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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:APAlyzer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings APAlyzer_1.9.4.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/APAlyzer.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'APAlyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'APAlyzer' version '1.9.4'
* 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 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
download_testbam  7.63  15.57  226.21
PASEXP_IPA       18.97   1.16   22.42
PASEXP_3UTR      11.16   0.14  117.91
GENEXP_CDS        6.81   0.09   62.88
PAS2GEF           0.01   0.28    6.64
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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: 1 WARNING, 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/APAlyzer.Rcheck/00check.log'
for details.