##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annmap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annmap_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/annmap.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘annmap’ version ‘1.48.0’
* 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 hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘annmap’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘rjson’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.make.hash’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.get.stats.cache: no visible global function definition for
  ‘flush.console’
.layout.genes: no visible global function definition for ‘strwidth’
.load.and.parse: no visible global function definition for ‘fromJSON’
.read.databases: no visible global function definition for ‘read.table’
.single.transcript.coords.to.genome: no visible global function
  definition for ‘tail’
.xmc.connect: no visible global function definition for ‘menu’
.xmcws.connect: no visible global function definition for ‘fromJSON’
.xmcws.connect: no visible global function definition for ‘menu’
annmapAddConnection: no visible global function definition for
  ‘write.table’
annmapConnect: no visible global function definition for
  ‘install.packages’
arrayType: no visible global function definition for ‘menu’
convertBamToRle: no visible global function definition for ‘RangedData’
convertBamToRle : <anonymous>: no visible global function definition
  for ‘Rle’
geneToGeneRegionTrack : generate: no visible global function definition
  for ‘GeneRegionTrack’
generateBridgeData: no visible global function definition for ‘rainbow’
genomicPlot : <anonymous>: no visible global function definition for
  ‘rgb’
genomicPlot: no visible global function definition for ‘rgb’
ngsTracePlotter : local.draw: no visible global function definition for
  ‘runValue’
ngsTracePlotter: no visible global function definition for ‘modifyList’
ngsTraceScale : <anonymous>: no visible global function definition for
  ‘runValue’
seqnameMapping: no visible global function definition for ‘seqlevels<-’
seqnameMapping: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
  GeneRegionTrack RangedData Rle flush.console fromJSON
  install.packages menu modifyList rainbow read.table rgb runValue
  seqlevels seqlevels<- strwidth tail write.table
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "strwidth")
  importFrom("utils", "flush.console", "install.packages", "menu",
             "modifyList", "read.table", "tail", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) NEWS.Rd:5: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:146: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:152: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:153: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'annmap.range.Rd':
  ‘RangedData’

Missing link or links in Rd file 'annmap.utils.Rd':
  ‘RangedData’

Missing link or links in Rd file 'plot.ngs.Rd':
  ‘[IRanges]{Rle}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/annmap.Rcheck/00check.log’
for details.