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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings APAlyzer_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/APAlyzer.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘APAlyzer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘APAlyzer’ version ‘1.16.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘APAlyzer’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘HybridMTest’
'library' or 'require' call to ‘HybridMTest’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GTF2LE: no visible binding for global variable ‘group_name’
.GTF2refUTRraw: no visible binding for global variable ‘GENEID’
.annotatePASRegion: no visible global function definition for
  ‘queryHits’
APABox: no visible binding for global variable ‘APAreg’
APABox: no visible binding for global variable ‘RED’
APAVolcano: no visible binding for global variable ‘APAreg’
APAVolcano: no visible binding for global variable ‘color’
PASEXP_IPA: no visible global function definition for ‘Print’
ThreeMostPairBam: no visible global function definition for ‘Print’
download_testbam: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  APAreg GENEID Print RED color download.file group_name queryHits
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: download_testbam.Rd:7-8: Dropping empty section \arguments
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 ‘APAlyzer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PAS2GEF
> ### Title: PAS2GEF, build reference regions for 3'UTR PASs
> ### Aliases: PAS2GEF
> 
> ### ** Examples
> 
> ## build Reference ranges for 3'UTR PASs in mouse
> 	download.file(url='ftp://ftp.ensembl.org/pub/release-99/gtf/mus_musculus/Mus_musculus.GRCm38.99.gtf.gz',
+               destfile='Mus_musculus.GRCm38.99.gtf.gz')			  
trying URL 'ftp://ftp.ensembl.org/pub/release-99/gtf/mus_musculus/Mus_musculus.GRCm38.99.gtf.gz'
Content type 'unknown' length 30321565 bytes (28.9 MB)
================================================
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 358531 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  ||    Meta-features : 222                                                     ||
  ||    Chromosomes/contigs : 1                                                 ||
  ||                                                                            ||
  || Process BAM file SRR316185.bam...                                          ||
  ||    Strand specific : stranded                                              ||
  ||    Single-end reads are included.                                          ||
  ||    Total alignments : 437626                                               ||
  ||    Successfully assigned alignments : 23378 (5.3%)                         ||
  ||    Running time : 0.01 minutes                                             ||
  ||                                                                            ||
  || Write the final count table.                                               ||
  || Write the read assignment summary.                                         ||
  ||                                                                            ||
  \\============================================================================//
  
* 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: 2 ERRORs, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/APAlyzer.Rcheck/00check.log’
for details.