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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings rtracklayer_1.71.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/rtracklayer.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.71.0’
* 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 ... WARNING
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
  ucsc/basicBed.c:449:1: warning: ‘__builtin_strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
  ucsc/udc.c:936:26: warning: ‘%02X’ directive output may be truncated writing between 2 and 8 bytes into a region of size 2 [-Wformat-truncation=]
See ‘/home/biocbuild/bbs-3.23-bioc/meat/rtracklayer.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
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 ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GRangesForUCSCGenome.Rd: genome
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:
  ‘Genome’ ‘Track’ ‘TrackContainer’ ‘cleanupBigBedCache’
  ‘descriptionUrl’ ‘descriptionUrl<-’ ‘email’ ‘email<-’ ‘genomeField’
  ‘genomeField<-’ ‘genomeInfo’ ‘genomeInfo<-’ ‘genomesFile’
  ‘genomesFile<-’ ‘getTracks’ ‘hub’ ‘hub<-’ ‘hubUrl<-’ ‘longLabel’
  ‘longLabel<-’ ‘readGFFAsGRanges’ ‘readGFFPragmas’ ‘shortLabel’
  ‘shortLabel<-’ ‘sniffGFFVersion’ ‘trackField’ ‘trackField<-’
Undocumented S4 classes:
  ‘Track’ ‘TrackContainer’
Undocumented S4 methods:
  generic 'genomesFile' and siglist 'TrackHub'
  generic 'genomesFile<-' and siglist 'TrackHub'
  generic 'names' and siglist 'GenomeContainer'
  generic 'names' and siglist 'TrackContainer'
  generic 'names' and siglist 'TrackHub'
  generic 'track<-' and siglist 'TrackHubGenome,BiocFile'
  generic 'trackNames' and siglist 'TrackHubGenome'
  generic 'trackNames' and siglist 'UCSCTableQuery'
  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 ... OK
* 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 is not available
File ‘rtracklayer/libs/rtracklayer.so’:
  Found non-API call to R: ‘R_ignore_SIGPIPE’

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’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
BigWigFile 22.464  4.413  26.879
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘rtracklayer_unit_tests.R’
 ERROR
Running the tests in ‘tests/rtracklayer_unit_tests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  rtracklayer RUnit Tests - 11 test functions, 1 error, 0 failures
  ERROR in test_ucsc: Error in if (file == "" || length(file) == 0) stop("empty or no content specified") : 
    missing value where TRUE/FALSE needed
  
  Test files with failing tests
  
     test_ucsc.R 
       test_ucsc 
  
  
  Error in BiocGenerics:::testPackage("rtracklayer") : 
    unit tests failed for package rtracklayer
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* 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: 1 ERROR, 2 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.