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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RTN_2.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RTN ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── RTN session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpEsAiHb/file126a815147eae8/RTN
→ BiocVersion: 3.24
→ Package: RTN
→ PackageVersion: 2.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RTN.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpEsAiHb/file126a815147eae8/RTN
→ installDir: /tmp/RtmpEsAiHb/file126a814b009184
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RTN ────────────────────────────────────────────────────
* 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 3.6.3 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpEsAiHb/file126a815147eae8/RTN/man/tni.area3.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpEsAiHb/file126a815147eae8/RTN/man/tni.gsea2.Rd'
* 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (37%).
* 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...
! WARNING: Evaluate more vignette chunks.
ℹ 27 out of 43 code chunks = 62% unevaluated
ℹ 
* Checking package installation calls in R code...
* Checking for library/require of RTN...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllChecks.R (line 785, column 21)
    • ...
    • R/TNI-subgroups.R (line 121, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllChecks.R (line 591, column 19)
    • ...
    • TNI-subgroups.R (line 122, column 61)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllChecks.R (line 992, column 16)
    • ...
    • print() in R/TNI-methods.R (line 1548, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllPlotsAVS.R (line 95, column 7)
    • ...
    • R/TNI-methods.R (line 1753, column 46)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AllChecks.R (line 17, column 12)
    • ...
    • R/TNI-subgroups.R (line 129, column 10)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 6 times:
    • F in R/AllPlotsTNA.R (line 239, column 44)
    • ...
    • F in R/TNI-methods.R (line 1696, column 75)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/TNI-methods.R (line 1925, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/AllSupplementsAVS.R (line 731, column 19)
  • <<- in R/AllSupplementsTNI.R (line 1485, column 16)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/AllPlotsAVS.R (line 248, column 3)
  • ...
  • suppressWarnings() in R/TNI-methods.R (line 1179, column 18)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 52
functions greater than 50 lines.
  The longest 5 functions are:
    • tnai.checks() (R/AllChecks.R): 934 lines
    • ...
    • _anonymous_.1590() (R/TNI-methods.R): 207 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • avs.evse.Rd
    • ...
    • upgradeTNI.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 67% of man
pages use at least one of these tags.
  Found in files:
    • AVS-class.Rd
    • ...
    • tni2tna.preprocess.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • AVS-class.Rd
    • ...
    • tni2tna.preprocess.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 403 lines (3%) are > 80 characters long.
  First few lines:
    • R/AllChecks.R#L53 "status","linkedMarkers","ra ...
    • ...
    • vignettes/RTN.Rmd#L490 * Chagas VS *et al.*, RTNduals: An R/Bio ...
ℹ NOTE: Consider 4 spaces instead of tabs; 143 lines (1%) contain tabs.
  First few lines:
    • R/AllSupplementsTNA.R#L13 nPermutations=1000, ...
    • ...
    • man/TNI-class.Rd#L107 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4970 lines (33%) are
not.
  First few lines:
    • R/AllChecks.R#L3 if(name=="alpha") { ...
    • ...
    • vignettes/RTN.Rmd#L448 filename = "fig5.pdf") ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the RTN.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.