##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings flagme_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/flagme.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'flagme/DESCRIPTION' ... OK
* this is package 'flagme' version '1.52.0'
* 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 'flagme' 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 ... OK
* 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
'::' or ':::' import not declared from: 'MSnbase'
Missing or unexported object: 'xcms::rectUnique'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addXCMSPeaks: no visible global function definition for 'bpparam'
addXCMSPeaks : <anonymous> : <anonymous>: no visible global function
  definition for 'setNames'
importSpec : <anonymous>: no visible global function definition for
  'setNames'
Undefined global functions or variables:
  bpparam setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotAlignment-peaksAlignment-method.Rd':
  'plotAlignment'

Missing link or links in documentation object 'plotClustAlignment-clusterAlignment-method.Rd':
  'plotAlignment'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'plotAlignment' 'plotChrom' 'plotClustAlignment'
Undocumented S4 methods:
  generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.15-bioc/R/library/flagme/libs/x64/flagme.dll':
  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. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                            user system elapsed
plotAlignedFrags                           33.54   0.39  109.95
addXCMSPeaks                               21.28   0.48   80.66
peaksAlignment-class                       20.77   0.27   73.94
ndpRT                                      20.56   0.37   74.71
corPrt                                     20.61   0.23   72.25
progressiveAlignment-class                 20.47   0.24   71.25
plotFrags                                  19.97   0.27   69.72
dynRT                                      19.72   0.29   74.57
plotAlignment-peaksAlignment-method        19.64   0.26   70.11
retFatMatrix                               19.24   0.30   70.17
imputePeaks                                10.14   0.39   13.25
plotChrom-peaksDataset-method               7.46   0.25    7.71
calcTimeDiffs                               6.79   0.16    7.31
gatherInfo                                  6.79   0.08    6.89
rmaFitUnit                                  6.76   0.09    6.86
multipleAlignment-class                     6.55   0.16    6.72
clusterAlignment                            6.07   0.08    6.14
normDotProduct                              5.60   0.17    5.77
dp                                          5.51   0.10    5.61
plotClustAlignment-clusterAlignment-method  5.37   0.06    5.43
peaksDataset                                4.98   0.10    5.07
addAMDISPeaks                               4.50   0.16    6.95
* 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: 3 WARNINGs, 2 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/flagme.Rcheck/00check.log'
for details.