##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:IRanges.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings IRanges_2.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/IRanges.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘2.41.1’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IRanges’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 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 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
setCompressedListSummaryMethod : <anonymous>: no visible binding for
  global variable ‘C_fun’
setCompressedListWhichSummaryMethod : def: no visible binding for
  global variable ‘C_fun’
Undefined global functions or variables:
  C_fun
* checking Rd files ... NOTE
checkRd: (-1) nearest-methods.Rd:69-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:88-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:94-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:100-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:140-143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:144-148: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'IntegerRangesList-class.Rd':
  ‘[IRanges]{RangesList}’

Missing link(s) in Rd file 'intra-range-methods.Rd':
  ‘RangesList’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AtomicList-class.Rd: List-class
  AtomicList-utils.Rd: unstrsplit
  CompressedHitsList-class.Rd: HitsList
  CompressedList-class.Rd: List
  DataFrameList-class.Rd: DataFrame-class, List-class
  Grouping-class.Rd: List
  IPosRanges-comparison.Rd: Hits
  NCList-class.Rd: Hits
  RleViews-class.Rd: Rle, Rle-class
  Views-class.Rd: Vector, Vector-class
  ViewsList-class.Rd: List-class
  coverage-methods.Rd: Rle
  extractList.Rd: Vector, List
  extractListFragments.Rd: List
  intra-range-methods.Rd: RangesList
  reverse-methods.Rd: revElements
  seqapply.Rd: List, Vector
  slice-methods.Rd: Rle
  view-summarization-methods.Rd: List, Rle
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘%poutside%’ ‘%pover%’ ‘%pwithin%’ ‘cvg’ ‘heads’ ‘slidingIRanges’
  ‘slidingViews’ ‘tails’ ‘windows’
Undocumented S4 classes:
  ‘BaseManyToManyGrouping’ ‘Pos’ ‘CompressedIntegerRangesList’
  ‘IPosList’ ‘CompressedRangesList’ ‘SimpleIPosList’ ‘RangesList’
  ‘CompressedPosList’ ‘CompressedIPosList’ ‘Ranges’ ‘SimplePosList’
  ‘PosList’ ‘SimpleRangesList’
Undocumented S4 methods:
  generic 'anyDuplicated' and siglist 'RangesNSBS'
  generic 'as.factor' and siglist 'ManyToOneGrouping'
  generic 'as.integer' and siglist 'NormalIRanges'
  generic 'as.integer' and siglist 'Pos'
  generic 'as.integer' and siglist 'RangesNSBS'
  generic 'cbind' and siglist 'Rle'
  generic 'cbind' and siglist 'RleList'
  generic 'chartr' and siglist 'ANY,ANY,CharacterList'
  generic 'chartr' and siglist 'ANY,ANY,RleList'
  generic 'coerce' and siglist 'ANY,IPosRanges'
  generic 'coerce' and siglist 'AtomicList,RleViews'
  generic 'coerce' and siglist 'IPosRanges,CompressedIntegerList'
  generic 'coerce' and siglist 'IPosRanges,IntegerList'
  generic 'coerce' and siglist 'IRanges,IPosList'
  generic 'coerce' and siglist 'IntegerRanges,CompressedIPosList'
  generic 'coerce' and siglist 'IntegerRanges,IPosList'
  generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
  generic 'coerce' and siglist 'factor,ManyToOneGrouping'
  generic 'commonColnames<-' and siglist 'SplitDataFrameList'
  generic 'cvg' and siglist 'IntegerRanges'
  generic 'cvg' and siglist 'IntegerRangesList'
  generic 'endsWith' and siglist 'CharacterList'
  generic 'endsWith' and siglist 'RleList'
  generic 'extractROWS' and siglist 'CompressedList,ANY'
  generic 'extractROWS' and siglist 'IPos,ANY'
  generic 'extractROWS' and siglist 'MaskCollection,ANY'
  generic 'extractROWS' and siglist 'NormalIRanges,ANY'
  generic 'extractROWS' and siglist 'Partitioning,ANY'
  generic 'extractROWS' and siglist 'Rle,RangesNSBS'
  generic 'extractROWS' and siglist 'vector_OR_factor,RangesNSBS'
  generic 'getListElement' and siglist 'CompressedList'
  generic 'getListElement' and siglist 'CompressedNormalIRangesList'
  generic 'getListElement' and siglist 'H2LGrouping'
  generic 'getListElement' and siglist 'MaskCollection'
  generic 'getListElement' and siglist 'NCLists'
  generic 'getListElement' and siglist 'Partitioning'
  generic 'getListElement' and siglist 'Views'
  generic 'gsub' and siglist 'ANY,ANY,CharacterList'
  generic 'gsub' and siglist 'ANY,ANY,RleList'
  generic 'ifelse2' and siglist 'ANY,List,List'
  generic 'is.unsorted' and siglist 'CompressedIntegerList'
  generic 'is.unsorted' and siglist 'CompressedLogicalList'
  generic 'is.unsorted' and siglist 'CompressedNumericList'
  generic 'isNormal' and siglist 'IntegerRanges'
  generic 'length' and siglist 'RangesNSBS'
  generic 'nchar' and siglist 'CharacterList'
  generic 'nchar' and siglist 'RleList'
  generic 'pcompareRecursively' and siglist 'IPosRanges'
  generic 'range' and siglist 'CompressedRleList'
  generic 'relist' and siglist 'grouping,missing'
  generic 'replaceROWS' and siglist 'IRanges'
  generic 'replaceROWS' and siglist 'NormalIRanges'
  generic 'slidingWindows' and siglist 'IntegerRanges'
  generic 'startsWith' and siglist 'CharacterList'
  generic 'startsWith' and siglist 'RleList'
  generic 'sub' and siglist 'ANY,ANY,CharacterList'
  generic 'sub' and siglist 'ANY,ANY,RleList'
  generic 'tile' and siglist 'IntegerRanges'
  generic 'tolower' and siglist 'CharacterList'
  generic 'tolower' and siglist 'RleList'
  generic 'toupper' and siglist 'CharacterList'
  generic 'toupper' and siglist 'RleList'
  generic 'updateObject' and siglist 'CompressedList'
  generic 'updateObject' and siglist 'IPosRanges'
  generic 'whichFirstNotNormal' and siglist 'IntegerRanges'
  generic 'windows' and siglist 'list_OR_List'
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.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'nearest-methods.Rd':
  ‘hits’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/libs/IRanges.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)

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 nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
IPos-class 6.174  0.349   6.525
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/IRanges.Rcheck/00check.log’
for details.