* using log directory 'd:/Rcompile/CRANpkg/local/3.4/clValid.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'clValid/DESCRIPTION' ... OK
* this is package 'clValid' version '0.6-6'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'moe430a.db'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'clValid' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'Biobase' 'GO.db' 'annotate' 'kohonen' 'mclust'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [7s] NOTE
BHI: no visible global function definition for 'getGO'
BHI: no visible binding for global variable 'dropECode'
BSI: no visible global function definition for 'xtabs'
BSI: no visible global function definition for 'getGO'
BSI: no visible binding for global variable 'dropECode'
clValid: no visible global function definition for 'as.dist'
clValid: no visible global function definition for 'cor'
clValid: no visible global function definition for 'dist'
connectivity: no visible global function definition for 'dist'
dist.fn: no visible global function definition for 'cor'
dunn: no visible global function definition for 'dist'
mysilhouette: no visible global function definition for 'dist'
plot.sota: no visible global function definition for 'par'
plot.sota: no visible global function definition for 'legend'
plot.sota: no visible global function definition for 'lines'
stability: no visible global function definition for 'xtabs'
stability: no visible global function definition for 'dist'
vClusters: no visible global function definition for 'hclust'
vClusters: no visible global function definition for 'cutree'
vClusters: no visible global function definition for 'kmeans'
vClusters: no visible global function definition for 'Mclust'
vClusters: no visible global function definition for 'som'
vClusters: no visible global function definition for 'as.dist'
vClusters: no visible global function definition for 'cor'
vClusters: no visible global function definition for 'dist'
plot,clValid-missing: no visible global function definition for 'par'
plot,clValid-missing: no visible global function definition for
  'dev.interactive'
plot,clValid-missing: no visible global function definition for
  'matplot'
plot,clValid-missing: no visible global function definition for 'axis'
summary,clValid: no visible global function definition for 'ftable'
Undefined global functions or variables:
  Mclust as.dist axis cor cutree dev.interactive dist dropECode ftable
  getGO hclust kmeans legend lines matplot par som xtabs
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "axis", "legend", "lines", "matplot", "par")
  importFrom("stats", "as.dist", "cor", "cutree", "dist", "ftable",
             "hclust", "kmeans", "xtabs")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [10s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [17s] WARNING
Error in re-building vignettes:
  ...
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML

Attaching package: 'XML'

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs