* using log directory 'd:/RCompile/CRANincoming/R-devel/pmartR.Rcheck'
* using R Under development (unstable) (2023-11-02 r85465 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'pmartR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pmartR' version '2.4.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Lisa Bramer <lisa.bramer@pnnl.gov>'

New submission

Possibly misspelled words in DESCRIPTION:
  NMR (8:302)
  PCA (8:507)
  Panomics (3:8, 4:13)
  lipidomic (8:201)
  metabolomic (8:216)
  omics (8:119)
  proteomic (8:145)
  spectrometry (8:101)
  summarization (8:479)

Unknown, possibly misspelled, fields in DESCRIPTION:
  'Remotes'

Suggests or Enhances not in mainstream repositories:
  pmartRdata

Package has a VignetteBuilder field but no prebuilt vignette index.

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'pmartRdata'
* 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 'pmartR' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  'LICENSE.txt' 'disclaimer.txt'
* 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 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 ... [31s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'trelli_abundance_heatmap.Rd':
  \examples lines wider than 100 characters:
     # Build the abundance heatmap with an omicsData object with emeta variables. Generate trelliData in as.trelliData.
          ggplot_params = c("ylab('')", "xlab('')"), interactive = TRUE, cognostics = c("biomolecule count"))  

Rd file 'trelli_abundance_histogram.Rd':
  \examples lines wider than 100 characters:
     # Build the abundance histogram with an omicsData and statRes object. Generate trelliData in as.trelliData.

Rd file 'trelli_missingness_bar.Rd':
  \examples lines wider than 100 characters:
     # Build the missingness bar plot with an omicsData and statRes object. Generate trelliData in as.trelliData.
        trelli_missingness_bar(test_mode = TRUE, test_example = 1:5, cognostics = "observed count", proportion = FALSE)

Rd file 'trelli_pvalue_filter.Rd':
  \examples lines wider than 100 characters:
     trelli_pvalue_filter(trelliData3, p_value_test = "anova", p_value_thresh = 0.1, comparison = "Phenotype3_vs_Phenotype2")
     trelli_pvalue_filter(trelliData4, p_value_test = "gtest", p_value_thresh = 0.25, comparison = "Phenotype3_vs_Phenotype2")

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'fmeta_matches.Rd':
  'omicsDataObjects'

Documented arguments not in \usage in Rd file 'gtest_heatmap.Rd':
  'count_text_size'

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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'Convenience_Functions.Rmd' 'Data_Normalization.Rmd'
  'Data_Object_Creation.Rmd' 'Filter_Functionality.Rmd'
  'Graphing_with_pmartR.Rmd' 'RNAseq_Data_Processing.R'
  'RNAseq_Processing_Workflow.Rmd' 'SPANS_isobaricpep.png'
  'SPANS_pep.png' 'Statistical_Analysis_with_pmartR.Rmd'
  'TrelliData_Plotting_Options.png' 'Trelliscope_Vignette.Rmd'
  'Typical_Processing_Workflow.Rmd' 'WorkflowFigure.png'
  'bibliography.bib' 'modify_mathjax.html' 'pmartR_graphic-final.jpg'
  'pmartR_logo_final.jpg' 'pmartRstat_lit.bib' 'spans_result.RDS'
* checking examples ... ERROR
Running examples in 'pmartR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RNA_filter
> ### Title: RNA Filter Object
> ### Aliases: RNA_filter
> 
> ### ** Examples
> 
> library(pmartRdata)
Error in library(pmartRdata) : there is no package called 'pmartRdata'
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [18m] ERROR
  Running 'testthat.R' [18m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pmartR)
  > 
  > test_check("pmartR")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 2699 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_plots.R:105:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_plot_errors.R:24:3'): plotting errors are triggered correctly ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'pmartRdata'
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(plot(pmartRdata::isobaric_object, transformation = "lcpm")) at test_plot_errors.R:24:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─base::plot(pmartRdata::isobaric_object, transformation = "lcpm")
    7. └─base::loadNamespace(x)
    8.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9.     └─base (local) withOneRestart(expr, restarts[[1L]])
   10.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 2699 ]
  Deleting unused snapshots:
  • plots/plot-corres.svg
  • plots/plot-cvfilt-log-scale.svg
  • plots/plot-cvfilt.svg
  • plots/plot-datares-bw-theme.svg
  • plots/plot-datares-palette.svg
  • plots/plot-dimres.svg
  • plots/plot-imdanovafilt.svg
  • plots/plot-isobaricnormres-bw-theme.svg
  • plots/plot-isobaricnormres-global-normalized.svg
  • plots/plot-isobaricnormres-palette.svg
  • plots/plot-isobaricnormres.svg
  • plots/plot-isobaricpepdata.svg
  • plots/plot-lipiddata.svg
  • plots/plot-metabdata.svg
  • plots/plot-moleculefilt-cumulative.svg
  • plots/plot-moleculefilt.svg
  • plots/plot-nares-bar-group-color.svg
  • plots/plot-nares-bar-group-order.svg
  • plots/plot-nares-scatter.svg
  • plots/plot-nmrdata.svg
  • plots/plot-nmrnormres-2.svg
  • plots/plot-nmrnormres-color-by.svg
  • plots/plot-nmrnormres.svg
  • plots/plot-normres.svg
  • plots/plot-pepdata.svg
  • plots/plot-prodata.svg
  • plots/plot-proteomicsfilt-redundancy.svg
  • plots/plot-proteomicsfilt.svg
  • plots/plot-rmdfilt.svg
  • plots/plot-rnafilt.svg
  • plots/plot-seqdata.svg
  • plots/plot-spansres-bw-theme.svg
  • plots/plot-spansres-color-high-color-low.svg
  • plots/plot-spansres.svg
  • plots/plot-statres-anova-volcano.svg
  • plots/plot-statres-anova.svg
  • plots/plot-statres-combined-volcano.svg
  • plots/plot-statres-combined.svg
  • plots/plot-statres-gtest.svg
  • plots/plot-totalcountfilt.svg
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  'Convenience_Functions.Rmd'
  'Data_Normalization.Rmd'
  'Data_Object_Creation.Rmd'
  'Filter_Functionality.Rmd'
  'Graphing_with_pmartR.Rmd'
  'RNAseq_Processing_Workflow.Rmd'
  'Statistical_Analysis_with_pmartR.Rmd'
  'Trelliscope_Vignette.Rmd'
  'Typical_Processing_Workflow.Rmd'
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'Convenience_Functions.Rmd' using rmarkdown

Quitting from lines 30-35 [unnamed-chunk-1] (Convenience_Functions.Rmd)
Error: processing vignette 'Convenience_Functions.Rmd' failed with diagnostics:
there is no package called 'pmartRdata'
--- failed re-building 'Convenience_Functions.Rmd'

--- re-building 'Data_Normalization.Rmd' using rmarkdown

Quitting from lines 20-24 [setup] (Data_Normalization.Rmd)
Error: processing vignette 'Data_Normalization.Rmd' failed with diagnostics:
there is no package called 'pmartRdata'
--- failed re-building 'Data_Normalization.Rmd'

--- re-building 'Data_Object_Creation.Rmd' using rmarkdown

Quitting from lines 69-79 [unnamed-chunk-2] (Data_Object_Creation.Rmd)
Error: processing vignette 'Data_Object_Creation.Rmd' failed with diagnostics:
there is no package called 'pmartRdata'
--- failed re-building 'Data_Object_Creation.Rmd'

--- re-building 'Filter_Functionality.Rmd' using rmarkdown

Quitting from lines 25-30 [logo] (Filter_Functionality.Rmd)
Error: processing vignette 'Filter_Functionality.Rmd' failed with diagnostics:
there is no package called 'pmartRdata'
--- failed re-building 'Filter_Functionality.Rmd'

--- re-building 'Graphing_with_pmartR.Rmd' using rmarkdown

Quitting from lines 25-30 [logo] (Graphing_with_pmartR.Rmd)
Error: processing vignette 'Graphing_with_pmartR.Rmd' failed with diagnostics:
there is no package called 'pmartRdata'
--- failed re-building 'Graphing_with_pmartR.Rmd'

--- re-building 'RNAseq_Processing_Workflow.Rmd' using rmarkdown

Quitting from lines 25-27 [unnamed-chunk-1] (RNAseq_Processing_Workflow.Rmd)
Error: processing vignette 'RNAseq_Processing_Workflow.Rmd' failed with diagnostics:
there is no package called 'pmartRdata'
--- failed re-building 'RNAseq_Processing_Workflow.Rmd'

--- re-building 'Statistical_Analysis_with_pmartR.Rmd' using rmarkdown

Quitting from lines 23-30 [setup] (Statistical_Analysis_with_pmartR.Rmd)
Error: processing vignette 'Statistical_Analysis_with_pmartR.Rmd' failed with diagnostics:
there is no package called 'pmartRdata'
--- failed re-building 'Statistical_Analysis_with_pmartR.Rmd'

--- re-building 'Trelliscope_Vignette.Rmd' using rmarkdown

Quitting from lines 19-24 [setup] (Trelliscope_Vignette.Rmd)
Error: processing vignette 'Trelliscope_Vignette.Rmd' failed with diagnostics:
there is no package called 'pmartRdata'
--- failed re-building 'Trelliscope_Vignette.Rmd'

--- re-building 'Typical_Processing_Workflow.Rmd' using rmarkdown

Quitting from lines 24-32 [logo] (Typical_Processing_Workflow.Rmd)
Error: processing vignette 'Typical_Processing_Workflow.Rmd' failed with diagnostics:
there is no package called 'pmartRdata'
--- failed re-building 'Typical_Processing_Workflow.Rmd'

SUMMARY: processing the following files failed:
  'Convenience_Functions.Rmd' 'Data_Normalization.Rmd'
  'Data_Object_Creation.Rmd' 'Filter_Functionality.Rmd'
  'Graphing_with_pmartR.Rmd' 'RNAseq_Processing_Workflow.Rmd'
  'Statistical_Analysis_with_pmartR.Rmd' 'Trelliscope_Vignette.Rmd'
  'Typical_Processing_Workflow.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [30s] OK
* DONE
Status: 3 ERRORs, 2 WARNINGs, 6 NOTEs