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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('TFARM_1.35.0.tar.gz','quit-with-status'=TRUE)"
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── Installing TFARM ────────────────────────────────────────────────────────────
✔ Package installed successfully
── TFARM session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpK275zP/file14bbd32769002f/TFARM
→ BiocVersion: 3.24
→ Package: TFARM
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/TFARM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpK275zP/file14bbd32769002f/TFARM
→ installDir: /tmp/RtmpK275zP/file14bbd37b187cb4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TFARM ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.5.0 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...
* 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 'URL', 'BugReports' 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • TFARM.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • TFARM.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/TFARM.Rnw
* Checking package installation calls in R code...
* Checking for library/require of TFARM...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/distribViz.R (line 31, column 14)
    • ...
    • R/presAbs.R (line 48, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • heatI.R (line 37, column 49)
    • ...
    • search_rule.R (line 21, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/rulesGen.R (line 71, column 5)
    • print() in R/search_rule.R (line 29, column 9)
    • print() in R/search_rule.R (line 36, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/distribViz.R (line 34, column 8)
    • ...
    • R/search_rule.R (line 32, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/rulesTF.R (line 43, column 21)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • F in R/heatI.R (line 49, column 57)
    • F in R/heatI.R (line 49, column 66)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • rulesTF0() (R/rulesTF0.R): 71 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • search_rule.Rd
* Checking package NEWS...
* 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; 123 lines (8%) are > 80 characters long.
  First few lines:
    • R/distribViz.R#L37 ...
    • ...
    • vignettes/TFARM.Rnw#L649 \item TCF12 has low mean Importance Inde ...
ℹ NOTE: Consider 4 spaces instead of tabs; 69 lines (4%) contain tabs.
  First few lines:
    • vignettes/TFARM.Rnw#L114 supp(X) = \frac {|\{t_i \in N ; X \su ...
    • ...
    • vignettes/TFARM.Rnw#L592 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 96 lines (6%) are not.
  First few lines:
    • R/distribViz.R#L37 ...
    • ...
    • vignettes/TFARM.Rnw#L593 }) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 18 NOTES
ℹ See the TFARM.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.