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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RiboCrypt.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RiboCrypt_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RiboCrypt.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘1.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RiboCrypt’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    images   2.2Mb
    rmd      4.3Mb
* 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
Unexported objects imported by ':::' calls:
  ‘ORFik:::name_decider’ ‘ORFik:::remove.file_ext’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘distribution_plot’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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’
RiboCrypt_app: no visible global function definition for ‘is’
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 ‘org’
RiboCrypt_app : server: no visible binding for global variable
  ‘gene_name_list’
RiboCrypt_app : server: no visible binding for global variable
  ‘df_with’
RiboCrypt_app_modular: no visible global function definition for ‘is’
RiboCrypt_app_modular : server: no visible binding for global variable
  ‘df’
RiboCrypt_app_modular : server: no visible binding for global variable
  ‘experiments’
RiboCrypt_app_modular : server: no visible binding for global variable
  ‘tx’
RiboCrypt_app_modular : server: no visible binding for global variable
  ‘org’
RiboCrypt_app_modular : server: no visible binding for global variable
  ‘gene_name_list’
RiboCrypt_app_modular : server: no visible binding for global variable
  ‘df_with’
browser_plot_assembler: no visible binding for global variable
  ‘profiles’
browser_plot_assembler: no visible binding for global variable
  ‘mainPlotControls’
browser_plot_assembler: no visible global function definition for
  ‘mainPlotControls’
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 global function
  definition for ‘shifts.load’
click_plot_heatmap_main_controller: no visible binding for global
  variable ‘fraction’
createSeqPanelPattern: no visible binding for global variable ‘frames’
distribution_plot: no visible binding for global variable ‘RPKM’
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’
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’
geneModelPanelPlot: no visible binding for global variable ‘layers’
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
  ‘labels_locations’
geneModelPanelPlot: no visible binding for global variable ‘gene_names’
geneTrackLayer: no visible binding for global variable ‘subjectHits’
geneTrackLayer: no visible binding for global variable ‘queryHits’
getCoverageProfile: no visible global function definition for ‘is’
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’
getRelativeFrames: no visible binding for global variable ‘cum_width’
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’
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’
load_custom_regions: no visible binding for global variable ‘.’
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’
multiOmicsPlot_internal: 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
  ‘display_dist’
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’
plotSeqPanel: no visible binding for global variable ‘frames’
profilesFetcher: no visible global function definition for ‘is’
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’
singlePlotsFetcher: no visible global function definition for ‘is’
singlePlotsFetcher: no visible binding for global variable ‘BPPARAM’
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 binding for global variable ‘position’
stopCoverage: 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_update_select: no visible binding for global variable ‘label’
unlistToExtremities: no visible global function definition for ‘.’
valuesToColors: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  . BPPARAM LFC RPKM Regulation amplitude capture.output cds_len
  colorRampPalette contrast cum_width df df_with display_dist dt
  experiments extend_trailers fraction frame frames gene_id
  gene_name_list gene_names index is label labels_locations layers
  mainPlotControls meanCounts merged_name nrun org periods position
  profiles queryHits ratio readLengthMeta read_length readlength
  rect_ends rect_starts rel_frame rfp rna seqType seqs shifts.load
  spec.pgram subjectHits tx tx_name utr5_len variable ylabels_full_name
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "frame")
  importFrom("methods", "is")
  importFrom("stats", "df", "dt", "spec.pgram")
  importFrom("utils", "capture.output")
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 ... ERROR
Running examples in ‘RiboCrypt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DEG_plot
> ### Title: Differential expression plots (1D or 2D)
> ### Aliases: DEG_plot
> 
> ### ** Examples
> 
> # Load experiment
> df <- ORFik.template.experiment()
> # 1 Dimensional analysis
> dt <- DEG.analysis(df[df$libtype == "RNA",])
----------------------
Input check: 
----------------------
Full exp design: ~replicate + condition
Target contrast: condition
----------------------
Creating DESeq model:
----------------------
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
Warning in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth,  :
  Estimated rdf < 1.0; not estimating variance
final dispersion estimates
fitting model and testing
----------------------
Comparison: Mutant vs WT
Regulation
No change 
        6 
----------------------
> dt$Regulation[1] <- "Significant" # Fake sig level
> DEG_plot(dt, draw_non_regulated = TRUE)
> # 2 Dimensional analysis
> dt_2d <- DTEG.analysis(df[df$libtype == "RFP",], df[df$libtype == "RNA",],
+                     output.dir = NULL)
----------------------
Input check:
----------------------
Input check: df.rfp
Loading default 80S counts, update count.folder to pshifted if wanted?
----------------------
Input check: df.rna
----------------------
----------------------
Full exper. design: ~condition
Interaction design: ~libtype + condition + libtype:condition
Target -- contrast: condition
----------------------
----------------------
Model 1/3: TE
----------------------
factor levels were dropped which had no samples
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
----------------------
Model 2/3: Ribo-seq
----------------------
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
Warning in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth,  :
  Estimated rdf < 1.0; not estimating variance
final dispersion estimates
fitting model and testing
----------------------
Model 3/3: RNA-seq
----------------------
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
Warning in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth,  :
  Estimated rdf < 1.0; not estimating variance
final dispersion estimates
fitting model and testing
----------------------
Comparison: Mutant vs WT

     No change    Translation      Buffering mRNA abundance 
             6              0              0              0 
----------------------
Plotting all results
> dt_2d$Regulation[4] <- "Translation" # Fake sig level
> dt_2d$Regulation[5] <- "Buffering" # Fake sig level
> DEG_plot(dt_2d, draw_non_regulated = TRUE)
Error in eval(substitute(expr), data, enclos = parent.frame()) : 
  dt must minimally contain the columns: contrast, Regulation, id, rna, rfp, te
Calls: DEG_plot ... DEG_plot_input_validation -> with -> with.default -> eval -> eval
Execution halted
* 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: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RiboCrypt.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RiboCrypt
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘RiboCrypt’ ...
** 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)