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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EventPointer.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings EventPointer_3.14.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/EventPointer.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'EventPointer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EventPointer' version '3.14.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'EventPointer' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'SGSeq:::addFeatureID' 'SGSeq:::addGeneID' 'SGSeq:::edges'
  'SGSeq:::exonGraph' 'SGSeq:::feature2name' 'SGSeq:::matchSGFeatures'
  'SGSeq:::nodes' 'SGSeq:::propagateAnnotation'
  'SGSeq:::splitCharacterList'
  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
EventDetection_transcriptome: no visible binding for global variable
  'jj'
SF_Prediction: no visible binding for global variable 'valueRanking'
SF_Prediction: no visible binding for global variable 'PSI_table'
annotate2: no visible global function definition for
  'addDummySpliceSites'
annotate2: no visible global function definition for 'annotatePaths'
annotateFeatures2: no visible global function definition for
  'matchTxFeatures'
callGRseq_parallel: no visible global function definition for
  'makeCluster'
callGRseq_parallel: no visible binding for global variable 'i'
callGRseq_parallel: no visible global function definition for
  'stopCluster'
call_get_table_Bootstrap: no visible global function definition for
  'makeCluster'
call_get_table_Bootstrap: no visible binding for global variable 'ii'
call_get_table_Bootstrap: no visible global function definition for
  'stopCluster'
fitgl: no visible binding for global variable 'hist'
myphyper: no visible global function definition for 'dhyper'
Undefined global functions or variables:
  PSI_table addDummySpliceSites annotatePaths dhyper hist i ii jj
  makeCluster matchTxFeatures stopCluster valueRanking
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dhyper")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ... NOTE
S3 methods shown with full name in Rd file 'InternalFunctions.Rd':
  'sort.exons'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/EventPointer/libs/x64/EventPointer.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/EventPointer.Rcheck/00check.log'
for details.