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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('sscu_2.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing sscu ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── sscu session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpBkp2gz/file1471306b936e1f/sscu
→ BiocVersion: 3.24
→ Package: sscu
→ PackageVersion: 2.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/sscu.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpBkp2gz/file1471306b936e1f/sscu
→ installDir: /tmp/RtmpBkp2gz/file14713057278b86
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on sscu ───────────────────────────────────────────────────
* 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 3.3 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...
* 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: 'Date:' field format is not 'YYYY-MM-DD': 2016-12-1
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (67%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/sscu.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • %\VignetteIndexEntry{title} knitr
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • sscu.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/sscu.Rmd
* Checking package installation calls in R code...
* Checking for library/require of sscu...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • op_corre_CodonW.R (line 30, column 10)
    • ...
    • op_highly.R (line 36, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat in R/op_highly_stats.R (line 6, column 5)
    • ...
    • cat in R/op_highly.R (line 9, column 35)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/akashi_test.R (line 14, column 11)
    • ...
    • R/akashi_test.R (line 17, column 12)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/op_corre_CodonW.R (line 49, column 19)
  • ...
  • suppressWarnings() in R/op_corre_NCprime.R (line 94, column 23)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
  The longest 5 functions are:
    • op_corre_NCprime() (R/op_corre_NCprime.R): 105 lines
    • ...
    • s_index() (R/s_index.R): 52 lines
* Checking man page documentation...
* 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; 192 lines (16%) are > 80 characters long.
  First few lines:
    • R/low_frequency_op.R#L1 low_frequency_op <- function(high_cds_fi ...
    • ...
    • vignettes/sscu.Rmd#L232 This folder contains two files as input ...
ℹ NOTE: Consider 4 spaces instead of tabs; 24 lines (2%) contain tabs.
  First few lines:
    • sscu/NAMESPACE#L12 s2c,GC3,uco,read.fasta) ...
    • ...
    • man/s_index.Rd#L20 a numeric vector with gc3 value, eg, 0. ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 415 lines (34%) are
not.
  First few lines:
    • R/genomic_gc3.R#L2 ...
    • ...
    • vignettes/sscu.Rmd#L215 ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 1 WARNINGS | ℹ 16 NOTES
ℹ See the sscu.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.