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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DIAlignR_2.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/DIAlignR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .dockerignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DIAlignR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.4Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    metabo    4.1Mb
    ptms      1.5Mb
* checking package 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 ... NOTE
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alignTargetedRuns: no visible binding for global variable ‘peptide_id’
alignTargetedRuns : <anonymous>: no visible global function definition
  for ‘.’
alignTargetedRuns: no visible binding for global variable ‘intensity’
alignToRoot4: no visible binding for global variable ‘trees’
alignToRoot4: no visible binding for global variable ‘precursors’
alignToRoot4: no visible binding for global variable ‘intensity’
childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf,
  x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x)))
dist4split: no visible global function definition for ‘as.dist’
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
  global variable ‘RT.ref’
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
  global variable ‘RT.eXp’
fetchPrecursorsInfo: no visible binding for global variable
  ‘transition_id’
fetchPrecursorsInfo: no visible global function definition for ‘.’
fetchPrecursorsInfo: no visible binding for global variable
  ‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
  ‘intensity’
fetchTransitionsFromRun: no visible global function definition for ‘.’
fetchTransitionsFromRun: no visible binding for global variable
  ‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
  ‘peak_group_rank’
fetchTransitionsFromRun: no visible global function definition for
  ‘head’
getNativeIDs: no visible binding for global variable ‘peptide_id’
getPeptideScores: no visible binding for global variable ‘col2’
getPeptideScores: no visible binding for global variable ‘run’
getQuery: no visible binding for global variable
  ‘identifying.transitionPEPfilter’
getRTdf: no visible binding for global variable ‘peak_group_rank’
getRTdf: no visible binding for global variable ‘m_score’
getRTdf: no visible global function definition for ‘.’
getRTdf: no visible binding for global variable ‘transition_group_id’
getRTdf: no visible binding for global variable ‘RT’
getRefRun : <anonymous>: no visible binding for global variable
  ‘pvalue’
ipfReassignFDR: no visible binding for global variable ‘ref_run’
ipfReassignFDR: no visible binding for global variable ‘run’
ipfReassignFDR: no visible global function definition for ‘.’
ipfReassignFDR: no visible binding for global variable ‘i.to’
ipfReassignFDR: no visible binding for global variable ‘m_score_new’
ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’
ipfReassignFDR: no visible binding for global variable ‘m_score’
mstAlignRuns: no visible binding for global variable ‘ropenms’
mstAlignRuns: no visible binding for global variable ‘peptide_id’
mstAlignRuns : <anonymous>: no visible global function definition for
  ‘.’
mstAlignRuns: no visible binding for global variable ‘intensity’
mstScript1: no visible binding for global variable ‘ropenms’
mstScript2: no visible binding for global variable ‘fileInfo’
mstScript2: no visible binding for global variable ‘peptide_id’
mstScript2: no visible binding for global variable ‘features’
mstScript2 : <anonymous>: no visible global function definition for ‘.’
mstScript2 : <anonymous>: no visible binding for global variable
  ‘features’
mstScript2: no visible binding for global variable ‘intensity’
progAlignRuns: no visible binding for global variable ‘peptide_id’
progAlignRuns : <anonymous>: no visible global function definition for
  ‘.’
progAlignRuns: no visible binding for global variable ‘intensity’
progComb3: no visible binding for global variable ‘precursors’
progComb3: no visible binding for global variable ‘ropenms’
progSplit2: no visible binding for global variable ‘trees’
progSplit2: no visible binding for global variable ‘scoreFile’
progSplit2: no visible binding for global variable ‘precursors’
progSplit2 : <anonymous>: no visible global function definition for ‘.’
progSplit2: no visible binding for global variable ‘ropenms’
progSplit4: no visible binding for global variable ‘precursors’
progSplit4 : <anonymous>: no visible global function definition for ‘.’
progSplit4: no visible binding for global variable ‘intensity’
progTree1: no visible binding for global variable ‘ropenms’
progTree1: no visible binding for global variable ‘peptide_id’
reIntensity: no visible binding for global variable ‘run’
reIntensity: no visible binding for global variable ‘alignment_rank’
recalculateIntensity: no visible binding for global variable
  ‘peptide_id’
recalculateIntensity: no visible binding for global variable
  ‘chromatogramIndex’
script2: no visible binding for global variable ‘fileInfo’
script2: no visible binding for global variable ‘peptide_id’
script2 : <anonymous>: no visible global function definition for ‘.’
script2: no visible binding for global variable ‘features’
script2: no visible binding for global variable ‘globalFits’
script2: no visible binding for global variable ‘RSE’
script2: no visible binding for global variable ‘intensity’
setRootRank : <anonymous>: no visible global function definition for
  ‘.’
writeTables: no visible binding for global variable ‘peptide_id’
writeTables: no visible binding for global variable ‘run’
writeTables: no visible binding for global variable ‘precursor’
Undefined global functions or variables:
  . RSE RT RT.eXp RT.ref alignment_rank as.dist chromatogramIndex col2
  features fileInfo globalFits head i.to
  identifying.transitionPEPfilter intensity m_score m_score_new
  ms2_m_score peak_group_rank peptide_id precursor precursors pvalue
  ref_run ropenms run scoreFile transition_group_id transition_id trees
Consider adding
  importFrom("datasets", "trees")
  importFrom("stats", "as.dist")
  importFrom("utils", "head")
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 ... OK
* 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 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DIAlignR/libs/DIAlignR.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)

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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
alignTargetedRuns 30.417 42.096  20.807
script1            3.371  7.067   4.164
script2            5.317  3.096   5.755
alignToMaster      6.026  0.103   6.137
traverseUp         5.930  0.084   6.028
traverseDown       5.592  0.044   5.642
mstScript2         4.296  1.075   4.480
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.