* using log directory 'd:/RCompile/CRANincoming/R-devel/RamEx.Rcheck'
* using R Under development (unstable) (2025-05-23 r88232 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 'RamEx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RamEx' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [10s] NOTE
Maintainer: 'Yanmei Zhang <zhangyanmei@qibebt.ac.cn>'

New submission

Possibly misspelled words in DESCRIPTION:
  RamEx (11:161, 11:274)
  Ramanomes (4:9)
  github (11:301)
  ramanomes (11:221, 11:431)
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: 'gpuR'
* 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 'RamEx' 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 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'doc'
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'RamEx' for: 'rbind2', 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... WARNING
'::' or ':::' import not declared from: 'scales'
* checking S3 generic/method consistency ... NOTE
Mismatches for apparent methods not registered:
select:
  function(.data, ...)
select.band:
  function(object, waves)

select:
  function(.data, ...)
select.value:
  function(object, wave)

cut:
  function(x, ...)
cut.spec:
  function(single_spec, cutoff)

mean:
  function(x, ...)
mean.spec:
  function(data, group, gap, col)
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [32s] NOTE
Feature.Reduction.Pcoa: no visible global function definition for
  'cmdscale'
Intraramanome.Analysis.Irca.Global : <anonymous>: no visible global
  function definition for 'jpeg'
Intraramanome.Analysis.Irca.Global : <anonymous>: no visible global
  function definition for 'title'
Intraramanome.Analysis.Irca.Global : <anonymous>: no visible global
  function definition for 'dev.off'
Intraramanome.Analysis.Irca.Global: no visible binding for global
  variable '.'
Intraramanome.Analysis.Irca.Local : <anonymous>: no visible global
  function definition for 'title'
Intraramanome.Analysis.Irca.Local : <anonymous>: no visible global
  function definition for 'dev.off'
Phenotype.Analysis.Louvaincluster: no visible global function
  definition for 'new'
Plot.Distribution: no visible binding for global variable 'Group_1'
Plot.Distribution: no visible binding for global variable 'Prop'
Plot.Distribution: no visible binding for global variable 'Group_2'
Plot.Heatmap.Markers: no visible global function definition for
  'aggregate'
Plot.Markers.Spectrum: no visible binding for global variable 'wave'
Plot.Markers.Spectrum: no visible binding for global variable
  'variable'
Plot.Markers.Spectrum: no visible binding for global variable 'value'
Plot.ViolinBox: no visible binding for global variable 'value'
Plot.ViolinBox: no visible binding for global variable 'variable'
Plot_global_chordDiagram_rpvalue: no visible binding for global
  variable 'value'
Plot_local_chordDiagram_rpvalue : <anonymous>: no visible binding for
  global variable 'Group'
Preprocessing.Background.Remove: no visible global function definition
  for 'aggregate'
Preprocessing.Background.Remove: no visible binding for global variable
  '.'
Preprocessing.OneStep: no visible binding for global variable '.'
Qualitycontrol.ICOD: no visible binding for global variable 'time_gap'
Qualitycontrol.ICOD: no visible binding for global variable
  'time_cluster'
Qualitycontrol.T2: no visible binding for global variable 'median'
Quantification.Glm: no visible global function definition for
  'gaussian'
Raman.Markers.Correlations: no visible binding for global variable
  'col1'
Raman.Markers.Correlations: no visible binding for global variable
  'col2'
Raman.Markers.Rbcs: no visible global function definition for
  'aggregate'
Raman.Markers.Rbcs: no visible binding for global variable '.'
Ramanome: no visible global function definition for 'new'
average_spectra: no visible global function definition for 'aggregate'
calculate_hotellings_t2: no visible global function definition for
  'var'
cluster.color: no visible binding for global variable 'cluster'
confusion.plot: no visible binding for global variable 'x'
confusion.plot: no visible binding for global variable 'y'
confusion.plot: no visible binding for global variable 'Freq'
covFastMCD: no visible global function definition for 'var'
get.nearest.dataset: no visible global function definition for 'tail'
gpupre_spike_matrix: no visible global function definition for
  'as.gpuVector'
mahalDistForEvery: no visible global function definition for 'cov'
matrix2vector: no visible global function definition for 'gpuMatrix'
mean.spec: no visible global function definition for 'aggregate'
mean.spec: no visible binding for global variable 'wavenumber'
mean.spec: no visible binding for global variable 'value'
mean.spec: no visible binding for global variable 'Group'
merge_groups: no visible global function definition for 'tail'
merge_wave_numbers: no visible global function definition for 'tail'
nmf_lee: no visible global function definition for 'runif'
outliers_mcdEst: no visible global function definition for 'na.omit'
read.spec: no visible global function definition for 'new'
read.spec.load: no visible global function definition for 'new'
save.renishaw: no visible binding for global variable '.'
save.rf.results.summary: no visible binding for global variable 'y'
vectorize_dm: no visible binding for global variable 'value'
[,Ramanome-ANY-ANY-ANY: no visible global function definition for 'new'
Undefined global functions or variables:
  . Freq Group Group_1 Group_2 Prop aggregate as.gpuVector cluster
  cmdscale col1 col2 cov dev.off gaussian gpuMatrix jpeg median na.omit
  new runif tail time_cluster time_gap title value var variable wave
  wavenumber x y
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "title")
  importFrom("methods", "new")
  importFrom("stats", "aggregate", "cmdscale", "cov", "gaussian",
             "median", "na.omit", "runif", "var")
  importFrom("utils", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'Feature.Reduction.Intensity.Rd':
  \examples lines wider than 100 characters:
     data_cleaned <- Feature.Reduction.Intensity(data_processed, list(c(2000,2250),c(2750,3050), 1450, 1665)) 

Rd file 'Intraramanome.Analysis.Irca.Local.Rd':
  \examples lines wider than 100 characters:
     bands_ann <- data.frame(rbind(cbind(c(742,850,872,971,997,1098,1293,1328,1426,1576),'Nucleic acid'),cbind(c(824,883,1005,1033,1051,1237 ... [TRUNCATED]

Rd file 'Phenotype.Analysis.Louvaincluster.Rd':
  \examples lines wider than 100 characters:
     #clusters_Louvaincluster <- Phenotype.Analysis.Louvaincluster(object = data_processed, resolutions = c(0.8))

Rd file 'Raman.Markers.Correlations.Rd':
  \examples lines wider than 100 characters:
     cor_markers <- Raman.Markers.Correlations(preprocessing.cutoff(data_processed, 800, 1300), min.cor = 0.6)

Rd file 'Raman.Markers.Roc.Rd':
  \examples lines wider than 100 characters:
     ROC_markers <- Raman.Markers.Roc(preprocessing.cutoff(data_processed, 800, 1300), threshold = 0.75, paired = FALSE, batch_size = 1000)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'cut.spec' 'read.single' 'read.spec.load'
All user-level objects in a package 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 ... WARNING
Undocumented arguments in Rd file 'Intraramanome.Analysis.Irca.Local.Rd'
  'threshold'

Undocumented arguments in Rd file 'Phenotype.Analysis.Gmm.Rd'
  'seed'

Undocumented arguments in Rd file 'Phenotype.Analysis.Louvaincluster.Rd'
  'n_cores'

Documented arguments not in \usage in Rd file 'Plot.Distribution.Rd':
  'alpha' 'curve_type'

Undocumented arguments in Rd file 'Plot.Heatmap.Markers.Rd'
  'cluster_cols' 'cluster_rows' 'show' 'save' 'width' 'height'

Undocumented arguments in Rd file 'Spectral.Decomposition.Nmf.Rd'
  'n_comp' 'max_iter' 'tol' 'verbose'
Documented arguments not in \usage in Rd file 'Spectral.Decomposition.Nmf.Rd':
  'ncomp'

Documented arguments not in \usage in Rd file 'predict_quantification.Rd':
  'show' 'save'

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 data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                 old_size new_size compress
  RamEx_data.rda    1.5Mb    863Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [28s] ERROR
Running examples in 'RamEx-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Intraramanome.Analysis.2Dcos
> ### Title: 2D Correlation Spectroscopy Analysis (2D-COS) Captures both
> ###   synchronous (simultaneous changes) and asynchronous (sequential
> ###   changes) relationships, providing detailed insights into spectral
> ###   changes
> ### Aliases: Intraramanome.Analysis.2Dcos
> 
> ### ** Examples
> 
> data(RamEx_data)
> data_processed <- Preprocessing.OneStep(RamEx_data)
The Ramanome contains 500 spectra
> corr_2d <- Intraramanome.Analysis.2Dcos(data_processed)
Error in .check_ncores(length(names)) : 96 simultaneous processes spawned
Calls: Intraramanome.Analysis.2Dcos ... corr2d -> <Anonymous> -> makePSOCKcluster -> .check_ncores
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [24s] ERROR
  Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RamEx)
  > 
  > test_check("RamEx")
  The Ramanome contains 500 spectra
  The Ramanome contains 500 spectra
  The Ramanome contains 500 spectra
  The Ramanome contains 500 spectra
  The Ramanome contains 500 spectra
  The Ramanome contains 500 spectra
  The Ramanome contains 500 spectra
  The Ramanome contains 500 spectra
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testthat-main-function.R:127:3'): UMAP plot generation works correctly ──
  Error in `Feature.Reduction.Umap(pca_obj, draw = TRUE, save = TRUE)`: unused argument (draw = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [375s] ERROR
Error(s) in re-building vignettes:
--- re-building 'RamEx.Rmd' using rmarkdown

Quitting from RamEx.Rmd:98-100 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.check_ncores()`:
! 96 simultaneous processes spawned
---
Backtrace:
    ▆
 1. └─RamEx::Intraramanome.Analysis.2Dcos(data_cleaned)
 2.   └─corr2D::corr2d(data)
 3.     └─parallel::makeCluster(corenumber)
 4.       └─parallel::makePSOCKcluster(names = spec, ...)
 5.         └─parallel:::.check_ncores(length(names))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RamEx.Rmd' failed with diagnostics:
96 simultaneous processes spawned
--- failed re-building 'RamEx.Rmd'

SUMMARY: processing the following file failed:
  'RamEx.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [20s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ⁻ (U+207B)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ⁻ (U+207B)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ⁻ (U+207B)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ⁻ (U+207B)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ⁻ (U+207B)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ⁻ (U+207B)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [12s] OK
* DONE
Status: 4 ERRORs, 5 WARNINGs, 7 NOTEs