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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:XVector.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings XVector_0.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/XVector.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘XVector/DESCRIPTION’ ... OK
* this is package ‘XVector’ version ‘0.46.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘XVector’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’
A package should be listed in only one of these fields.
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'XRawList-comparison.Rd':
  ‘[IRanges]{Ranges-comparison}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘RdaCollection’ ‘RdsCollection’ ‘open_input_files’ ‘rdaPath’
Undocumented S4 classes:
  ‘RdaCollection’ ‘RdsCollection’
Undocumented S4 methods:
  generic '[[' and siglist 'RdaCollection'
  generic 'coerce' and siglist 'XVector,Rle'
  generic 'extractList' and siglist 'XVector,IntegerRanges'
  generic 'extractROWS' and siglist 'RdsCollection,ANY'
  generic 'extractROWS' and siglist 'XVector,ANY'
  generic 'extractROWS' and siglist 'XVectorList,ANY'
  generic 'getListElement' and siglist 'RdsCollection'
  generic 'getListElement' and siglist 'XVectorList'
  generic 'length' and siglist 'RdaCollection'
  generic 'names' and siglist 'RdaCollection'
  generic 'names' and siglist 'RdsCollection'
  generic 'parallel_slot_names' and siglist 'RdsCollection'
  generic 'path' and siglist 'RdsCollection'
  generic 'rdaPath' and siglist 'RdaCollection'
  generic 'relist' and siglist 'XVector,PartitioningByEnd'
  generic 'relistToClass' and siglist 'XVector'
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/XVector.Rcheck/00check.log’
for details.