##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rtracklayer_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.54.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rtracklayer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   3.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  Artistic-2.0 + file LICENSE
* 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 dependencies in R code ... NOTE
':::' call which should be '::': ‘XVector:::open_input_files’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘GenomicRanges:::INVALID.GR.COLNAMES’
  ‘S4Vectors:::labeledLine’
  ‘S4Vectors:::make_XYZxyz_to_XxYyZz_subscript’
  ‘S4Vectors:::new_SimpleList_from_list’ ‘XVector:::rewind_filexp’
  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 ... NOTE
import,BEDPEFile-ANY-ANY: no visible binding for global variable
  ‘chrom2’
import,BEDPEFile-ANY-ANY: no visible binding for global variable
  ‘start2’
import,BEDPEFile-ANY-ANY: no visible binding for global variable ‘end2’
import,BEDPEFile-ANY-ANY: no visible binding for global variable
  ‘strand2’
Undefined global functions or variables:
  chrom2 end2 start2 strand2
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'uri':
  ‘Quickload-class.Rd’ ‘TrackHub-class.Rd’
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IntegerRangesList-methods.Rd':
  ‘[IRanges]{names}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘FileForFormat’ ‘Genome’ ‘Track’ ‘TrackContainer’ ‘browserSession<-’
  ‘cleanupBigBedCache’ ‘descriptionUrl’ ‘descriptionUrl<-’ ‘email’
  ‘email<-’ ‘genomeField’ ‘genomeField<-’ ‘genomeInfo’ ‘genomeInfo<-’
  ‘genomesFile’ ‘genomesFile<-’ ‘getTracks’ ‘hub’ ‘hub<-’ ‘hubUrl<-’
  ‘longLabel’ ‘longLabel<-’ ‘readGFFAsGRanges’ ‘readGFFPragmas’
  ‘resource’ ‘shortLabel’ ‘shortLabel<-’ ‘sniffGFFVersion’ ‘trackField’
  ‘trackField<-’ ‘trackName’ ‘trackName<-’
Undocumented S4 classes:
  ‘RTLFile’ ‘Track’ ‘TrackContainer’ ‘RTLFileList’
Undocumented S4 methods:
  generic 'as.character' and siglist 'RTLFile'
  generic 'browserSession' and siglist 'UCSCTableQuery'
  generic 'browserSession<-' and siglist 'UCSCTableQuery'
  generic 'export' and siglist 'CompressedGRangesList,BEDFile,ANY'
  generic 'export' and siglist 'CompressedGRangesList,GFFFile,ANY'
  generic 'export' and siglist 'GRangesList,UCSCFile,ANY'
  generic 'export' and siglist 'SimpleGRangesList,BEDFile,ANY'
  generic 'export' and siglist 'SimpleGRangesList,GFFFile,ANY'
  generic 'export' and siglist 'SimpleGRangesList,WIGFile,ANY'
  generic 'fileFormat' and siglist 'Bed15TrackLine'
  generic 'fileFormat' and siglist 'GraphTrackLine'
  generic 'fileFormat' and siglist 'RTLFile'
  generic 'fileFormat' and siglist 'TrackLine'
  generic 'genomesFile' and siglist 'TrackHub'
  generic 'genomesFile<-' and siglist 'TrackHub'
  generic 'initialize' and siglist 'RTLFile'
  generic 'liftOver' and siglist 'GRangesList,Chain'
  generic 'names' and siglist 'GenomeContainer'
  generic 'names' and siglist 'Quickload'
  generic 'names' and siglist 'TrackContainer'
  generic 'names' and siglist 'TrackHub'
  generic 'path' and siglist 'RTLFile'
  generic 'show' and siglist 'RTLFile'
  generic 'show' and siglist 'UCSCSchema'
  generic 'track<-' and siglist 'TrackHubGenome,BiocFile'
  generic 'track<-' and siglist 'UCSCSession,SimpleGRangesList'
  generic 'trackName' and siglist 'UCSCTableQuery'
  generic 'trackName<-' and siglist 'UCSCTableQuery'
  generic 'trackNames' and siglist 'QuickloadGenome'
  generic 'trackNames' and siglist 'TrackHubGenome'
  generic 'trackNames' and siglist 'UCSCTableQuery'
  generic 'uri' and siglist 'Quickload'
  generic 'uri' and siglist 'TrackHub'
  generic 'writeTrackHub' and siglist 'TrackHub'
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 ... WARNING
S4 class codoc mismatches from documentation object 'UCSCView-class':
Slots for class 'UCSCView'
  Code: form hgsid session
  Inherited: session
  Docs: hgsid session

* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rtracklayer/libs/rtracklayer.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘__exit’, possibly from ‘_exit’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
File ‘rtracklayer/libs/rtracklayer.so’:
  Found non-API calls to R: ‘R_ReadConnection’, ‘R_ignore_SIGPIPE’,
    ‘getConnection’

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
BigWigFile    30.300  2.373  32.712
BEDFile-class  6.238  0.730   6.974
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘rtracklayer_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.