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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RiboCrypt.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RiboCrypt_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RiboCrypt.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RiboCrypt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RiboCrypt’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 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 ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/RiboCrypt.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
DEG_plot 23.083  1.206  24.344
* 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: 5 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RiboCrypt.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL RiboCrypt
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘RiboCrypt’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (RiboCrypt)