* using log directory ‘/srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck’
* using R Under development (unstable) (2025-05-23 r88232)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux 13 (trixie)
* 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 ... [3s/5s] 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 ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RamEx’ can be installed ... [14s/14s] OK
* used C++ compiler: ‘Debian clang version 19.1.7 (3)’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] NOTE
Warning: no function found corresponding to methods exports from ‘RamEx’ for: ‘rbind2’

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 ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [14s/14s] 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 ... [0s/0s] 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 ... [2s/2s] 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 ... [13s/13s] 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)) : 32 simultaneous processes spawned
Calls: Intraramanome.Analysis.2Dcos ... corr2d -> <Anonymous> -> makePSOCKcluster -> .check_ncores
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [12s/12s] OK
  Running ‘testthat.R’ [12s/11s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [208s/207s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘RamEx.Rmd’ using rmarkdown
** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14309 bytes
Input file size = 14399 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11142
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11142

Output IDAT size = 11142 bytes (3167 bytes decrease)
Output file size = 11220 bytes (3179 bytes = 22.08% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24853 bytes
Input file size = 24967 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20633
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20633

Output IDAT size = 20633 bytes (4220 bytes decrease)
Output file size = 20711 bytes (4256 bytes = 17.05% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23585 bytes
Input file size = 23687 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20303
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20303

Output IDAT size = 20303 bytes (3282 bytes decrease)
Output file size = 20381 bytes (3306 bytes = 13.96% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-6-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24507 bytes
Input file size = 24609 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20975
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20975

Output IDAT size = 20975 bytes (3532 bytes decrease)
Output file size = 21053 bytes (3556 bytes = 14.45% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-6-3.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26144 bytes
Input file size = 26258 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21798
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21798

Output IDAT size = 21798 bytes (4346 bytes decrease)
Output file size = 21876 bytes (4382 bytes = 16.69% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-6-4.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27407 bytes
Input file size = 27521 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 22745
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 22745

Output IDAT size = 22745 bytes (4662 bytes decrease)
Output file size = 22823 bytes (4698 bytes = 17.07% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19495 bytes
Input file size = 19597 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15749
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15749

Output IDAT size = 15749 bytes (3746 bytes decrease)
Output file size = 15827 bytes (3770 bytes = 19.24% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-8-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32595 bytes
Input file size = 32709 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26642
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26642

Output IDAT size = 26642 bytes (5953 bytes decrease)
Output file size = 26720 bytes (5989 bytes = 18.31% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-8-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 30737 bytes
Input file size = 30851 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 25537
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 25537

Output IDAT size = 25537 bytes (5200 bytes decrease)
Output file size = 25615 bytes (5236 bytes = 16.97% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-8-3.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 30110 bytes
Input file size = 30224 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 24166
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 24166

Output IDAT size = 24166 bytes (5944 bytes decrease)
Output file size = 24244 bytes (5980 bytes = 19.79% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-8-4.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29883 bytes
Input file size = 29997 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 24814
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 24814

Output IDAT size = 24814 bytes (5069 bytes decrease)
Output file size = 24892 bytes (5105 bytes = 17.02% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-9-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 22475 bytes
Input file size = 22577 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16000
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16000

Output IDAT size = 16000 bytes (6475 bytes decrease)
Output file size = 16078 bytes (6499 bytes = 28.79% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-9-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 22104 bytes
Input file size = 22206 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15856
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15856

Output IDAT size = 15856 bytes (6248 bytes decrease)
Output file size = 15934 bytes (6272 bytes = 28.24% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-9-3.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23361 bytes
Input file size = 23463 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16708
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16708

Output IDAT size = 16708 bytes (6653 bytes decrease)
Output file size = 16786 bytes (6677 bytes = 28.46% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/RamEx.Rcheck/vign_test/RamEx/vignettes/RamEx_files/figure-html/unnamed-chunk-9-4.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25429 bytes
Input file size = 25543 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 17833
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 17833

Output IDAT size = 17833 bytes (7596 bytes decrease)
Output file size = 17911 bytes (7632 bytes = 29.88% decrease)


Quitting from RamEx.Rmd:98-100 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.check_ncores()`:
! 32 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:
32 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 ... [4s/4s] 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 ... [1s/1s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘RamEx-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 ERRORs, 5 WARNINGs, 6 NOTEs