noriakis / biotextgraph Goto Github PK

* using log directory ‘/Users/guz/project/development/wcGeneSummary.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘wcGeneSummary/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wcGeneSummary’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘wcGeneSummary’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compareWordNet: no visible global function definition for
  ‘geom_mark_hull’
compareWordNet: no visible binding for global variable ‘x’
compareWordNet: no visible binding for global variable ‘y’
compareWordNet: no visible global function definition for
  ‘colorRampPalette’
compareWordNet: no visible binding for global variable ‘name’
getWordsOnDendro: no visible binding for global variable ‘x’
makeBar: no visible binding for global variable ‘freq’
pathviewText: no visible global function definition for ‘download.kegg’
pathviewText: no visible global function definition for ‘node.info’
pathviewText: no visible global function definition for ‘node.map’
pathviewText: no visible global function definition for
  ‘colorRampPalette’
pathviewText: no visible global function definition for
  ‘keggview.native’
pathviewText: no visible global function definition for ‘readPNG’
pathviewText: no visible binding for global variable ‘query’
pathviewText: no visible global function definition for ‘summarise’
pathviewText: no visible global function definition for ‘group_by’
pathviewText: no visible binding for global variable ‘X1’
pathviewText: no visible global function definition for ‘n’
pathviewText: no visible global function definition for ‘reorder’
pathviewText: no visible binding for global variable ‘X3’
pathviewText: no visible binding for global variable ‘stack’
pathviewText: no visible binding for global variable ‘X2’
plotDynamic: no visible binding for global variable ‘Freq’
plotDynamic: no visible binding for global variable ‘name’
plotORA: no visible binding for global variable ‘freq’
plotORA: no visible binding for global variable ‘p’
plotORA: no visible global function definition for ‘geom_text_repel’
retUdpipeNet: no visible global function definition for ‘summarise’
retUdpipeNet: no visible global function definition for ‘group_by’
retUdpipeNet: no visible binding for global variable ‘term’
retUdpipeNet: no visible binding for global variable ‘ID’
retUdpipeNet: no visible binding for global variable ‘sentence_id’
retUdpipeNet: no visible binding for global variable ‘token_id’
retUdpipeNet: no visible binding for global variable ‘name’
returnPyramid: no visible binding for global variable ‘ME’
returnPyramid: no visible binding for global variable ‘Word’
returnPyramid: no visible binding for global variable ‘Label’
returnPyramid: no visible binding for global variable ‘Count’
returnPyramid: no visible binding for global variable ‘plotID’
returnPyramid: no visible binding for global variable ‘value’
returnPyramid: no visible binding for global variable ‘plotCol’
returnQuanteda: no visible global function definition for ‘corpus’
returnQuanteda: no visible global function definition for
  ‘tokens_remove’
returnQuanteda: no visible global function definition for
  ‘tokens_ngrams’
returnQuanteda: no visible global function definition for ‘dfm’
returnQuanteda: no visible global function definition for ‘dfm_tfidf’
textORA: no visible binding for global variable ‘Gene_ID’
wcAbst: no visible global function definition for ‘boot.strength’
wcAbst: no visible global function definition for ‘averaged.network’
wcAbst: no visible binding for global variable ‘weight’
wcAbst: no visible binding for global variable ‘Freq’
wcAbst: no visible binding for global variable ‘name’
wcBSDB: no visible binding for global variable ‘Title’
wcBSDB: no visible binding for global variable ‘ID’
wcBSDB: no visible binding for global variable ‘orgDb’
wcBSDB: no visible binding for global variable ‘weight’
wcBSDB: no visible binding for global variable ‘Freq’
wcBSDB: no visible binding for global variable ‘name’
wcGeneSummary: no visible global function definition for
  ‘enrichPathway’
wcGeneSummary: no visible global function definition for ‘enrichKEGG’
wcGeneSummary: no visible binding for global variable ‘Gene_ID’
wcGeneSummary: no visible global function definition for ‘setReadable’
wcGeneSummary: no visible global function definition for
  ‘boot.strength’
wcGeneSummary: no visible global function definition for
  ‘averaged.network’
wcGeneSummary: no visible binding for global variable ‘weight’
wcGeneSummary: no visible binding for global variable ‘Freq’
wcGeneSummary: no visible binding for global variable ‘name’
wcGeneSummary: no visible global function definition for
  ‘geom_mark_hull’
wcMan: no visible global function definition for ‘boot.strength’
wcMan: no visible global function definition for ‘averaged.network’
wcMan: no visible binding for global variable ‘weight’
wcMan: no visible binding for global variable ‘Freq’
wcMan: no visible binding for global variable ‘name’
wcMan: no visible binding for global variable ‘redo’
plot,osplot-ANY: no visible global function definition for
  ‘colorRampPalette’
plot,osplot-ANY: no visible global function definition for ‘brewer.pal’
plot,osplot-ANY: no visible global function definition for
  ‘adjustcolor’
show,osplot: no visible global function definition for ‘object.size’
Undefined global functions or variables:
  Count Freq Gene_ID ID Label ME Title Word X1 X2 X3 adjustcolor
  averaged.network boot.strength brewer.pal colorRampPalette corpus dfm
  dfm_tfidf download.kegg enrichKEGG enrichPathway freq geom_mark_hull
  geom_text_repel group_by keggview.native n name node.info node.map
  object.size orgDb p plotCol plotID query readPNG redo reorder
  sentence_id setReadable stack summarise term token_id tokens_ngrams
  tokens_remove value weight x y
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette")
  importFrom("stats", "reorder")
  importFrom("utils", "object.size", "stack")
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 R/sysdata.rda ... NOTE

  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    1.4Mb    311Kb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘basic_usage.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/guz/project/development/wcGeneSummary.Rcheck/00check.log’
for details.