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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omXplore.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings omXplore_1.1.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'omXplore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'omXplore' version '1.1.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'omXplore' can be installed ... OK
* 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 ... WARNING
Found the following file with non-ASCII characters:
  R/plot_pca.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function 'tools::showNonASCIIfile' can help in finding non-ASCII
characters in files.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'nipals'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Build_X_CC: no visible global function definition for 'metadata'
Build_X_CC: no visible global function definition for 'metadata<-'
Check_MSnSet_Consistency : <anonymous>: no visible global function
  definition for 'experimentData'
MAE_Compatibility_with_Prostar_1x : <anonymous>: no visible binding for
  global variable '.colData'
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for 'experimentData'
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for 'metadata'
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for 'metadata<-'
densityPlot: no visible global function definition for 'head'
plots_tracking_server : <anonymous>: no visible global function
  definition for 'updateTextInput'
Undefined global functions or variables:
  .colData experimentData head metadata metadata<- updateTextInput
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density-plot.Rd: RColorBrewer
  intensity-plots.Rd: RColorBrewer
  palette.Rd: RColorBrewer
  plot-variance.Rd: RColorBrewer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'density-plot.Rd':
omXplore_density_server
  Code: function(id, obj = reactive({ NULL}), i = reactive({ 1}),
                 pal.name = reactive({ NULL}))
  Docs: function(id, obj = reactive({ NULL}), i = reactive({ NULL}),
                 pal.name = reactive({ NULL}))
  Mismatches in argument default values:
    Name: 'i'
    Code: reactive({
          1
      })
    Docs: reactive({
          NULL
      })

Codoc mismatches from Rd file 'ds-pca.Rd':
wrapper_pca
  Code: function(qdata, group, var.scaling = TRUE, ncp = NULL, method =
                 NULL, gramschmidt = TRUE)
  Docs: function(qdata, group, var.scaling = TRUE, ncp = NULL)
  Argument names in code not in docs:
    method gramschmidt

Codoc mismatches from Rd file 'plots_tracking.Rd':
plots_tracking_server
  Code: function(id, obj = reactive({ NULL}), remoteReset = reactive({
                 NULL}), is.enabled = reactive({ TRUE}))
  Docs: function(id, obj = reactive({ NULL}), i = reactive({ NULL}),
                 remoteReset = reactive({ NULL}), is.enabled =
                 reactive({ TRUE}))
  Argument names in docs not in code:
    i
  Mismatches in argument names:
    Position: 3 Code: remoteReset Docs: i
    Position: 4 Code: is.enabled Docs: remoteReset
plots_tracking
  Code: function(obj)
  Docs: function(obj, i)
  Argument names in docs not in code:
    i

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'intensity-plots.Rd'
  'remoteReset' 'is.enabled'

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 ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'omXplore-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ds-pca
> ### Title: Bar plot of missing values per lines using highcharter.
> ### Aliases: ds-pca omXplore_pca_ui omXplore_pca_server omXplore_pca
> ###   wrapper_pca plotPCA_Eigen plotPCA_Var plotPCA_Ind plotPCA_Eigen_hc
> 
> ### ** Examples
> 
> ## Don't show: 
> if (interactive()) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+   data(vdata)
+   # Replace missing values for the example
+   sel <- is.na(SummarizedExperiment::assay(vdata, 1))
+   SummarizedExperiment::assay(vdata[[1]])[sel] <- 0
+   omXplore_pca(vdata, 1)
+ ## Don't show: 
+ }) # examplesIf
> ## End(Don't show)
> data(vdata)
> obj <- vdata[[1]]
> res.pca <- wrapper_pca(SummarizedExperiment::assay(obj), get_group(obj))
[1] "gramschmidt wrapper pca : TRUE"
[1] "gramschmidt wrapper pca après modif : TRUE"
[1] "gramschmidt my_pca TRUE"
[1] "method_nip : "
Error in if (method == "NIPALS") X.init <- X : argument is of length zero
Calls: wrapper_pca -> my_PCA
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
density-plot 1.28   0.17    9.82
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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: 1 ERROR, 4 WARNINGs, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck/00check.log'
for details.