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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('rifi_1.17.0.tar.gz','quit-with-status'=TRUE)"
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── Installing rifi ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── rifi session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpXt7t7h/file11f3c76441c609/rifi
→ BiocVersion: 3.24
→ Package: rifi
→ PackageVersion: 1.17.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/rifi.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpXt7t7h/file11f3c76441c609/rifi
→ installDir: /tmp/RtmpXt7t7h/file11f3c75f32f4b2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on rifi ───────────────────────────────────────────────────
* 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 4.2 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: Transcription
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...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (12%).
* 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:
    • vignette.Rmd
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpXt7t7h/file11f3c76441c609/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpXt7t7h/file11f3c76441c609/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
* Checking for library/require of rifi...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dataframe_summary_events_HL_int.r (line 89, column 32)
    • ...
    • event_dataframe.r (line 81, column 20)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/empty_data_negative.r (line 9, column 3)
    • ...
    • print() in R/TI_fit.r (line 205, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/rifi_visualization.r (line 295, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 51
functions greater than 50 lines.
  The longest 5 functions are:
    • positive_strand_function() (R/positive_strand_function.r): 996 lines
    • ...
    • dataframe_summary_events_HL_int() (R/dataframe_summary_events_HL_int.r):
    325 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpXt7t7h/file11f3c76441c609/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpXt7t7h/file11f3c76441c609/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpXt7t7h/file11f3c76441c609/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpXt7t7h/file11f3c76441c609/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpXt7t7h/file11f3c76441c609/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpXt7t7h/file11f3c76441c609/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
* Checking package NEWS...
! WARNING: news(package='rifi') failed with news file: inst/NEWS.md:news()
failed to parse news file: inst/NEWS.md Refer to
https://contributions.bioconductor.org/news.html to 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; 184 lines (1%) are > 80 characters long.
  First few lines:
    • R/apply_manova.r#L10 #' therefore this function sets first fr ...
    • ...
    • vignettes/vignette.Rmd#L1577 ``` {r genomeplot2, echo=F, fig.cap="**F ...
ℹ NOTE: Consider 4 spaces instead of tabs; 8 lines (0%) contain tabs.
  First few lines:
    • R/dataframe_summary_events_HL_int.r#L195 } ...
    • ...
    • vignettes/vignette.Rmd#L1578 knitr::include_graphics("genome_plot_2. ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4931 lines (33%) are
not.
  First few lines:
    • R/annotation_plot.r#L3 function(data_p = df1, ...
    • ...
    • vignettes/vignette.Rmd#L1662 ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the rifi.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.