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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RiboCrypt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RiboCrypt_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RiboCrypt.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RiboCrypt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RiboCrypt’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RiboCrypt’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    images   5.7Mb
    rmd      5.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ORFik:::name_decider’ ‘ORFik:::remove.file_ext’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
collection_to_metawindow: warning in rbindlist(output, id = "genes"):
  partial argument match of 'id' to 'idcol'
DEG_plot: no visible binding for global variable ‘rna’
DEG_plot: no visible binding for global variable ‘rfp’
DEG_plot: no visible binding for global variable ‘Regulation’
DEG_plot: no visible binding for global variable ‘contrast’
DEG_plot: no visible binding for global variable ‘meanCounts’
DEG_plot: no visible binding for global variable ‘LFC’
DEG_server : <anonymous>: no visible binding for global variable
  ‘value’
DEG_server : <anonymous>: no visible global function definition for
  ‘URLencode’
DE_model_results: no visible binding for global variable ‘Regulation’
RiboCrypt_app: no visible binding for global variable ‘names_init’
RiboCrypt_app: no visible binding for global variable ‘libs’
RiboCrypt_app: no visible binding for global variable ‘time_before’
RiboCrypt_app : server: no visible binding for global variable
  ‘without_readlengths_env’
RiboCrypt_app : server: no visible binding for global variable ‘df’
RiboCrypt_app : server: no visible binding for global variable
  ‘experiments’
RiboCrypt_app : server: no visible binding for global variable ‘tx’
RiboCrypt_app : server: no visible binding for global variable ‘libs’
RiboCrypt_app : server: no visible binding for global variable ‘org’
RiboCrypt_app : server: no visible binding for global variable
  ‘gene_name_list’
RiboCrypt_app : server: no visible binding for global variable
  ‘df_meta’
RiboCrypt_app : server: no visible binding for global variable
  ‘names_init’
RiboCrypt_app : server: no visible binding for global variable
  ‘with_readlengths_env’
RiboCrypt_app : server: no visible binding for global variable
  ‘df_with’
RiboCrypt_app : server: no visible binding for global variable
  ‘exp_init_meta’
RiboCrypt_app : server: no visible binding for global variable
  ‘time_before’
allsamples_enrich_bar_plot: no visible binding for global variable
  ‘variable’
allsamples_enrich_bar_plot: no visible binding for global variable ‘rn’
allsamples_enrich_bar_plot: no visible binding for global variable
  ‘value’
allsamples_meta_stats: no visible binding for global variable ‘index’
allsamples_meta_stats: no visible binding for global variable
  ‘grouping_numeric_bins’
allsamples_meta_stats: no visible global function definition for
  ‘chisq.test’
allsamples_metadata_clustering: no visible global function definition
  for ‘pdf’
allsamples_metadata_clustering: no visible global function definition
  for ‘dev.off’
allsamples_metadata_clustering: no visible binding for global variable
  ‘cluster’
allsamples_metadata_clustering: no visible binding for global variable
  ‘index’
allsamples_metadata_clustering: no visible binding for global variable
  ‘grouping_numeric_bins_temp’
allsamples_metadata_clustering: no visible binding for global variable
  ‘grouping_numeric_bins’
allsamples_sidebar : <anonymous>: no visible binding for global
  variable ‘index’
allsamples_sidebar_ggproto: no visible binding for global variable
  ‘index’
annotation_controller: no visible global function definition for ‘is’
annotation_controller: no visible global function definition for ‘wmsg’
annotation_track_allsamples: no visible binding for global variable
  ‘tx_name’
append_gene_symbols: no visible global function definition for ‘is’
append_gene_symbols: no visible binding for global variable ‘id’
append_gene_symbols: no visible binding for global variable
  ‘external_gene_name’
append_gene_symbols: no visible binding for global variable ‘label’
browseRC: no visible global function definition for ‘browseURL’
browser_allsamp_server : <anonymous>: no visible binding for global
  variable ‘gene_name_list’
browser_track_panel_shiny: no visible binding for global variable
  ‘ylabels_full_name’
browser_track_panel_shiny: no visible binding for global variable
  ‘total_libs’
browser_track_panel_shiny: no visible binding for global variable
  ‘display_dist’
click_plot_browser_main_controller: no visible global function
  definition for ‘is’
click_plot_browser_new_controller: no visible binding for global
  variable ‘extend_trailers’
click_plot_codon: no visible binding for global variable ‘variable’
click_plot_codon: no visible binding for global variable ‘seqs’
click_plot_heatmap_main_controller: no visible binding for global
  variable ‘fraction’
collection_path_from_exp: no visible binding for global variable
  ‘label’
collection_path_from_exp: no visible binding for global variable
  ‘value’
collection_to_metawindow: no visible binding for global variable ‘.’
collection_to_metawindow: no visible global function definition for
  ‘mcmapply’
collection_to_wide: no visible binding for global variable ‘position’
compute_collection_table_grouping: no visible binding for global
  variable ‘lib_sizes’
compute_collection_table_grouping: no visible global function
  definition for ‘.’
compute_collection_table_grouping: no visible binding for global
  variable ‘score’
createSeqPanelPattern: no visible binding for global variable ‘frames’
distribution_plot: no visible binding for global variable ‘RPKM’
distribution_plot: no visible binding for global variable ‘transcript’
dt_fft: no visible global function definition for ‘spec.pgram’
dt_fft: no visible binding for global variable ‘fraction’
extend_all_to: no visible binding for global variable ‘tx_name’
filter_collection_on_count: no visible global function definition for
  ‘.’
filter_collection_on_count: no visible binding for global variable
  ‘count’
filter_collection_on_count: no visible binding for global variable
  ‘valid’
fivePlots: no visible binding for global variable ‘seqType’
fivePlots: no visible global function definition for ‘readLengthMeta’
fivePlots: no visible binding for global variable ‘position’
fivePlots: no visible binding for global variable ‘index’
fivePlots: no visible binding for global variable ‘frames’
fivePlots: no visible binding for global variable ‘ratio’
fourPlots: no visible binding for global variable ‘seqType’
fourPlots: no visible binding for global variable ‘position’
fourPlots: no visible binding for global variable ‘index’
fourPlots: no visible binding for global variable ‘frames’
geneBoxFromRanges: no visible binding for global variable ‘no_ex’
geneBoxFromRanges: no visible global function definition for ‘.’
geneBoxFromRanges: no visible binding for global variable ‘rect_ends’
geneBoxFromRanges: no visible binding for global variable ‘rect_starts’
geneModelPanelPlot: no visible binding for global variable ‘type’
geneModelPanelPlot: no visible binding for global variable
  ‘rect_starts’
geneModelPanelPlot: no visible binding for global variable ‘rect_ends’
geneModelPanelPlot: no visible binding for global variable ‘layers’
geneModelPanelPlot: no visible binding for global variable ‘gene_names’
geneModelPanelPlot: no visible global function definition for ‘.’
geneModelPanelPlot: no visible binding for global variable
  ‘labels_locations’
geneTrackLayer: no visible binding for global variable ‘subjectHits’
geneTrackLayer: no visible binding for global variable ‘queryHits’
genomic_string_to_grl: no visible global function definition for ‘as’
genomic_string_to_grl: no visible global function definition for ‘is’
genomic_string_to_grl: no visible global function definition for
  ‘seqlevelsStyle<-’
genomic_string_to_grl: no visible global function definition for
  ‘seqlevelsStyle’
getCoverageProfile: no visible global function definition for ‘is’
getCoverageProfile: no visible binding for global variable ‘position’
getIndexes: no visible global function definition for ‘nrun’
getMetaCoverage: no visible global function definition for ‘.’
getMetaCoverage: no visible binding for global variable ‘position’
getMetaCoverage: no visible binding for global variable ‘index’
getMetaCoverage: no visible binding for global variable ‘frames’
getPlotAnimate: no visible binding for global variable ‘position’
getPlotAnimate: no visible binding for global variable ‘frame’
getProfileAnimate: no visible global function definition for ‘is’
getProfileWrapper: no visible binding for global variable ‘frame’
getProfileWrapper: no visible binding for global variable ‘count’
getRelativeFrames: no visible binding for global variable ‘cum_width’
getRelativeFrames: no visible global function definition for ‘.’
getRelativeFrames: no visible binding for global variable ‘type’
getRelativeFrames: no visible binding for global variable ‘rel_frame’
getRiboProfile: no visible global function definition for ‘is’
getRiboProfile: no visible binding for global variable ‘frame’
getStartWindow: no visible binding for global variable ‘.’
getStopWindow: no visible binding for global variable ‘.’
get_gene_name_categories: no visible binding for global variable
  ‘merged_name’
get_gene_name_categories: no visible binding for global variable
  ‘uniprot_id’
get_gene_name_categories_collection: no visible binding for global
  variable ‘value’
heatmap_data: no visible binding for global variable ‘position’
heatmap_data: no visible binding for global variable ‘readlength’
heatmap_data: no visible binding for global variable ‘fraction’
internalGetterSubsetter: no visible binding for global variable
  ‘position’
load_collection: no visible binding for global variable ‘position’
load_custom_regions: no visible binding for global variable ‘.’
make_rc_url: no visible binding for global variable ‘merged_name’
make_summary_track: no visible global function definition for ‘.’
make_summary_track: no visible binding for global variable ‘position’
make_summary_track: no visible binding for global variable ‘frame’
metaPlot: no visible binding for global variable ‘index’
metaPlot: no visible binding for global variable ‘frames’
metadata_ui: no visible binding for global variable ‘libtypes’
multiLib_to_metaWindow: no visible global function definition for
  ‘mclapply’
multiLib_to_metaWindow : <anonymous>: no visible binding for global
  variable ‘position’
multiLib_to_metaWindow : <anonymous>: no visible binding for global
  variable ‘genes’
multiOmicsPlot_all_profiles: no visible global function definition for
  ‘is’
multiOmicsPlot_all_track_plots: no visible global function definition
  for ‘is’
multiOmicsPlot_internal: no visible binding for global variable
  ‘ylabels_full_name’
multiOmicsPlot_internal: no visible binding for global variable
  ‘total_libs’
multiOmicsPlot_internal: no visible binding for global variable
  ‘display_dist’
normalize_collection: no visible binding for global variable
  ‘score_tpm’
normalize_collection: no visible binding for global variable ‘count’
normalize_collection: no visible binding for global variable ‘score’
normalize_collection: no visible global function definition for ‘sd’
normalize_collection: no visible binding for global variable ‘logscore’
observed_cds_heatmap: no visible binding for global variable ‘gene_id’
observed_cds_heatmap: no visible binding for global variable ‘cds_len’
observed_cds_heatmap: no visible binding for global variable ‘utr5_len’
periodicity_plot: no visible binding for global variable ‘fraction’
periodicity_plot: no visible binding for global variable ‘frame’
periodicity_plot : <anonymous>: no visible binding for global variable
  ‘read_length’
periodicity_plot : <anonymous>: no visible binding for global variable
  ‘periods’
periodicity_plot : <anonymous>: no visible binding for global variable
  ‘amplitude’
phylo_custom_seq_track_panel: no visible global function definition for
  ‘seqlevelsStyle<-’
phylo_custom_seq_track_panel: no visible global function definition for
  ‘seqlevelsStyle’
phylo_custom_seq_track_panel: no visible global function definition for
  ‘relist’
phylo_custom_seq_track_panel: no visible binding for global variable
  ‘position’
phylo_custom_seq_track_panel: no visible binding for global variable
  ‘phyloP’
plotSeqPanel: no visible binding for global variable ‘frames’
quality_server : <anonymous>: no visible binding for global variable
  ‘frame’
quality_server : <anonymous>: no visible binding for global variable
  ‘position’
quality_server : <anonymous>: no visible binding for global variable
  ‘fraction’
singlePlot_select_plot_type: no visible binding for global variable
  ‘position’
singlePlot_select_plot_type: no visible binding for global variable
  ‘frame’
smoothenMultiSampCoverage: no visible binding for global variable
  ‘count’
smoothenMultiSampCoverage: no visible binding for global variable
  ‘frame’
smoothenMultiSampCoverage: no visible global function definition for
  ‘.’
smoothenSingleSampCoverage: no visible binding for global variable
  ‘count’
smoothenSingleSampCoverage: no visible binding for global variable
  ‘genes’
smoothenSingleSampCoverage: no visible binding for global variable
  ‘frame’
smoothenSingleSampCoverage: no visible binding for global variable
  ‘position’
sra_search_server : <anonymous>: no visible global function definition
  for ‘capture.output’
sra_search_server : <anonymous>: no visible binding for global variable
  ‘dt’
startCoverage: no visible global function definition for ‘distance’
startCoverage: no visible binding for global variable ‘position’
stopCoverage: no visible global function definition for ‘distance’
stopCoverage: no visible binding for global variable ‘position’
subset_fst_by_interval: no visible global function definition for ‘is’
subset_fst_by_interval: no visible binding for global variable
  ‘position’
subset_fst_by_region: no visible global function definition for ‘is’
subset_fst_by_region: no visible binding for global variable ‘position’
subset_fst_interval_sum: no visible binding for global variable
  ‘position’
subset_fst_interval_sum: no visible global function definition for ‘.’
subset_fst_interval_sum: no visible binding for global variable ‘score’
summary_track_allsamples: no visible binding for global variable
  ‘position’
threePlots: no visible binding for global variable ‘seqType’
threePlots: no visible binding for global variable ‘position’
threePlots: no visible binding for global variable ‘index’
tx_from_gene_list: no visible binding for global variable ‘value’
tx_from_gene_list: no visible binding for global variable ‘label’
tx_update_select: no visible binding for global variable ‘value’
valuesToColors: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  . LFC RPKM Regulation URLencode amplitude as browseURL capture.output
  cds_len chisq.test cluster colorRampPalette contrast count cum_width
  dev.off df df_meta df_with display_dist distance dt exp_init_meta
  experiments extend_trailers external_gene_name fraction frame frames
  gene_id gene_name_list gene_names genes grouping_numeric_bins
  grouping_numeric_bins_temp id index is label labels_locations layers
  lib_sizes libs libtypes logscore mclapply mcmapply meanCounts
  merged_name names_init no_ex nrun org pdf periods phyloP position
  queryHits ratio readLengthMeta read_length readlength rect_ends
  rect_starts rel_frame relist rfp rn rna score score_tpm sd seqType
  seqlevelsStyle seqlevelsStyle<- seqs spec.pgram subjectHits
  time_before total_libs transcript tx tx_name type uniprot_id utr5_len
  valid value variable with_readlengths_env without_readlengths_env
  wmsg ylabels_full_name
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "frame")
  importFrom("methods", "as", "is")
  importFrom("stats", "chisq.test", "df", "dt", "sd", "spec.pgram")
  importFrom("utils", "URLencode", "browseURL", "capture.output",
             "relist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'compute_collection_table.Rd'
  ‘decreasing_order’

Undocumented arguments in Rd file 'make_rc_url.Rd'
  ‘add_translons’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiOmicsPlot_animate
> ### Title: Multi-omics animation using list input
> ### Aliases: multiOmicsPlot_animate
> 
> ### ** Examples
> 
> library(RiboCrypt)
> df <- ORFik.template.experiment()[9:10,]
> cds <- loadRegion(df, "cds")
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
> mrna <- loadRegion(df, "mrna")
> multiOmicsPlot_animate(mrna[1], annotation = cds[1], reference_sequence = findFa(df),
+                     frames_type = "columns", leader_extension = 30, trailer_extension = 30, withFrames = c(T, T),
+                     reads = outputLibs(df, type = "pshifted", output.mode = "envirlist",
+                                   naming = "full", BPPARAM = BiocParallel::SerialParam()))
Outputting libraries from: ORFik
1 :  RFP_Mutant_r1
2 :  RFP_Mutant_r2
Error in eval(substitute(expr), data, enclos = parent.frame()) : 
  T used instead of TRUE
Calls: multiOmicsPlot_animate ... multiOmicsControllerView -> with -> with.default -> eval -> eval
Execution halted
* 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, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/RiboCrypt.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RiboCrypt
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘RiboCrypt’ ...
** this is package ‘RiboCrypt’ version ‘1.15.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RiboCrypt)