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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:alabaster.ranges.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings alabaster.ranges_1.7.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/alabaster.ranges.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘alabaster.ranges/DESCRIPTION’ ... OK
* this is package ‘alabaster.ranges’ version ‘1.7.0’
* 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 ‘alabaster.ranges’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  readAtomicVectorList.Rd: CompressedAtomicList-class, readObject,
    saveObject, readObjectFile, altReadObject
  readDataFrameList.Rd: CompressedSplitDataFrameList-class, readObject,
    saveObject, readObjectFile, altReadObject
  readGRanges.Rd: GRanges-class, readObject, stageObject,
    readObjectFile, altReadObject
  readGRangesList.Rd: GRangesList-class, saveObject, readObjectFile,
    altReadObject
  readSeqinfo.Rd: Seqinfo-class, readObject, saveObject, readObjectFile
  saveAtomicVectorList.Rd: CompressedAtomicList-class
  saveCompressedSplitDataFrameList.Rd:
    CompressedSplitDataFrameList-class
  saveGRanges.Rd: GRanges-class
  saveGRangesList.Rd: GRangesList-class
  saveSeqinfo.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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘alabaster.ranges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readGRanges
> ### Title: Read a GRanges from disk
> ### Aliases: readGRanges loadGRanges
> 
> ### ** Examples
> 
> gr <- GRanges(c("chrA", "chrB"), IRanges(c(1, 5), c(100, 200)))
> seqlengths(gr) <- c(chrA=1000, chrB=2000)
> 
> tmp <- tempfile()
> saveObject(gr, tmp)
Error in H5Dclose(dhandle) : 
  HDF5. Dataset. Unable to decrement reference count.
Calls: saveObject -> saveObject -> h5_write_vector -> H5Dclose
Error in H5Fclose(fhandle) : 
  HDF5. File accessibility. Unable to close file.
Calls: saveObject -> saveObject -> H5Fclose
Execution halted

 *** caught segfault ***
address 0x558, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
Re-running with no redirection of stdout/stderr.
Fatal error: cannot create 'R_TempDir'
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/alabaster.ranges.Rcheck/00check.log’
for details.