Check results for 'MetaPCA'

using R version 4.0.2 (2020-06-22)
using platform: x86_64-apple-darwin17.0 (64-bit)
using session charset: UTF-8
checking for file ‘MetaPCA/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘MetaPCA’ version ‘0.1.4’
checking package namespace information ... OK
checking package dependencies ... NOTE
Packages suggested but not available for checking:
'hgu133plus2.db', 'doSMP'
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘MetaPCA’ can be installed ... [2s/3s] OK
checking installed package size ... OK
checking package 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘pcaPP:::l1median_HoCr’ ‘pcaPP:::l1median_VaZh’
  See the note in ?`:::` about the use of this operator.
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [3s/3s] NOTE
.MetaSparsePCA: no visible global function definition for ‘%do%’
.MetaSparsePCA: no visible global function definition for ‘foreach’
.MetaSparsePCA: no visible global function definition for ‘iter’
DropDupGenes: no visible global function definition for ‘registerDoMC’
DropDupGenes: no visible global function definition for ‘startWorkers’
DropDupGenes: no visible global function definition for ‘registerDoSMP’
DropDupGenes: no visible global function definition for ‘%dopar%’
DropDupGenes: no visible global function definition for ‘foreach’
DropDupGenes: no visible global function definition for ‘iter’
DropDupGenes: no visible binding for global variable ‘IQR’
DropDupGenes: no visible global function definition for ‘stopWorkers’
MetaPCA: no visible global function definition for ‘PCAgrid’
MetaPCA: no visible global function definition for ‘cov’
PlotPC2D: no visible global function definition for ‘quartz’
PlotPC2D: no visible global function definition for ‘X11’
PlotPC2D: no visible global function definition for ‘cov.mve’
PlotPC2D: no visible global function definition for ‘ellipse’
PlotPC2D: no visible global function definition for ‘lines’
PlotPC2D: no visible global function definition for ‘points’
PlotPC2D: no visible global function definition for ‘axis’
PlotPC2D: no visible global function definition for ‘box’
PlotPC2D: no visible global function definition for ‘abline’
PlotPC2D: no visible global function definition for ‘legend’
PlotPC2D: no visible global function definition for ‘title’
PreprocessMetaAnalysis: no visible global function definition for
  ‘%do%’
PreprocessMetaAnalysis: no visible global function definition for
  ‘foreach’
PreprocessMetaAnalysis: no visible global function definition for
  ‘iter’
PreprocessMetaAnalysis: no visible binding for global variable ‘dat’
PreprocessMetaAnalysis: no visible global function definition for
  ‘na.omit’
PreprocessMetaAnalysis: no visible global function definition for
  ‘impute.knn’
legend2: no visible global function definition for ‘par’
legend2: no visible global function definition for ‘as.graphicsAnnot’
legend2: no visible global function definition for ‘xy.coords’
legend2 : rect2: no visible global function definition for ‘rect’
legend2 : segments2: no visible global function definition for
  ‘segments’
legend2 : points2: no visible global function definition for ‘points’
legend2 : text2: no visible global function definition for ‘text’
legend2: no visible global function definition for ‘strwidth’
legend2: no visible global function definition for ‘xinch’
legend2: no visible global function definition for ‘yinch’
legend2: no visible global function definition for ‘strheight’
requireAll: no visible global function definition for
  ‘installed.packages’
requireAll: no visible global function definition for ‘biocLite’
Undefined global functions or variables:
  %do% %dopar% IQR PCAgrid X11 abline as.graphicsAnnot axis biocLite
  box cov cov.mve dat ellipse foreach impute.knn installed.packages
  iter legend lines na.omit par points quartz rect registerDoMC
  registerDoSMP segments startWorkers stopWorkers strheight strwidth
  text title xinch xy.coords yinch
Consider adding
  importFrom("grDevices", "X11", "as.graphicsAnnot", "quartz",
             "xy.coords")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "par", "points", "rect", "segments", "strheight",
             "strwidth", "text", "title", "xinch", "yinch")
  importFrom("stats", "IQR", "cov", "na.omit")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
checking Rd files ... NOTE
prepare_Rd: DropDupGenes.Rd:29-31: Dropping empty section \details
prepare_Rd: DropDupGenes.Rd:41-43: Dropping empty section \note
prepare_Rd: DropDupGenes.Rd:47-49: Dropping empty section \seealso
prepare_Rd: MetaPCA-package.Rd:29-30: Dropping empty section \seealso
prepare_Rd: MetaPCA.Rd:76-78: Dropping empty section \details
prepare_Rd: MetaPCA.Rd:88-90: Dropping empty section \note
prepare_Rd: MetaPCA.Rd:94-96: Dropping empty section \seealso
prepare_Rd: PlotPC2D.Rd:80-82: Dropping empty section \details
prepare_Rd: PlotPC2D.Rd:92-94: Dropping empty section \note
prepare_Rd: PlotPC2D.Rd:98-100: Dropping empty section \seealso
prepare_Rd: PreprocessMetaAnalysis.Rd:39-41: Dropping empty section \details
prepare_Rd: PreprocessMetaAnalysis.Rd:51-53: Dropping empty section \note
prepare_Rd: PreprocessMetaAnalysis.Rd:57-59: Dropping empty section \seealso
prepare_Rd: requireAll.Rd:19-21: Dropping empty section \details
prepare_Rd: requireAll.Rd:31-33: Dropping empty section \note
prepare_Rd: requireAll.Rd:25-27: Dropping empty section \references
prepare_Rd: requireAll.Rd:37-39: Dropping empty section \seealso
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 examples ... [1s/1s] OK
checking PDF version of manual ... OK
DONE
Status: 4 NOTEs