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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RiboCrypt.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RiboCrypt_1.15.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RiboCrypt.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘RiboCrypt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RiboCrypt’ version ‘1.15.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 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 11.5Mb
  sub-directories of 1Mb or more:
    images   5.7Mb
    rmd      5.2Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘ORFik:::DEG_gorilla’
  See the note in ?`:::` about the use of this operator.
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 ‘y_axis’
DEG_plot: no visible binding for global variable ‘rfp.lfc’
DEG_plot: no visible binding for global variable ‘LFC’
DEG_plot: no visible binding for global variable ‘x_axis’
DEG_plot: no visible binding for global variable ‘rna.lfc’
DEG_plot: no visible binding for global variable ‘meanCounts’
DEG_plot: no visible binding for global variable ‘id’
DEG_plot: no visible binding for global variable ‘Regulation’
DEG_plot : <anonymous>: no visible binding for global variable
  ‘contrast’
DEG_server : <anonymous>: no visible binding for global variable
  ‘value’
DEG_server : <anonymous>: no visible global function definition for
  ‘URLencode’
DEG_server : <anonymous>: no visible global function definition for
  ‘organism’
DEG_server : <anonymous>: no visible binding for global variable
  ‘external_gene_name’
DEG_server : <anonymous>: no visible binding for global variable
  ‘label’
DE_model_results: no visible binding for global variable ‘Regulation’
DE_model_results: no visible binding for global variable ‘LFC’
DE_model_results: no visible binding for global variable ‘meanCounts’
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 ‘names_init_meta’
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_meta’
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
  ‘names_init’
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
  ‘tooltip_text’
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’
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_allsamp_controller: no visible global function
  definition for ‘%over%’
click_plot_browser_allsamp_controller: no visible global function
  definition for ‘reduce’
click_plot_browser_main_controller: no visible global function
  definition for ‘%over%’
click_plot_browser_main_controller: no visible global function
  definition for ‘reduce’
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 ‘seqs’
click_plot_codon: no visible binding for global variable
  ‘relative_to_max_score’
click_plot_codon: no visible global function definition for ‘.’
click_plot_codon: no visible binding for global variable ‘variable’
click_plot_codon: no visible binding for global variable
  ‘..score_column_name’
click_plot_codon: no visible binding for global variable
  ‘simulated_error’
click_plot_codon: no visible global function definition for ‘runif’
click_plot_codon: no visible binding for global variable ‘N_min’
click_plot_codon: no visible binding for global variable ‘p_value’
click_plot_codon: no visible global function definition for
  ‘wilcox.test’
click_plot_codon: no visible binding for global variable ‘significant’
click_plot_codon: no visible binding for global variable ‘tooltip_text’
click_plot_codon: no visible binding for global variable ‘N_sites’
click_plot_codon: no visible binding for global variable ‘x’
click_plot_codon: no visible binding for global variable ‘y’
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’
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 ‘reduce’
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’
generate_filename: no visible global function definition for ‘organism’
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_meta_browser_plot: no visible global function definition for
  ‘kmeans’
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’
library_input_select: no visible global function definition for ‘is’
load_collection: no visible binding for global variable ‘position’
load_custom_regions: no visible binding for global variable ‘.’
load_data_umap: no visible binding for global variable ‘color_column’
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’
observed_cds_point: no visible global function definition for
  ‘vmatchPattern’
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’
row_order: no visible global function definition for ‘is’
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_coord_by_region: no visible global function definition for
  ‘organism’
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’
subset_tx_by_region: no visible global function definition for
  ‘organism’
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’
umap_centroids_plot: no visible global function definition for ‘.’
umap_centroids_plot: no visible binding for global variable ‘UMAP 1’
umap_centroids_plot: no visible binding for global variable ‘UMAP 2’
umap_centroids_plot: no visible binding for global variable
  ‘color_column’
umap_centroids_plot: no visible binding for global variable
  ‘centroid_x’
umap_centroids_plot: no visible binding for global variable
  ‘centroid_y’
umap_centroids_plot: no visible global function definition for ‘dist’
umap_centroids_plot: no visible binding for global variable ‘Group1’
umap_centroids_plot: no visible binding for global variable ‘Group2’
umap_centroids_plot: no visible binding for global variable
  ‘Comparison’
umap_plot: no visible binding for global variable ‘UMAP 1’
umap_plot: no visible binding for global variable ‘UMAP 2’
umap_plot: no visible binding for global variable ‘color_column’
valuesToColors: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  %over% . ..score_column_name Comparison Group1 Group2 LFC N_min
  N_sites RPKM Regulation UMAP 1 UMAP 2 URLencode amplitude as
  browseURL capture.output cds_len centroid_x centroid_y chisq.test
  cluster colorRampPalette color_column contrast count cum_width
  dev.off df df_meta df_with display_dist dist distance dt 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 kmeans label labels_locations
  layers lib_sizes libs libtypes logscore mclapply mcmapply meanCounts
  merged_name names_init names_init_meta no_ex nrun org organism
  p_value pdf periods phyloP position queryHits ratio readLengthMeta
  read_length readlength rect_ends rect_starts reduce rel_frame
  relative_to_max_score relist rfp.lfc rn rna.lfc runif score score_tpm
  sd seqType seqlevelsStyle seqlevelsStyle<- seqs significant
  simulated_error spec.pgram subjectHits time_before tooltip_text
  total_libs transcript tx type uniprot_id utr5_len valid value
  variable vmatchPattern wilcox.test with_readlengths_env
  without_readlengths_env wmsg x x_axis y y_axis ylabels_full_name
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "frame")
  importFrom("methods", "as", "is")
  importFrom("stats", "chisq.test", "df", "dist", "dt", "kmeans",
             "runif", "sd", "spec.pgram", "wilcox.test")
  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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
DEG_plot 15.525  0.402   15.93
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/RiboCrypt.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RiboCrypt
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘RiboCrypt’ ...
** this is package ‘RiboCrypt’ version ‘1.15.3’
** 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)