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### Running command:
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###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:srnadiff.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings srnadiff_1.22.2.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/srnadiff.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'srnadiff/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'srnadiff' version '1.22.2'
* 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 'srnadiff' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocManager' 'BiocStyle'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION
Most likely 'inst/CITATION' should be used instead.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
useEdgeR: no visible global function definition for 'model.matrix'
useEdgeR: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  model.matrix p.adjust
Consider adding
  importFrom("stats", "model.matrix", "p.adjust")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: parameters.Rd:38-40: Dropping empty section \details
checkRd: (5) plotRegions.Rd:115: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:116: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:117: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:118-119: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:120-121: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotRegions.Rd':
  'GdObject'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 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-3.18-bioc/R/library/srnadiff/libs/x64/srnadiff.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (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
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotRegions               14.24   0.13   41.89
parameters                11.64   0.08   64.32
countMatrix               10.65   0.11   41.20
srnadiff                   6.89   0.05   33.12
srnadiffDefaultParameters  6.46   0.08   34.10
regions                    6.30   0.16   32.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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: 2 WARNINGs, 5 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/srnadiff.Rcheck/00check.log'
for details.