##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rtracklayer.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings rtracklayer_1.67.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/rtracklayer.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.67.0'
* 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 whether package 'rtracklayer' can be installed ... WARNING
Found the following significant warnings:
  bigBedHelper.c:148:3: warning: 'strncpy' destination unchanged after copying no bytes [-Wstringop-truncation]
  ucsc/basicBed.c:449:1: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
  ucsc/udc.c:1070:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  ucsc/net.c:36:1: warning: control reaches end of non-void function [-Wreturn-type]
  ucsc/net.c:57:1: warning: control reaches end of non-void function [-Wreturn-type]
  ucsc/net.c:187:1: warning: control reaches end of non-void function [-Wreturn-type]
See 'E:/biocbuild/bbs-3.21-bioc/meat/rtracklayer.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... INFO
  installed size is 12.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   9.6Mb
* 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 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
':::' 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 ... WARNING
checkRd: (5) BigBedFile.Rd:96-101: \item in \describe must have non-empty label
checkRd: (5) BigBedSelection.rd:23-30: \item in \describe must have non-empty label
checkRd: (5) BigBedSelection.rd:36-42: \item in \describe must have non-empty label
checkRd: (5) BigWigFile.Rd:137-142: \item in \describe must have non-empty label
checkRd: (5) BigWigFile.Rd:143-172: \item in \describe must have non-empty label
checkRd: (5) BigWigSelection-class.Rd:21-29: \item in \describe must have non-empty label
checkRd: (5) BigWigSelection-class.Rd:35-41: \item in \describe must have non-empty label
checkRd: (5) BrowserViewList-class.Rd:19-22: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:49-55: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:56-59: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:60-62: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:63-65: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:66-69: \item in \describe must have non-empty label
checkRd: (5) Chain-class.Rd:83-88: \item in \describe must have non-empty label
checkRd: (5) GFFFile-class.Rd:248-250: \item in \describe must have non-empty label
checkRd: (5) GenomicData.Rd:24-28: \item in \describe must have non-empty label
checkRd: (5) GenomicData.Rd:29-35: \item in \describe must have non-empty label
checkRd: (5) GenomicData.Rd:41-57: \item in \describe must have non-empty label
checkRd: (5) IntegerRangesList-methods.Rd:26-30: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:36-43: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:52-55: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:56-57: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:58-60: \item in \describe must have non-empty label
checkRd: (5) Quickload-class.Rd:61-63: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:48-72: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:81-86: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:87-90: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:91-94: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:95-98: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:99-102: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:103-106: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:112-114: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:115-117: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:118-120: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:121-123: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:124-150: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:151-154: \item in \describe must have non-empty label
checkRd: (5) QuickloadGenome-class.Rd:155-159: \item in \describe must have non-empty label
checkRd: (-1) TabixFile-methods.Rd:16: Lost braces
    16 |   \code{Rsamtools:TabixFile}{TabixFile} objects. These are generally
       |                             ^
checkRd: (5) TrackDb-class.Rd:30-32: \item in \describe must have non-empty label
checkRd: (5) TrackDb-class.Rd:33-35: \item in \describe must have non-empty label
checkRd: (5) TrackDb-class.Rd:36-38: \item in \describe must have non-empty label
checkRd: (5) TrackDb-class.Rd:39-42: \item in \describe must have non-empty label
checkRd: (5) TrackDb-class.Rd:43-49: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:56-63: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:72-75: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:76-77: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:78-80: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:81-83: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:84-88: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:95-97: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:98-100: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:101-103: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:104-106: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:107-109: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:110-112: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:113-115: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:116-118: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:119-121: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:122-124: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:125-127: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:128-130: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:131-133: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:134-136: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:137-139: \item in \describe must have non-empty label
checkRd: (5) TrackHub-class.Rd:140-144: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:45-59: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:67-70: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:71-74: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:75-77: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:78-80: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:81-83: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:84-87: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:88-91: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:92-94: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:95-97: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:98-100: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:106-108: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:109-128: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:129-132: \item in \describe must have non-empty label
checkRd: (5) TrackHubGenome-class.Rd:133-137: \item in \describe must have non-empty label
checkRd: (5) TwoBitFile-class.Rd:106-111: \item in \describe must have non-empty label
checkRd: (5) UCSCSchema-class.Rd:25: \item in \describe must have non-empty label
checkRd: (5) UCSCSchema-class.Rd:26: \item in \describe must have non-empty label
checkRd: (5) UCSCSchema-class.Rd:27: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:92-102: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:110-114: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:115-122: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:123-126: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:135-137: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:138-140: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:141-145: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:146-152: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:153-156: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:157-158: \item in \describe must have non-empty label
checkRd: (5) UCSCTableQuery-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (-1) layTrack-methods.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) layTrack-methods.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (5) ucscSession-class.Rd:100-105: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BigBedFile.Rd: BiocFile-class
  BigWigSelection-class.Rd: IntegerRangesList-class
  GRangesForUCSCGenome.Rd: genome
  TrackHubGenome-class.Rd: BiocFile-class
  UCSCData-class.Rd: import, export
  browserSession-class.Rd: genome
  readGFF.Rd: import
  ucscSession-class.Rd: GRanges
  wigToBigWig.Rd: Seqinfo-class
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:
  'FileForFormat' 'Genome' 'Track' 'TrackContainer' 'browserSession<-'
  'cleanupBigBedCache' 'descriptionUrl' 'descriptionUrl<-' 'email'
  'email<-' 'genomeField' 'genomeField<-' 'genomeInfo' 'genomeInfo<-'
  'genomesFile' 'genomesFile<-' 'getTracks' 'hub' 'hub<-' 'hubUrl<-'
  'longLabel' 'longLabel<-' 'readGFFAsGRanges' 'readGFFPragmas'
  'shortLabel' 'shortLabel<-' 'sniffGFFVersion' 'trackField'
  'trackField<-' 'trackName' 'trackName<-'
Undocumented S4 classes:
  'Track' 'RTLFile' '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 Rd file 'ucscView-class.Rd':
Slots for class 'UCSCView'
  Code: form hgsid session
  Inherited: session
  Docs: hgsid session

* checking Rd \usage sections ... OK
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'readGFF.Rd':
  'filter' 'raw_data' 'GFF1'
* 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 ... 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/rtracklayer/libs/x64/rtracklayer.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
File 'rtracklayer/libs/x64/rtracklayer.dll':
  Found non-API calls to R: 'R_ReadConnection', '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 nor [v]sprintf. 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,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
* 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
BEDFile-class 4.89   1.47    6.36
* 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 ... 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
  'E:/biocbuild/bbs-3.21-bioc/meat/rtracklayer.Rcheck/00check.log'
for details.