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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MSstatsPTM_2.5.4.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MSstatsPTM.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsPTM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsPTM' version '2.5.4'
* 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:
  .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 'MSstatsPTM' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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:
  'MSstats:::.getMedianSigmaSubject' 'MSstats:::.getVarComponent'
  'MSstatsConvert:::.filterFewMeasurements'
  'MSstatsConvert:::.filterManyColumns'
  'MSstatsConvert:::.getChannelColumns'
  'MSstatsConvert:::.standardizeColnames'
  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
.extract_pd_mods: no visible binding for global variable
  '..sequence_col'
.format.data.process.plots: no visible binding for global variable
  'ABUNDANCE'
.pivotPS: no visible binding for global variable '..keep_cols'
.plot.model.volcano: no visible binding for global variable
  'text.angle'
.progensis.add.sites: no visible binding for global variable
  '..col_order'
.qc.all.plot.lf: no visible binding for global variable 'text.angle'
.qc.single.plot.lf: no visible binding for global variable 'text.angle'
.removeCutoffSites: no visible binding for global variable
  '..mod_pep_col'
.rmConfounded: no visible binding for global variable '..col_res'
DIANNtoMSstatsPTMFormat: no visible binding for global variable
  '..protein_id_col'
FragPipetoMSstatsPTMFormat: no visible binding for global variable
  '..msstats_cols'
MSstatsPTMSiteLocator: no visible binding for global variable
  '..mod_pep_col'
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  'TMT.keyword'
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  'ptm.keyword'
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  'mod.num'
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  'which.proteinid.ptm'
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  'PeptideSequence'
PStoMSstatsPTMFormat: no visible binding for global variable
  'Intensity'
ProgenesistoMSstatsPTMFormat: no visible binding for global variable
  'Type'
SkylinetoMSstatsPTMFormat: no visible binding for global variable
  'annotation_prot'
dataProcessPlotsPTM: no visible binding for global variable
  'PROTEINNAME'
dataProcessPlotsPTM: no visible binding for global variable
  'GLOBALPROTEIN'
dataSummarizationPTM: no visible binding for global variable 'address'
locatePTM: no visible binding for global variable '..col_seq'
locatePTM: no visible binding for global variable '..col_fasta'
Undefined global functions or variables:
  ..col_fasta ..col_order ..col_res ..col_seq ..keep_cols ..mod_pep_col
  ..msstats_cols ..protein_id_col ..sequence_col ABUNDANCE
  GLOBALPROTEIN Intensity PROTEINNAME PeptideSequence TMT.keyword Type
  address annotation_prot mod.num ptm.keyword text.angle
  which.proteinid.ptm
* 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
Documented arguments not in \usage in Rd file 'dot-fixTerminus.Rd':
  'fasta_file'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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-3.19-bioc/R/library/MSstatsPTM/libs/x64/MSstatsPTM.dll':
  Found '_exit', possibly from '_exit' (C)
  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
groupComparisonPlotsPTM  14.44   0.28   14.75
designSampleSizePTM       5.51   0.08    5.63
dataSummarizationPTM_TMT  5.00   0.25    5.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.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: 5 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/MSstatsPTM.Rcheck/00check.log'
for details.