MCdesign: no visible global function definition for 'runif'
MCdesign: no visible global function definition for 'rt'
Undefined global functions or variables:
  qnorm qt qunif rnorm rt runif
Consider adding
  importFrom("stats", "qnorm", "qt", "qunif", "rnorm", "rt", "runif")
to your NAMESPACE file.
PlotAtm.lin : scale_image: no visible global function definition for
  'heat.colors'
PlotAtm.lin : scale_image: no visible global function definition for
  'par'
PlotAtm.lin : scale_image: no visible global function definition for
  'sd'
PlotAtm.lin : scale_image: no visible global function definition for
  'approx'
PlotAtm.lin : scale_image: no visible global function definition for
  'image'
PlotAtm.lin : scale_image: no visible global function definition for
  'axis'
PlotAtm.lin : scale_image: no visible global function definition for
  'mtext'
PlotAtm.lin: no visible global function definition for 'arrows'
PlotAtm.lin: no visible global function definition for 'text'
PlotAtm.lin: no visible global function definition for 'polygon'
sky.colors: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
parse_response: 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.
attribrisk: no visible global function definition for 'terms'
attribrisk: no visible global function definition for '.getXlevels'
attribrisk: no visible global function definition for 'model.response'
attribrisk: no visible global function definition for 'model.weights'
attribrisk: no visible global function definition for 'model.offset'
attribrisk: no visible global function definition for 'model.matrix'
attribrisk: no visible global function definition for 'model.frame'
attribrisk.fit: no visible global function definition for 'glm.fit'
attribrisk.fit: no visible global function definition for 'binomial'
attribrisk.fit: no visible global function definition for 'glm.control'
attribrisk.fit: no visible global function definition for 'coef'
attribrisk.fit: no visible global function definition for
  'coefficients'
attribrisk_boot: no visible global function definition for 'var'
print.attribrisk: no visible global function definition for 'qnorm'
summary.attribrisk: no visible global function definition for 'hasArg'
summary.attribrisk: no visible global function definition for 'var'
Undefined global functions or variables:
  .getXlevels binomial coef coefficients glm.control glm.fit hasArg
  model.frame model.matrix model.offset model.response model.weights
  qnorm terms var
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", ".getXlevels", "binomial", "coef", "coefficients",
             "glm.control", "glm.fit", "model.frame", "model.matrix",
             "model.offset", "model.response", "model.weights", "qnorm",
             "terms", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.AUC: no visible global function definition for 'plot'
plot.AUC: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for 'predict'
plot.AUCRF: no visible global function definition for 'par'
plot.AUCRF: no visible global function definition for 'dotchart'
plot.AUCRF: no visible global function definition for 'title'
plot.AUCRF: no visible global function definition for 'text'
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RJSONIO' 'hexbin' 'plotrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for 'hist'
audioHist: no visible global function definition for 'rescale'
audioHist: no visible global function definition for 'toJSON'
audioScatter: no visible binding for global variable 'formula'
audioScatter: no visible global function definition for 'hexbinplot'
audioScatter: no visible global function definition for 'cor'
audioScatter: no visible global function definition for 'toJSON'
audioSplom: no visible global function definition for 'hexplom'
audioSplom: no visible binding for global variable 'BTY'
audioSplom: no visible binding for global variable 'panel.hexboxplot'
audioSplom: no visible global function definition for 'combn'
audioSplom : <anonymous>: no visible global function definition for
  'cor'
audioSplom : <anonymous>: no visible global function definition for
  'toJSON'
audiolyzRcheck: no visible global function definition for
  'download.file'
audiolyzRcheck: no visible global function definition for 'unzip'
matricize: no visible global function definition for 'hexbin'
panel.audiolyzR: no visible global function definition for
  'panel.hexbinplot'
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/audio.Rcheck/00install.out' for details.
simulateD: no visible global function definition for 'rgamma'
simulateT: no visible global function definition for 'runif'
simulateT: no visible global function definition for 'rbeta'
simulateT: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbeta rbinom rgamma runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rgamma", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'rPython'
'library' or 'require' calls in package code:
  'ggplot2' 'gpclib' 'maptools'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
gLog.ep: no visible global function definition for 'quantile'
gedestp: no visible global function definition for 'na.omit'
gedestp: no visible global function definition for 'optim'
gets.mean: no visible global function definition for 'start'
gets.mean: no visible global function definition for 'end'
gets.mean: no visible global function definition for 'window'
gets.mean: no visible global function definition for 'pt'
gets.mean: no visible global function definition for 'Box.test'
gets.mean: no visible global function definition for 'pchisq'
gets.vol: no visible global function definition for 'start'
gets.vol: no visible global function definition for 'end'
gets.vol: no visible global function definition for 'window'
gets.vol: no visible global function definition for 'pt'
gets.vol: no visible global function definition for 'Box.test'
gets.vol: no visible global function definition for 'pchisq'
jb.test: no visible global function definition for 'pchisq'
skewness.test: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'start'
sm: no visible global function definition for 'end'
sm: no visible global function definition for 'window'
sm: no visible global function definition for 'pt'
sm: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'Box.test'
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 448 SKIPPED: 0 FAILED: 4
  1. Error: autovar function returns hello world (@test_autovar.r#14) 
  2. Error: model_score calls its subfunctions correctly for AIC (@test_model_score.r#50) 
  3. Error: model_score calls its subfunctions correctly for BIC (@test_model_score.r#81) 
  4. Error: select_valid_masks calls bitwAnd correctly (@test_select_valid_masks.r#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 448 SKIPPED: 0 FAILED: 4
  1. Error: autovar function returns hello world (@test_autovar.r#14) 
  2. Error: model_score calls its subfunctions correctly for AIC (@test_model_score.r#50) 
  3. Error: model_score calls its subfunctions correctly for BIC (@test_model_score.r#81) 
  4. Error: select_valid_masks calls bitwAnd correctly (@test_select_valid_masks.r#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
best: no visible global function definition for 'optim'
randomboards: no visible global function definition for 'runif'
randomprobs: no visible global function definition for 'runif'
Undefined global functions or variables:
  optim runif
Consider adding
  importFrom("stats", "optim", "runif")
to your NAMESPACE file.
File 'aylmer/libs/i386/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.o'
File 'aylmer/libs/x64/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.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.
CRexp_set: no visible global function definition for 'runif'
b6e6rl: no visible global function definition for 'runif'
derand_RL: no visible global function definition for 'runif'
derandexp_RL: no visible global function definition for 'runif'
nahvyb_expt: no visible global function definition for 'runif'
roulete: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for 'sd'
.generateUnitHyperCube: no visible global function definition for
  'runif'
.makeBoundedSingleStep: no visible global function definition for
  'runif'
.makeBoundedStep: no visible global function definition for 'runif'
.makeStep: no visible global function definition for 'runif'
.staircaseSampling: no visible global function definition for 'runif'
GaussianPrior: no visible global function definition for 'qnorm'
LogNormalPrior: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BACA.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'sybilSBML'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
BACprior.CV: no visible global function definition for 'na.fail'
BACprior.CV: no visible global function definition for 'plot'
BACprior.CV: no visible global function definition for 'abline'
BACprior.boot: no visible global function definition for 'na.fail'
BACprior.boot: no visible global function definition for 'plot'
BACprior.boot: no visible global function definition for 'abline'
BACprior.lm: no visible global function definition for 'na.fail'
BACprior.lm: no visible global function definition for 'coef'
BACprior.lm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
bagging: no visible global function definition for 'predict'
samme: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Package suggested but not available for checking: 'mzR'
best_binomial_bandit : f: no visible global function definition for
  'dbeta'
best_binomial_bandit : f: no visible global function definition for
  'pbeta'
best_binomial_bandit: no visible global function definition for
  'integrate'
best_poisson_bandit : f: no visible global function definition for
  'dgamma'
best_poisson_bandit : f: no visible global function definition for
  'pgamma'
best_poisson_bandit: no visible global function definition for
  'integrate'
deseasonalized_trend: no visible global function definition for
  'predict'
distribution_estimate: no visible global function definition for
  'quantile'
distribution_estimate: no visible global function definition for
  'qbeta'
significance_analysis: no visible global function definition for
  'prop.test'
sim_post: no visible global function definition for 'rbeta'
summarize_metrics: no visible global function definition for 'median'
summarize_metrics: no visible global function definition for
  'prop.test'
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
extractAffybatch: 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').
'library' or 'require' calls to packages already attached by Depends:
  'grid' 'lattice'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'grid' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for 'unit'
barcode: no visible global function definition for 'grid.newpage'
barcode: no visible global function definition for 'grid.text'
barcode: no visible global function definition for 'gpar'
barcode: no visible global function definition for 'pushViewport'
barcode: no visible global function definition for 'viewport'
barcode: no visible global function definition for 'convertHeight'
barcode: no visible global function definition for 'convertWidth'
barcode: no visible global function definition for 'grid.rect'
barcode: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for 'unit'
barcode.panel: no visible global function definition for 'hist'
barcode.panel: no visible global function definition for 'pushViewport'
barcode.panel: no visible global function definition for 'viewport'
barcode.panel: no visible global function definition for 'grid.xaxis'
barcode.panel: no visible global function definition for 'gpar'
barcode.panel: no visible global function definition for 'grid.text'
barcode.panel: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for
  'grid.segments'
barcode.panel: no visible global function definition for 'grid.points'
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 0 FAILED: 70
  1. Failure: encode and decode on random strings (@test_base32.R#10) 
  2. Failure: encode and decode on random strings (@test_base32.R#10) 
  3. Failure: encode and decode on random strings (@test_base32.R#10) 
  4. Failure: encode and decode on random strings (@test_base32.R#10) 
  5. Failure: encode and decode on random strings (@test_base32.R#10) 
  6. Failure: encode and decode on random strings (@test_base32.R#10) 
  7. Failure: encode and decode on random strings (@test_base32.R#10) 
  8. Failure: encode and decode on random strings (@test_base32.R#10) 
  9. Failure: encode and decode on random strings (@test_base32.R#10) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 0 FAILED: 70
  1. Failure: encode and decode on random strings (@test_base32.R#10) 
  2. Failure: encode and decode on random strings (@test_base32.R#10) 
  3. Failure: encode and decode on random strings (@test_base32.R#10) 
  4. Failure: encode and decode on random strings (@test_base32.R#10) 
  5. Failure: encode and decode on random strings (@test_base32.R#10) 
  6. Failure: encode and decode on random strings (@test_base32.R#10) 
  7. Failure: encode and decode on random strings (@test_base32.R#10) 
  8. Failure: encode and decode on random strings (@test_base32.R#10) 
  9. Failure: encode and decode on random strings (@test_base32.R#10) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'doMC' 'rPython'
'library' or 'require' call to 'hwriter' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
asyncRunCommands: no visible global function definition for 'runif'
mergeCsv: no visible global function definition for 'read.csv'
mergeCsv: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv runif write.csv
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Running examples in 'batchtools-Ex.R' failed
The error most likely occurred in:

> ### Name: addExperiments
> ### Title: Add Experiments to the Registry
> ### Aliases: addExperiments
> 
> ### ** Examples
> 
> tmp = makeExperimentRegistry(file.dir = NA, make.default = FALSE)
No configuration file found
Created registry in 'D:/temp/RtmpaMSUhB/registry708462a132f0' using cluster functions 'Interactive'
> 
> # add first problem
> fun = function(job, data, n, mean, sd, ...) rnorm(n, mean = mean, sd = sd)
> addProblem("rnorm", fun = fun, reg = tmp)
Adding problem 'rnorm'
> 
> # add second problem
> fun = function(job, data, n, lambda, ...) rexp(n, rate = lambda)
> addProblem("rexp", fun = fun, reg = tmp)
Adding problem 'rexp'
> 
> # add first algorithm
> fun = function(instance, method, ...) if (method == "mean") mean(instance) else median(instance)
> addAlgorithm("average", fun = fun, reg = tmp)
Adding algorithm 'average'
> 
> # add second algorithm
> fun = function(instance, ...) sd(instance)
> addAlgorithm("deviation", fun = fun, reg = tmp)
Adding algorithm 'deviation'
> 
> # define problem and algorithm designs
> prob.designs = algo.designs = list()
> prob.designs$rnorm = CJ(n = 100, mean = -1:1, sd = 1:5)
> prob.designs$rexp = data.table(n = 100, lambda = 1:5)
> algo.designs$average = data.table(method = c("mean", "median"))
> algo.designs$deviation = data.table()
> 
> # add experiments and submit
> addExperiments(prob.designs, algo.designs, reg = tmp)
Adding 30 experiments ('rnorm'[15] x 'average'[2] x repls[1]) ...
Error in length(ans$indices) : type must be LANGSXP at this point
Calls: addExperiments ... merge -> merge.data.table -> [ -> [.data.table -> length
Execution halted
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 929 SKIPPED: 12 FAILED: 24
  1. Error: addAlgorithm (@test_Algorithm.R#13) 
  2. Error: addAlgorithm overwrites old algo (@test_Algorithm.R#31) 
  3. Error: External directory is created (@test_Job.R#71) 
  4. Error: addProblem / removeProblem (@test_Problem.R#28) 
  5. Error: instance caching (@test_Problem.R#50) 
  6. Error: makeRegistry (@test_Registry.R#17) 
  7. Error: loadRegistry (@test_Registry.R#87) 
  8. Error: clearRegistry (@test_Registry.R#130) 
  9. Error: addExperiments handles parameters correctly (@test_addExperiments.R#10) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BayClone2.Rcheck/00install.out' for details.
bridge.nmix.R: no visible global function definition for 'rnorm'
draw.alpha: no visible global function definition for 'runif'
draw.alpha: no visible global function definition for 'dbeta'
draw.alpha.2: no visible global function definition for 'runif'
draw.beta.2: no visible global function definition for 'runif'
draw.sig2: no visible global function definition for 'rgamma'
draw.tau: no visible global function definition for 'rgamma'
draw.u: no visible global function definition for 'runif'
draw.w: no visible global function definition for 'runif'
draw.w: no visible global function definition for 'rgamma'
draw.w.marg: no visible global function definition for 'runif'
draw.w.marg: no visible global function definition for 'rgamma'
trace.beta: no visible global function definition for 'plot'
trace.beta: no visible global function definition for 'lines'
trace.beta: no visible global function definition for 'legend'
trace.beta.mcmc: no visible global function definition for 'sd'
trace.beta.mcmc: no visible binding for global variable 'sd'
trace.beta.mcmc: no visible global function definition for 'plot'
trace.beta.mcmc: no visible global function definition for 'title'
trace.beta.mcmc: no visible global function definition for 'hsv'
trace.beta.mcmc: no visible global function definition for 'lines'
trace.beta.mcmc: no visible global function definition for 'points'
Undefined global functions or variables:
  dbeta hsv legend lines plot points rgamma rnorm runif sd title
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "lines", "plot", "points", "title")
  importFrom("stats", "dbeta", "rgamma", "rnorm", "runif", "sd")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/bayesCL.Rcheck/00install.out' for details.
FECRT: no visible global function definition for 'pdf'
FECRT: no visible global function definition for 'hist'
FECRT: no visible global function definition for 'abline'
FECRT: no visible global function definition for 'dev.off'
FECRT.analysis: no visible global function definition for 'pdf'
FECRT.analysis: no visible global function definition for 'hist'
FECRT.analysis: no visible global function definition for 'abline'
FECRT.analysis: no visible global function definition for 'dev.off'
fecrt: no visible global function definition for 'pdf'
fecrt: no visible global function definition for 'hist'
fecrt: no visible global function definition for 'abline'
fecrt: no visible global function definition for 'dev.off'
fecrt.analysis: no visible global function definition for 'pdf'
fecrt.analysis: no visible global function definition for 'hist'
fecrt.analysis: no visible global function definition for 'abline'
fecrt.analysis: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
BMAnimalTrack: no visible global function definition for 'nlm'
BMAnimalTrack: no visible global function definition for 'qnorm'
dataSim: no visible global function definition for 'rnorm'
rBBridge: no visible global function definition for 'rnorm'
rBMotion: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
BayesianbetaregEst: no visible global function definition for 'runif'
BayesianbetaregEst: no visible global function definition for 'as.ts'
BayesianbetaregEst: no visible global function definition for 'dev.new'
BayesianbetaregEst: no visible global function definition for 'ts.plot'
BayesianbetaregEst: no visible binding for global variable 'sd'
BayesianbetaregEst: no visible global function definition for
  'quantile'
betaresiduals : lt: no visible global function definition for 'dbeta'
diagnostics: no visible global function definition for 'plot'
diagnostics: no visible global function definition for 'abline'
diagnostics: no visible global function definition for 'qqnorm'
diagnostics: no visible global function definition for 'qqline'
dpostb: no visible global function definition for 'dbeta'
dpostg: no visible global function definition for 'dbeta'
plotresiduals: no visible global function definition for 'plot'
print.summary.Bayesianbetareg: no visible global function definition
  for 'printCoefmat'
summary.Bayesianbetareg: no visible global function definition for
  'coef'
Undefined global functions or variables:
  abline as.ts coef dbeta dev.new plot printCoefmat qqline qqnorm
  quantile runif sd ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "as.ts", "coef", "dbeta", "printCoefmat", "qqline",
             "qqnorm", "quantile", "runif", "sd", "ts.plot")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Depends: includes the non-default packages:
  'gplots' 'xtable' 'mnormt' 'MASS' 'bayesm' 'boa' 'e1071' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'MASS' 'bayesm' 'boa' 'e1071' 'gplots' 'gtools' 'mnormt' 'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: working directory was changed to 'd:/Rcompile/CRANpkg/local/3.5/bayesMCClust.Rcheck/bayesMCClust-wd', resetting
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.1Mb
noninform_prior : a : f1: no visible global function definition for
  'pbeta'
noninform_prior : a : f1: no visible global function definition for
  'dbeta'
noninform_prior : a: no visible global function definition for
  'integrate'
noninform_prior: no visible global function definition for 'rbeta'
noninform_prior: no visible global function definition for 'optim'
postNullFun : b : f1: no visible global function definition for 'pbeta'
postNullFun : b : f1: no visible global function definition for 'dbeta'
postNullFun : b: no visible global function definition for 'integrate'
prior_prob : a : f1: no visible global function definition for 'pbeta'
prior_prob : a : f1: no visible global function definition for 'dbeta'
prior_prob : a: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
MHratioPopPref: no visible global function definition for 'runif'
MratioPopMult: no visible global function definition for 'dunif'
MratioPopMult: no visible global function definition for 'runif'
bayesPref: no visible global function definition for 'runif'
calcP: no visible global function definition for 'dunif'
calcP: no visible global function definition for 'dmultinom'
calcdic: no visible global function definition for 'median'
calcdic: no visible binding for global variable 'median'
calcdic: no visible global function definition for 'dmultinom'
calcdicExtern: no visible global function definition for 'median'
calcdicExtern: no visible global function definition for 'dmultinom'
calcdicExtern: no visible binding for global variable 'median'
credibleIntervals: no visible global function definition for 'quantile'
prefPlot: no visible global function definition for 'postscript'
prefPlot: no visible global function definition for 'plot'
prefPlot: no visible global function definition for 'lines'
prefPlot: no visible global function definition for 'density'
prefPlot: no visible global function definition for 'median'
prefPlot: no visible global function definition for 'legend'
prefPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
BayesFH: no visible global function definition for 'rnorm'
BayesFH: no visible global function definition for 'rgamma'
BayesSAE: no visible global function definition for 'runif'
BayesSAE: no visible global function definition for 'as.formula'
BayesSAE: no visible global function definition for 'terms'
BayesSAE: no visible global function definition for 'delete.response'
BayesSAE: no visible global function definition for 'model.response'
BayesSAE: no visible global function definition for 'model.matrix'
BayesSAE: no visible global function definition for 'coef'
BayesSAE: no visible global function definition for 'lm'
BayesSFH: no visible global function definition for 'rnorm'
BayesSFH: no visible global function definition for 'runif'
BayesSFH: no visible global function definition for 'rgamma'
BayesSYC: no visible global function definition for 'rnorm'
BayesSYC: no visible global function definition for 'runif'
BayesSYC: no visible global function definition for 'rgamma'
BayesUFH: no visible global function definition for 'rnorm'
BayesUFH: no visible global function definition for 'rgamma'
BayesUYC: no visible global function definition for 'rnorm'
BayesUYC: no visible global function definition for 'rgamma'
BayesYC: no visible global function definition for 'rnorm'
BayesYC: no visible global function definition for 'rgamma'
model.compare: no visible global function definition for 'dnorm'
print.summary.BayesSAE: no visible global function definition for
  'printCoefmat'
replication: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  as.formula coef delete.response dnorm lm model.matrix model.response
  printCoefmat rgamma rnorm runif terms
Consider adding
  importFrom("stats", "as.formula", "coef", "delete.response", "dnorm",
             "lm", "model.matrix", "model.response", "printCoefmat",
             "rgamma", "rnorm", "runif", "terms")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some 'make' programs ignore lines not ending in LF.
File 'BayesSAE/libs/i386/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.o'
File 'BayesSAE/libs/x64/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.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.
mlike.alt.g.AR: no visible global function definition for 'integrate'
mlike.alt.gtheta.AR: no visible global function definition for 'dbeta'
mlike.null.AR: no visible global function definition for 'dbeta'
multilevel.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
multilevel.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
trendtest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for 'dcauchy'
trendtest.Gibbs.AR: no visible global function definition for 'pcauchy'
trendtest.MC.AR: no visible global function definition for
  'txtProgressBar'
trendtest.MC.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.nullMargLikeAR: no visible global function definition for
  'integrate'
ttest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
ttest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
ttest.Gibbs.AR: no visible global function definition for 'dcauchy'
ttest.Gibbs.AR: no visible global function definition for 'pcauchy'
ttest.MCGQ.AR: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta dcauchy integrate pcauchy setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "dbeta", "dcauchy", "integrate", "pcauchy")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'combinat' 'gplots' 'mnormt'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bayes.regress: no visible binding for global variable 'var'
bayesregressB1S1: no visible global function definition for 'rgamma'
bayesregressB1S2: no visible global function definition for 'rgamma'
bayesregressB2S1: no visible global function definition for 'rgamma'
bayesregressB2S2: no visible global function definition for 'rgamma'
bayesregressB3S1: no visible global function definition for 'rWishart'
bayesregressB3S1: no visible global function definition for 'rgamma'
bayesregressB3S2: no visible global function definition for 'rWishart'
bayesregressB3S2: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rWishart rgamma var
Consider adding
  importFrom("stats", "rWishart", "rgamma", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'lme4' 'MASS' 'VGAM' 'mvtnorm' 'matrixcalc' 'coda'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'MASS' 'VGAM' 'coda' 'lme4' 'matrixcalc' 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
validate: no visible binding for global variable 'qnorm'
validate: no visible global function definition for 'pchisq'
validate: no visible global function definition for 'qnorm'
validate: no visible global function definition for 'plot'
validate: no visible global function definition for 'axis'
validate: no visible global function definition for 'points'
validate: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Found the following file(s) containing GNU extensions:
  src/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'boa:::boa.getparms'
  See the note in ?`:::` about the use of this operator.
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'coda' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'mvnmle' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
BilogData: no visible global function definition for 'write.table'
CohensD.rawData: no visible global function definition for 'var'
EtaSq: no visible global function definition for 'summary.aov'
HedgesG.rawData: no visible global function definition for 'var'
LittleMCAR: no visible global function definition for 'mlest'
LittleMCAR: no visible global function definition for 'pchisq'
PseudoR2: no visible global function definition for 'predict'
Undefined global functions or variables:
  mlest pchisq predict summary.aov var write.table
Consider adding
  importFrom("stats", "pchisq", "predict", "summary.aov", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'fields' 'poibin' 'rjags'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for 'heat.colors'
BMR.plot: no visible global function definition for 'image.plot'
BMR.plot: no visible global function definition for 'title'
BMR.plot: no visible global function definition for 'mtext'
BMR.plot: no visible global function definition for 'par'
baysic.data: no visible global function definition for 'layout'
baysic.data: no visible global function definition for 'barplot'
baysic.data: no visible global function definition for 'rainbow'
baysic.fit: no visible global function definition for 'jags.model'
baysic.fit: no visible global function definition for 'update'
baysic.fit: no visible global function definition for 'coda.samples'
baysic.test: no visible global function definition for 'ppois'
baysic.test : <anonymous>: no visible global function definition for
  'ppoibin'
baysic.test: no visible global function definition for 'pbinom'
fuzzy.FDR.approx: no visible global function definition for 'p.adjust'
fuzzy.FDR.approx: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
BAYSTAR: no visible global function definition for 'median'
BAYSTAR: no visible global function definition for 'ar'
BAYSTAR: no visible global function definition for 'quantile'
BAYSTAR: no visible global function definition for 'dev.new'
BAYSTAR: no visible global function definition for 'ts.plot'
BAYSTAR: no visible global function definition for 'title'
BAYSTAR: no visible global function definition for 'par'
BAYSTAR: no visible global function definition for 'plot.ts'
BAYSTAR: no visible global function definition for 'lines'
BAYSTAR: no visible global function definition for 'acf'
TAR.lagd: no visible global function definition for 'runif'
TAR.sigma: no visible global function definition for 'rgamma'
TAR.simu: no visible global function definition for 'rnorm'
TAR.summary: no visible global function definition for 'quantile'
TAR.summary: no visible global function definition for 'sd'
TAR.thres: no visible global function definition for 'rnorm'
TAR.thres: no visible global function definition for 'runif'
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
Package in Depends field not imported from: 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaplaceMetropolis_admkr: no visible binding for global variable
  'median'
LaplaceMetropolis_admkr: no visible global function definition for
  'mad'
LaplaceMetropolis_gaussian: no visible binding for global variable
  'median'
LaplaceMetropolis_gaussian: no visible global function definition for
  'mad'
cost_admkr: no visible global function definition for 'sd'
cov_chol: no visible global function definition for 'qchisq'
cov_chol_admkr: no visible global function definition for 'qchisq'
gibbs_admkr_erro: no visible global function definition for 'rnorm'
gibbs_admkr_erro: no visible global function definition for 'runif'
gibbs_admkr_nw: no visible global function definition for 'qnorm'
gibbs_admkr_nw: no visible global function definition for 'rnorm'
gibbs_admkr_nw: no visible global function definition for 'runif'
loglikelihood_admkr: no visible global function definition for 'sd'
margin_like_admkr: no visible global function definition for 'sd'
np_gibbs: no visible global function definition for 'qnorm'
np_gibbs: no visible global function definition for 'rnorm'
np_gibbs: no visible global function definition for 'runif'
np_gibbs: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
bbmm.contour: no visible global function definition for 'na.omit'
bbmm.contour: no visible global function definition for 'optimize'
bbmm.contour: no visible global function definition for 'contour'
bbmm.contour: no visible global function definition for 'points'
bbmm.contour: no visible global function definition for 'lines'
brownian.bridge: no visible global function definition for 'sd'
brownian.motion.variance: no visible global function definition for
  'optimize'
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for 'runif'
bbo: no visible global function definition for 'tail'
plot.bbo: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'HI' 'lme4' 'locfit' 'secr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BBRecap: no visible global function definition for 'optimize'
BBRecap: no visible global function definition for 'arms'
BBRecap: no visible global function definition for 'median'
BBRecap : HPD.interval: no visible global function definition for
  'density'
BBRecap : HPD.interval: no visible global function definition for
  'quantile'
BBRecap.custom.part: no visible global function definition for
  'optimize'
LBRecap: no visible global function definition for 'findbars'
LBRecap: no visible global function definition for 'as.formula'
LBRecap: no visible global function definition for 'glm'
LBRecap: no visible global function definition for 'binomial'
LBRecap: no visible global function definition for 'glmer'
LBRecap: no visible global function definition for 'logLik'
LBRecap: no visible global function definition for 'coef'
LBRecap: no visible global function definition for 'na.omit'
LBRecap: no visible global function definition for 'fixef'
LBRecap: no visible global function definition for 'ranef'
LBRecap: no visible global function definition for 'qnorm'
LBRecap: no visible global function definition for 'plot'
LBRecap: no visible global function definition for 'points'
LBRecap: no visible global function definition for 'axis'
LBRecap: no visible global function definition for 'abline'
LBRecap.custom.part: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  abline arms as.formula axis binomial coef density findbars fixef glm
  glmer logLik median na.omit optimize plot points qnorm quantile ranef
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "as.formula", "binomial", "coef", "density", "glm",
             "logLik", "median", "na.omit", "optimize", "qnorm",
             "quantile")
to your NAMESPACE file.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
pairs.bce : panel.cor: no visible global function definition for 'text'
pairs.bce : panel.cor: no visible global function definition for 'cor'
pairs.bce : panel.hist: no visible global function definition for 'par'
pairs.bce : panel.hist: no visible global function definition for
  'hist'
pairs.bce : panel.hist: no visible global function definition for
  'rect'
pairs.bce: no visible global function definition for 'pairs'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
rdirichlet2: no visible global function definition for 'rgamma'
summary.bce: no visible global function definition for 'cov'
summary.bce: no visible binding for global variable 'sd'
summary.bce: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
Packages suggested but not available for checking: 'bcmaps.rdata' 'doMC'
Missing or unexported object: 'sf::st_make_valid'
check.summary: no visible global function definition for 'sd'
risk.summary: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  sd write.csv
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
plot.cvsvd: no visible binding for global variable 'sd'
plot.cvsvd: no visible global function definition for 'plot'
plot.cvsvd: no visible global function definition for 'lines'
plot.cvsvd: no visible global function definition for 'segments'
plot.cvsvd: no visible global function definition for 'points'
print.cvsvd: no visible binding for global variable 'sd'
summary.cvsvd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  lines plot points sd segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
mise: no visible global function definition for 'integrate'
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for 'dbeta'
density,Chen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,Vitale : <anonymous>: no visible global function definition for
  'dbeta'
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for 'integrate'
distribution,KernelDensity : <anonymous>: no visible global function
  definition for 'integrate'
print,BoundedDensity: no visible global function definition for 'str'
print,KernelDensity: no visible global function definition for 'str'
rsample,BoundedDensity: no visible global function definition for
  'runif'
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for 'integrate'
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for 'integrate'
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for 'integrate'
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  'dbeta'
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for 'integrate'
show,BoundedDensity: no visible global function definition for 'str'
show,KernelDensity: no visible global function definition for 'str'
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
BDtest: no visible global function definition for 'binom.test'
CIlnpv: no visible global function definition for 'qnorm'
CIlnpvak: no visible global function definition for 'qnorm'
CIlppv: no visible global function definition for 'qnorm'
CIlppvak: no visible global function definition for 'qnorm'
CIpvBI: no visible global function definition for 'rbeta'
CIpvBI: no visible global function definition for 'quantile'
CIpvBI: no visible global function definition for 'median'
CIpvBII: no visible global function definition for 'rbeta'
CIpvBII: no visible global function definition for 'quantile'
CIpvBII: no visible global function definition for 'median'
nNPV: no visible global function definition for 'qnorm'
nPPV: no visible global function definition for 'qnorm'
plotnPV: no visible global function definition for 'na.omit'
plotnPV: no visible global function definition for 'lines'
plotnPV2 : defplot: no visible global function definition for 'plot'
plotnPV2 : defplot: no visible global function definition for 'lines'
plotnPV2: no visible global function definition for 'par'
plotnPV2: no visible global function definition for 'layout'
simPV: no visible global function definition for 'rbinom'
simPV: no visible global function definition for 'quantile'
Undefined global functions or variables:
  binom.test layout lines median na.omit par plot qnorm quantile rbeta
  rbinom
Consider adding
  importFrom("graphics", "layout", "lines", "par", "plot")
  importFrom("stats", "binom.test", "median", "na.omit", "qnorm",
             "quantile", "rbeta", "rbinom")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BEACH.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'RColorBrewer' 'beadarray'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for 'na.omit'
beadtypeFilter: no visible global function definition for 'exprs'
beadtypeFilter: no visible global function definition for 'se.exprs'
beadtypeFilter: no visible global function definition for 'beadNum'
beadtypeFilter: no visible global function definition for 'fData'
emCDF: no visible global function definition for 'brewer.pal'
emCDF: no visible global function definition for 'plot'
emCDF: no visible global function definition for 'ecdf'
emCDF: no visible global function definition for 'legend'
emCDF: no visible global function definition for 'lines'
emCDF: no visible global function definition for 'text'
emCDF: no visible global function definition for 'reshape'
iccFun : <anonymous>: no visible global function definition for
  'quantile'
varianceplot: no visible global function definition for 'reshape'
varianceplot: no visible global function definition for 'plot'
varianceplot: no visible global function definition for 'points'
varianceplot: no visible global function definition for 'legend'
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:128:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:152:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/beanz.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
beep: 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.
'library' or 'require' call to 'multcomp' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
beqi2: no visible global function definition for 'na.omit'
beqi2: no visible global function definition for 'browseURL'
readAMBI: no visible global function definition for 'read.csv'
readBEQI: no visible global function definition for 'read.csv'
readERF: no visible global function definition for 'read.csv'
readTWN: no visible global function definition for 'read.csv'
read_ITI_FIBI: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  browseURL na.omit read.csv
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
ber: no visible global function definition for 'model.matrix'
ber: no visible global function definition for 'as.formula'
ber_bg: no visible global function definition for 'model.matrix'
ber_bg: no visible global function definition for 'as.formula'
combat_np: no visible global function definition for 'as.formula'
combat_np: no visible global function definition for 'model.matrix'
combat_p: no visible global function definition for 'as.formula'
combat_p: no visible global function definition for 'model.matrix'
combat_p: no visible binding for global variable 'var'
combat_p: no visible global function definition for 'par'
combat_p: no visible global function definition for 'density'
combat_p: no visible global function definition for 'plot'
combat_p: no visible global function definition for 'lines'
combat_p: no visible global function definition for 'dnorm'
combat_p: no visible global function definition for 'qqnorm'
combat_p: no visible global function definition for 'qqline'
combat_p: no visible global function definition for 'rgamma'
combat_p: no visible global function definition for 'qqplot'
combat_p: no visible global function definition for 'title'
mean_centering: no visible global function definition for
  'model.matrix'
standardization: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  as.formula density dnorm lines model.matrix par plot qqline qqnorm
  qqplot rgamma title var
Consider adding
  importFrom("graphics", "lines", "par", "plot", "title")
  importFrom("stats", "as.formula", "density", "dnorm", "model.matrix",
             "qqline", "qqnorm", "qqplot", "rgamma", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'Rmpfr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bI: no visible global function definition for 'is'
bI: no visible global function definition for 'mpfr'
bI: no visible binding for global variable 'slot'
bI: no visible global function definition for 'as'
Undefined global functions or variables:
  as is mpfr slot
Consider adding
  importFrom("methods", "as", "is", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
betafam: no visible global function definition for 'pnorm'
betafam: no visible global function definition for 'pchisq'
betafam: no visible global function definition for 'lm'
betafam: no visible global function definition for 'coefficients'
betafam: no visible global function definition for 'glm.fit'
betafam: no visible global function definition for 'gaussian'
betafam: no visible global function definition for 'glmnet'
Undefined global functions or variables:
  coefficients gaussian glm.fit glmnet lm pchisq pnorm
Consider adding
  importFrom("stats", "coefficients", "gaussian", "glm.fit", "lm",
             "pchisq", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'vegan' which was already attached by Depends.
  Please remove these calls from your code.
S3 methods shown with full name in documentation object 'cca.pertables':
  'cca.pertables'

S3 methods shown with full name in documentation object 'rda.pertables':
  'rda.pertables'

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.
betas.lm: no visible binding for global variable 'sd'
betas.lm: no visible global function definition for 'sd'
my.wtd.var: no visible global function definition for 'var'
Undefined global functions or variables:
  sd var
Consider adding
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
bezierArcLength: no visible global function definition for 'sd'
bezierArcLength: no visible global function definition for 'lm'
bezierCurveFit: no visible global function definition for 'nls'
bezierCurveFit: no visible global function definition for 'nls.control'
bezierCurveFit: no visible global function definition for 'lm'
bezierCurveFit: no visible global function definition for 'na.omit'
pointsOnBezier: no visible global function definition for 'optim'
Undefined global functions or variables:
  lm na.omit nls nls.control optim sd
Consider adding
  importFrom("stats", "lm", "na.omit", "nls", "nls.control", "optim",
             "sd")
to your NAMESPACE file.
binommh.default : log_lik: no visible global function definition for
  'dbinom'
binommh.default: no visible global function definition for 'dbinom'
binommh.default: no visible global function definition for 'runif'
binommh.formula: no visible global function definition for
  'model.frame'
binommh.formula: no visible global function definition for
  'model.matrix'
binommh.formula: no visible global function definition for
  'model.response'
expmh.default : log_lik: no visible global function definition for
  'dexp'
expmh.default: no visible global function definition for 'dexp'
expmh.default: no visible global function definition for 'runif'
expmh.formula: no visible global function definition for 'model.frame'
expmh.formula: no visible global function definition for 'model.matrix'
expmh.formula: no visible global function definition for
  'model.response'
poissmh.default : log_lik: no visible global function definition for
  'dpois'
poissmh.default: no visible global function definition for 'dpois'
poissmh.default: no visible global function definition for 'runif'
poissmh.formula: no visible global function definition for
  'model.frame'
poissmh.formula: no visible global function definition for
  'model.matrix'
poissmh.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  dbinom dexp dpois model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "dbinom", "dexp", "dpois", "model.frame",
             "model.matrix", "model.response", "runif")
to your NAMESPACE file.
block.gibbs: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
global: no visible global function definition for 'par'
global: no visible global function definition for 'runif'
global: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'par'
mymcmc: no visible global function definition for 'rnorm'
mymcmc: no visible global function definition for 'runif'
mymcmc: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'lines'
plkhci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
installed size is 140.7Mb
  sub-directories of 1Mb or more:
    include  139.7Mb
File which contains pragma(s) suppressing important diagnostics:
  'inst/include/boost/lexical_cast/try_lexical_convert.hpp'
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/boost/atomic/detail/bitwise_cast.hpp'
  'inst/include/boost/get_pointer.hpp'
  'inst/include/boost/interprocess/detail/config_begin.hpp'
  'inst/include/boost/log/detail/header.hpp'
  'inst/include/boost/move/detail/std_ns_begin.hpp'
  'inst/include/boost/multi_index/detail/ignore_wstrict_aliasing.hpp'
  'inst/include/boost/random/detail/disable_warnings.hpp'
  'inst/include/boost/regex/v4/instances.hpp'
  'inst/include/boost/smart_ptr/detail/shared_count.hpp'
  'inst/include/boost/smart_ptr/scoped_ptr.hpp'
  'inst/include/boost/smart_ptr/shared_ptr.hpp'
  'inst/include/boost/tuple/detail/tuple_basic.hpp'
  'inst/include/boost/type_traits/has_logical_not.hpp'
Package in Depends field not imported from: 'betareg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for 'predict'
bias: no visible global function definition for 'pnorm'
bias: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  -- 1. Failure: bib2df() throws error messages (@tests.R#53)  -------------------
  `bib2df("https://www.ottlngr.de/data/x.bib")` threw an error with unexpected message.
  Expected match: "Invalid URL: File is not readable."
  Actual message: "cannot open the connection"
  
  == testthat results  ===========================================================
  OK: 16 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
BiDimRegression: no visible global function definition for 'lm'
BiDimRegression: no visible global function definition for 'pf'
print.BiDimRegression: no visible global function definition for
  'printCoefmat'
print.summary.BiDimRegression: no visible global function definition
  for 'printCoefmat'
Undefined global functions or variables:
  lm pf printCoefmat
Consider adding
  importFrom("stats", "lm", "pf", "printCoefmat")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Rcpp' 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'bifactorial/libs/i386/bifactorial.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'misc.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'krit.o', 'pv.o'
File 'bifactorial/libs/x64/bifactorial.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'misc.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'krit.o', 'pv.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.
anon_matrix: no visible global function definition for
  'filebacked.big.matrix'
anon_matrix: no visible global function definition for 'capture.output'
finalize_anon_matrix: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output filebacked.big.matrix
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'DBI' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbSendQuery'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbSendQuery'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'fetch'
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Package which this enhances but not available for checking: 'synchronicity'
Package unavailable to check Rd xrefs: 'synchronicity'
quickModel: no visible global function definition for 'tail'
quickSource: no visible global function definition for 'write.table'
Undefined global functions or variables:
  tail write.table
Consider adding
  importFrom("utils", "tail", "write.table")
to your NAMESPACE file.
bigRR: no visible global function definition for 'gaussian'
bigRR.default: no visible global function definition for 'gaussian'
bigRR.formula: no visible global function definition for 'gaussian'
bigRR.formula: no visible global function definition for 'as.formula'
bigRR.formula: no visible global function definition for 'model.frame'
bigRR.formula: no visible global function definition for 'model.matrix'
bigRR.formula: no visible global function definition for
  'model.response'
bigRR_update: no visible global function definition for 'gaussian'
hugeRR: no visible global function definition for 'gaussian'
hugeRR_update: no visible global function definition for 'gaussian'
plot.bigRR: no visible global function definition for 'par'
plot.bigRR: no visible global function definition for 'plot'
plot.bigRR: no visible global function definition for 'rgb'
Undefined global functions or variables:
  as.formula gaussian model.frame model.matrix model.response par plot
  rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "gaussian", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.6Mb
Packages in Depends field not imported from:
  'gbm' 'glmnet' 'randomForest' 'tree'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LDCAEst: no visible global function definition for 'glmnet'
cv.LDCA: no visible global function definition for 'cv.glmnet'
predict.LDCA: no visible global function definition for 'predict'
predict.cv.LDCA: no visible global function definition for 'predict'
predict.tsp.gbm: no visible global function definition for 'predict'
predict.tsp.randomForest: no visible global function definition for
  'predict'
predict.tsp.tree: no visible global function definition for 'predict'
tsp.gbm: no visible global function definition for 'gbm.fit'
tsp.randomForest: no visible global function definition for
  'randomForest'
tsp.tree: no visible global function definition for 'tree.control'
tsp.tree: no visible global function definition for 'tree'
Undefined global functions or variables:
  cv.glmnet gbm.fit glmnet predict randomForest tree tree.control
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
plot,bild-missing: no visible global function definition for
  'dev.interactive'
plot,bild-missing: no visible global function definition for
  'devAskNewPage'
plot,bild-missing: no visible global function definition for
  'extendrange'
Undefined global functions or variables:
  dev.interactive devAskNewPage extendrange
Consider adding
  importFrom("grDevices", "dev.interactive", "devAskNewPage",
             "extendrange")
to your NAMESPACE file.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for 'chisq.test'
rmultnom: no visible global function definition for 'runif'
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
commonprob2sigma: no visible global function definition for 'approxfun'
rmvbin: no visible global function definition for 'qnorm'
simul.commonprob: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  approxfun qnorm
Consider adding
  importFrom("stats", "approxfun", "qnorm")
to your NAMESPACE file.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 3
  1. Error: canDownloadFiles (@test-download_files.R#9) 
  2. Error: canReturnEmptyDFWhenEmptyDownloadFiles (@test-download_files.R#27) 
  3. Error: canProcessYaml (@test-process_yaml.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Mtoquant: no visible global function definition for 'qnorm'
NHS: no visible global function definition for 'qnorm'
NHS : WilsonScore: no visible global function definition for 'qnorm'
binMto.formula: no visible global function definition for 'model.frame'
plot.binMto: no visible global function definition for 'plot.new'
plot.binMto: no visible global function definition for 'par'
plot.binMto: no visible global function definition for 'strwidth'
plot.binMto: no visible global function definition for 'axis'
plot.binMto: no visible global function definition for 'box'
plot.binMto: no visible global function definition for 'segments'
plot.binMto: no visible global function definition for 'points'
plot.binMto: no visible global function definition for 'abline'
simPowerI: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline axis box model.frame par plot.new points qnorm rbinom segments
  strwidth
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "plot.new",
             "points", "segments", "strwidth")
  importFrom("stats", "model.frame", "qnorm", "rbinom")
to your NAMESPACE file.
bin_ps: no visible global function definition for 'runif'
bin_ps: no visible global function definition for 'dbinom'
draw_i: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  'flush.console'
dRUMAuxMix: no visible global function definition for 'flush.console'
dRUMHAM: no visible global function definition for 'flush.console'
dRUMIndMH: no visible global function definition for 'flush.console'
print.binomlogit: no visible global function definition for 'is'
summary.binomlogit: no visible global function definition for 'is'
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'ggplot2' 'lattice' 'polynom' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bins.quantiles: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'ape' 'cladoRcpp' 'phylobase' 'rexpokit'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ape' 'cladoRcpp' 'methods' 'phylobase' 'rexpokit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'ape:::floating.pie.asp' 'cladoRcpp:::areas_list_to_states_list_old'
  See the note in ?`:::` about the use of this operator.
Running examples in 'biomartr-Ex.R' failed
The error most likely occurred in:

> ### Name: getFilters
> ### Title: Retrieve All Available Filters for a Specific Dataset
> ### Aliases: getFilters
> 
> ### ** Examples
> 
> # search for available datasets
> getMarts()
Error in getSubMarts(submarts[i]) : Internal Server Error (HTTP 500).
Calls: getMarts -> getSubMarts -> <Anonymous>
Execution halted
'library' or 'require' call to 'MGRASTer' 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'
biom.matrix: no visible global function definition for 'packageVersion'
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
extractPDB : atom.select : sel.txt2nums: no visible global function
  definition for 'na.omit'
extractPDB : read.pdb: no visible global function definition for
  'na.omit'
mat.read: no visible global function definition for 'read.table'
mat.write: no visible global function definition for 'write.table'
scpcp: no visible global function definition for 'pgamma'
sim : sim.func: no visible global function definition for 'write.table'
simc: no visible global function definition for 'write.table'
simc : simc.func: no visible global function definition for
  'write.table'
sims: no visible global function definition for 'write.table'
sims : sims.func: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  na.omit pgamma read.table write.table
Consider adding
  importFrom("stats", "na.omit", "pgamma")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/index.Rmd'
(Is a VignetteBuilder field missing?)
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.5/biorxivr.Rcheck/vign_test/biorxivr") :
  Files named as vignettes but with no recognized vignette engine:
   'vignettes/index.Rmd'
(Is a VignetteBuilder field missing?)
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 17-20 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
failed to load external entity "http://www.biorxiv.org/search/Ecology?page=0"
Execution halted
binom.ci : bc: no visible global function definition for 'qf'
binom.ci : bc: no visible global function definition for 'qnorm'
cvar: no visible global function definition for 'sd'
eta2: no visible global function definition for 'lm'
eta2: no visible global function definition for 'as.formula'
gg_qqplot: no visible binding for global variable 'qnorm'
gg_qqplot: no visible global function definition for 'quantile'
panel.hist: no visible global function definition for 'par'
panel.hist: no visible global function definition for 'hist'
panel.hist: no visible global function definition for 'rect'
plotcdf2: no visible global function definition for 'colorRampPalette'
plotcdf2 : jet.colors: no visible global function definition for 'gray'
plotcdf2: no visible global function definition for 'persp'
poi.ci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  as.formula colorRampPalette gray hist lm par persp qchisq qf qnorm
  quantile rect sd
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "hist", "par", "persp", "rect")
  importFrom("stats", "as.formula", "lm", "qchisq", "qf", "qnorm",
             "quantile", "sd")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'colorspace' 'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.BIPOD: no visible global function definition for 'par'
plot.BIPOD: no visible global function definition for 'matplot'
plot.BIPOD: no visible global function definition for 'abline'
plot.BIPOD: no visible global function definition for 'plot'
plot.BIPOD: no visible global function definition for 'density'
plot.BIPOD: no visible global function definition for 'curve'
plot.BIPOD: no visible global function definition for 'dlnorm'
plot.BIPOD: no visible global function definition for 'dnorm'
plot.BIPOD: no visible global function definition for 'acf'
plot.BIPOD: no visible global function definition for 'pairs'
plot.BIPOD : standfun: no visible global function definition for 'sd'
plot.BIPOD: no visible global function definition for 'sd'
plot.BIPOD: no visible global function definition for 'points'
plot.BIPOD: no visible global function definition for 'tail'
plot.BIPOD: no visible global function definition for 'matlines'
plot.BIPOD: no visible binding for global variable 'quantile'
plot.BIPOD: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline acf curve density dlnorm dnorm lines matlines matplot pairs
  par plot points quantile sd tail
Consider adding
  importFrom("graphics", "abline", "curve", "lines", "matlines",
             "matplot", "pairs", "par", "plot", "points")
  importFrom("stats", "acf", "density", "dlnorm", "dnorm", "quantile",
             "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
aveslope: no visible global function definition for 'pbeta'
bisoreg : <anonymous>: no visible global function definition for
  'pbeta'
bisoreg: no visible global function definition for 'rgamma'
bisoreg: no visible global function definition for 'rbeta'
bisoreg: no visible global function definition for 'rnorm'
bisoreg: no visible global function definition for 'rbinom'
bisoreg: no visible global function definition for 'dnorm'
bisoreg: no visible global function definition for 'var'
fitted.biso : <anonymous>: no visible global function definition for
  'median'
get.W : <anonymous>: no visible global function definition for 'pbeta'
loess.wrapper : theta.fit: no visible global function definition for
  'loess'
loess.wrapper : theta.predict: no visible global function definition
  for 'predict'
loess.wrapper: no visible global function definition for 'loess'
nd2004 : initfun: no visible global function definition for 'rnorm'
nd2004 : initfun: no visible global function definition for 'rgamma'
plot.biso: no visible global function definition for 'plot'
plot.biso : <anonymous>: no visible global function definition for
  'quantile'
plot.biso: no visible global function definition for 'polygon'
plot.biso: no visible global function definition for 'gray'
plot.biso: no visible global function definition for 'points'
plot.biso : <anonymous>: no visible global function definition for
  'median'
plot.biso: no visible global function definition for 'lines'
summary.biso: no visible binding for global variable 'fivenum'
Undefined global functions or variables:
  dnorm fivenum gray lines loess median pbeta plot points polygon
  predict quantile rbeta rbinom rgamma rnorm var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "dnorm", "fivenum", "loess", "median", "pbeta",
             "predict", "quantile", "rbeta", "rbinom", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
bivarcalcn: no visible global function definition for 'qnorm'
bivarcalcn: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
biwt.cor: no visible global function definition for 'covMcd'
biwt.cor: no visible binding for global variable 'mad'
biwt.est: no visible global function definition for 'covMcd'
biwt.est: no visible global function definition for 'mahalanobis'
chi.int: no visible global function definition for 'pchisq'
chi.int.p: no visible global function definition for 'dchisq'
chi.int2: no visible global function definition for 'pchisq'
chi.int2.p: no visible global function definition for 'dchisq'
rejpt.bw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: 'RQuantLib'
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
blighty: no visible global function definition for 'par'
blighty: no visible global function definition for 'polygon'
blighty: no visible global function definition for 'points'
blighty: no visible global function definition for 'box'
blighty: no visible global function definition for 'axis'
blighty: no visible global function definition for 'abline'
map.scale: no visible global function definition for 'locator'
map.scale: no visible global function definition for 'segments'
map.scale: no visible global function definition for 'text'
north.pointer: no visible global function definition for 'locator'
north.pointer: no visible global function definition for 'text'
north.pointer: no visible global function definition for 'arrows'
north.pointer: no visible global function definition for 'segments'
sqlimits: no visible global function definition for 'frame'
sqlimits: no visible global function definition for 'par'
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
Package suggested but not available for checking: 'bigrf'
Missing or unexported object: 'xgboost::predict'
bglmer: no visible global function definition for 'packageVersion'
getBglmerDevianceFunctionBody: no visible global function definition
  for 'packageVersion'
getParInfo : <anonymous>: no visible global function definition for
  'sd'
makeRefitDevFun: no visible global function definition for
  'packageVersion'
mkBglmerDevfun: no visible global function definition for
  'packageVersion'
namedList: no visible global function definition for 'setNames'
refit.bmerMod: no visible global function definition for
  'packageVersion'
refit.bmerMod: no visible global function definition for 'model.frame'
refit.bmerMod: no visible global function definition for 'family'
refit.bmerMod: no visible global function definition for 'getCall'
Undefined global functions or variables:
  family getCall model.frame packageVersion sd setNames
Consider adding
  importFrom("stats", "family", "getCall", "model.frame", "sd",
             "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
blockMessage : <anonymous>: no visible global function definition for
  'head'
blockMessage: no visible global function definition for 'head'
blockMessage: no visible global function definition for 'tail'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.mat':
  'plot.mat' 'plot.mat.nm'

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.