* using log directory 'd:/RCompile/CRANincoming/R-devel/apLCMS.Rcheck'
* using R Under development (unstable) (2025-06-06 r88283 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'apLCMS/DESCRIPTION' ... OK
* this is package 'apLCMS' version '6.8.3'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Tianwei Yu <yutianwei@cuhk.edu.cn>'

New submission

Possibly misspelled words in DESCRIPTION:
  metabolomics (7:43)

Uses the non-portable package: 'mzR'

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tianwei",
                    family = "Yu",
                    role = c("aut", "cre"),
                    email = "yutianwei@cuhk.edu.cn")
as necessary.

The Title field should be in title case. Current version is:
  'Adaptive processing of LC-MS data'
In title case that is:
  'Adaptive Processing of LC-MS Data'

Size of tarball: 10048197 bytes
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'MASS', 'rgl', 'mzR', 'doParallel', 'foreach', 'splines',
  'iterators', 'gbm', 'e1071', 'randomForest', 'ROCR', 'ROCS', 'Rcpp'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 serialization versions ... OK
* checking whether package 'apLCMS' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [35s] NOTE
EIC.plot: no visible binding for global variable 'raw.prof'
EIC.plot: no visible global function definition for 'predict'
EIC.plot: no visible global function definition for 'par'
EIC.plot: no visible global function definition for 'lines'
EIC.plot.learn: no visible binding for global variable 'raw.prof'
EIC.plot.learn: no visible global function definition for 'predict'
EIC.plot.learn: no visible global function definition for 'lines'
adaptive.bin: no visible global function definition for 'density'
adaptive.bin: no visible global function definition for 'approx'
adaptive.bin: no visible global function definition for 'median'
adaptive.bin: no visible global function definition for 'runif'
adaptive.bin.2: no visible global function definition for 'density'
adaptive.bin.2: no visible global function definition for 'approx'
adaptive.bin.2: no visible global function definition for 'median'
adaptive.bin.2: no visible global function definition for
  'weighted.mean'
adjust.time: no visible global function definition for 'par'
adjust.time: no visible global function definition for 'text'
adjust.time: no visible binding for global variable 'j'
adjust.time: no visible global function definition for 'ksmooth'
adjust.time: no visible global function definition for 'points'
cdf.to.ftr: no visible global function definition for 'makeCluster'
cdf.to.ftr: no visible global function definition for 'clusterEvalQ'
cdf.to.ftr: no visible global function definition for 'stopCluster'
cont.index : collapse: no visible global function definition for
  'median'
cont.index: no visible global function definition for 'ksmooth'
eic.disect : my.dens: no visible global function definition for
  'density'
eic.disect : my.dens: no visible global function definition for
  'approx'
eic.disect: no visible global function definition for 'median'
eic.disect: no visible global function definition for 'quantile'
eic.pred: no visible global function definition for 'median'
eic.pred: no visible global function definition for 'predict'
eic.pred: no visible global function definition for 'glm'
eic.pred: no visible binding for global variable 'binomial'
eic.pred: no visible global function definition for 'boxplot'
eic.qual: no visible global function definition for 'par'
eic.qual: no visible global function definition for 'lines'
eic.qual: no visible global function definition for 'abline'
feature.align: no visible global function definition for 'par'
feature.align: no visible global function definition for 'text'
feature.align : to.attach: no visible global function definition for
  'median'
feature.align: no visible global function definition for 'density'
feature.align: no visible global function definition for 'median'
feature.align: no visible global function definition for 'sd'
feature.align: no visible global function definition for 'hist'
feature.align: no visible binding for global variable 'sd'
find.tol: no visible global function definition for 'density'
find.tol: no visible global function definition for 'dexp'
find.tol: no visible global function definition for 'lines'
find.tol: no visible global function definition for 'abline'
find.tol.time: no visible global function definition for 'dist'
find.tol.time: no visible global function definition for 'density'
find.tol.time: no visible global function definition for 'lm'
find.tol.time: no visible global function definition for 'lines'
find.tol.time: no visible global function definition for 'abline'
find.turn.point : peaks2: no visible global function definition for
  'embed'
interpol.area: no visible global function definition for 'approx'
learn.cdf: no visible global function definition for 'par'
learn.cdf: no visible global function definition for 'text'
merge_seq_3: no visible global function definition for 'median'
peak.characterize : merge.new: no visible global function definition
  for 'sd'
plot_cdf_2d: no visible global function definition for 'lines'
plot_txt_2d: no visible global function definition for 'read.table'
plot_txt_2d: no visible global function definition for 'lines'
present.cdf.3d: no visible global function definition for 'median'
present.cdf.3d: no visible global function definition for 'topo.colors'
proc.cdf: no visible global function definition for 'par'
proc.cdf: no visible global function definition for 'text'
proc.cdf: no visible global function definition for 'density'
proc.cdf: no visible global function definition for 'abline'
proc.cdf: no visible global function definition for 'quantile'
proc.cdf: no visible global function definition for 'lines'
proc.cdf: no visible global function definition for 'hist'
proc.cdf.2d: no visible global function definition for
  'colorRampPalette'
proc.cdf.2d: no visible global function definition for 'quantile'
proc.cdf.2d: no visible global function definition for 'points'
proc.txt: no visible global function definition for 'par'
proc.txt: no visible global function definition for 'text'
proc.txt: no visible global function definition for 'read.table'
proc.txt: no visible global function definition for 'density'
proc.txt: no visible global function definition for 'abline'
proc.txt: no visible global function definition for 'quantile'
proc.txt: no visible global function definition for 'lines'
proc.txt: no visible global function definition for 'hist'
prof.to.features : bigauss.esti.EM: no visible global function
  definition for 'median'
prof.to.features : bigauss.esti.EM: no visible global function
  definition for 'dnorm'
prof.to.features : bigauss.esti: no visible global function definition
  for 'median'
prof.to.features : bigauss.esti: no visible global function definition
  for 'dnorm'
prof.to.features : bigauss.esti: no visible global function definition
  for 'lines'
prof.to.features : bigauss.esti: no visible global function definition
  for 'abline'
prof.to.features : bigauss.mix: no visible global function definition
  for 'par'
prof.to.features : bigauss.mix: no visible global function definition
  for 'ksmooth'
prof.to.features : bigauss.mix: no visible global function definition
  for 'dnorm'
prof.to.features : bigauss.mix: no visible global function definition
  for 'lines'
prof.to.features : bigauss.mix: no visible global function definition
  for 'abline'
prof.to.features : normix: no visible global function definition for
  'dnorm'
prof.to.features : normix.bic: no visible global function definition
  for 'par'
prof.to.features : normix.bic: no visible global function definition
  for 'ksmooth'
prof.to.features : normix.bic: no visible global function definition
  for 'dnorm'
prof.to.features : normix.bic: no visible global function definition
  for 'abline'
prof.to.features : normix.bic: no visible global function definition
  for 'lines'
prof.to.features: no visible global function definition for 'sd'
prof.to.features: no visible global function definition for 'median'
prof.to.features: no visible global function definition for 'par'
prof.to.features: no visible global function definition for 'text'
prof.to.features: no visible global function definition for 'hist'
recover.weaker: no visible binding for global variable 'na.omit'
recover.weaker: no visible global function definition for 'predict'
recover.weaker: no visible global function definition for 'density'
recover.weaker: no visible global function definition for 'approx'
recover.weaker: no visible global function definition for 'median'
recover.weaker: no visible global function definition for 'ksmooth'
recover.weaker: no visible global function definition for 'dnorm'
rm.ridge: no visible global function definition for 'quantile'
rm.ridge: no visible global function definition for 'ksmooth'
semi.sup: no visible global function definition for 'makeCluster'
semi.sup: no visible global function definition for 'clusterEvalQ'
semi.sup: no visible global function definition for 'stopCluster'
semi.sup: no visible global function definition for 'median'
semi.sup.2d: no visible global function definition for 'makeCluster'
semi.sup.2d: no visible global function definition for 'clusterEvalQ'
semi.sup.2d: no visible global function definition for 'stopCluster'
semi.sup.2d: no visible global function definition for 'median'
semi.sup.learn: no visible global function definition for 'makeCluster'
semi.sup.learn: no visible global function definition for
  'clusterEvalQ'
semi.sup.learn: no visible global function definition for 'stopCluster'
semi.sup.learn: no visible global function definition for 'median'
target.search : target.onefile: no visible global function definition
  for 'density'
target.search : target.onefile: no visible global function definition
  for 'approx'
target.search : target.onefile: no visible global function definition
  for 'median'
target.search : target.onefile: no visible global function definition
  for 'ksmooth'
target.search : target.onefile: no visible global function definition
  for 'dnorm'
target.search: no visible global function definition for 'makeCluster'
target.search: no visible global function definition for 'clusterEvalQ'
target.search: no visible global function definition for 'stopCluster'
target.search: no visible binding for global variable 'mz.tol'
two.step.hybrid: no visible binding for global variable 'median'
two.step.hybrid: no visible global function definition for
  'makeCluster'
two.step.hybrid: no visible global function definition for
  'clusterEvalQ'
two.step.hybrid: no visible global function definition for
  'stopCluster'
two.step.hybrid.2d: no visible binding for global variable 'median'
two.step.hybrid.2d: no visible global function definition for
  'makeCluster'
two.step.hybrid.2d: no visible global function definition for
  'clusterEvalQ'
two.step.hybrid.2d: no visible global function definition for
  'stopCluster'
Undefined global functions or variables:
  abline approx binomial boxplot clusterEvalQ colorRampPalette density
  dexp dist dnorm embed glm hist j ksmooth lines lm makeCluster median
  mz.tol na.omit par points predict quantile raw.prof read.table runif
  sd stopCluster text topo.colors weighted.mean
Consider adding
  importFrom("grDevices", "colorRampPalette", "topo.colors")
  importFrom("graphics", "abline", "boxplot", "hist", "lines", "par",
             "points", "text")
  importFrom("stats", "approx", "binomial", "density", "dexp", "dist",
             "dnorm", "embed", "glm", "ksmooth", "lm", "median",
             "na.omit", "predict", "quantile", "runif", "sd",
             "weighted.mean")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [18s] OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 NOTEs