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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RiboCrypt_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RiboCrypt ────────────────────────────────────────────────────────
✔ Package installed successfully
── RiboCrypt session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmptx4rq9/file11dfea7d1b27c9/RiboCrypt
→ BiocVersion: 3.24
→ Package: RiboCrypt
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RiboCrypt.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmptx4rq9/file11dfea7d1b27c9/RiboCrypt
→ installDir: /tmp/Rtmptx4rq9/file11dfea11522438
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RiboCrypt ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.6.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Coverage, DifferentialExpression, Alignment,
FunctionalGenomics, ImmunoOncology, DataImport
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (27%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • RiboCrypt_app_tutorial.rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/RiboCrypt_app_tutorial.rmd
    • vignettes/RiboCrypt_overview.rmd
* Checking package installation calls in R code...
* Checking for library/require of RiboCrypt...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/annotation_plots.R (line 61, column 3)
    • R/annotation_plots.R (line 234, column 30)
    • R/multi_lib_metacoverage.R (line 2, column 10)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • annotation_plots.R (line 67, column 15)
    • ...
    • profile_getters.R (line 32, column 20)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/browser_helpers.R (line 87, column 3)
    • ...
    • print() in R/URL_helpers.R (line 245, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/other_helpers.R (line 65, column 15)
    • ...
    • R/Reactive_controllers.R (line 266, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/browser_helpers.R (line 255, column 36)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/multi_lib_metacoverage.R (line 28, column 22)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11 times)
  • suppressWarnings() in R/annotation_plots.R (line 290, column 3)
  • ...
  • suppressMessages() in R/Reactive_getters.R (line 3, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 26
functions greater than 50 lines.
  The longest 5 functions are:
    • module_protein() (R/Module_controllers.R): 189 lines
    • ...
    • _anonymous_.48() (R/page_DEG.R): 139 lines
* Checking man page documentation...
Warning: no function found corresponding to methods exports from ‘ORFik’ for: ‘organism’
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 824 lines (11%) are > 80 characters long.
  First few lines:
    • R/annotation_plots.R#L10 createSeqPanelPattern <- function(sequen ...
    • ...
    • vignettes/RiboCrypt_overview.rmd#L156 RiboCrypt offers interactive NGS
    profile ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3403 lines (45%) are
not.
  First few lines:
    • R/3dbeacons_utils.R#L2 'https://www.ebi.ac.uk/pdbe/pdbe-kb/3d ...
    • ...
    • vignettes/RiboCrypt_overview.rmd#L151 ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 19 NOTES
ℹ See the RiboCrypt.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.