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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GeneGA_1.63.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GeneGA ───────────────────────────────────────────────────────────
✔ Package installed successfully
── GeneGA session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpkXULSe/filea35892ec652d8/GeneGA
→ BiocVersion: 3.24
→ Package: GeneGA
→ PackageVersion: 1.63.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GeneGA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpkXULSe/filea35892ec652d8/GeneGA
→ installDir: /tmp/RtmpkXULSe/filea3589257f30ba
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GeneGA ─────────────────────────────────────────────────
* 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...
* 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': 2013-3-6
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • GeneGA.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GeneGA.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/GeneGA.Rnw
* Checking package installation calls in R code...
* Checking for library/require of GeneGA...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/GeneCodon.R (line 20, column 33)
    • ...
    • R/GeneGA.R (line 171, column 61)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • evaluationFunction.R (line 40, column 44)
    • ...
    • GeneGA.R (line 194, column 42)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/GeneFoldGA.R (line 51, column 25)
    • cat() in R/GeneGA_internal.R (line 59, column 25)
    • cat() in R/GeneGA.R (line 70, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/evaluationFunction.R (line 4, column 15)
    • ...
    • R/GeneGA.R (line 204, column 34)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/GeneGA-internal.R (line 77, column 30)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 11 times:
    • T in R/evaluationFunction.R (line 4, column 66)
    • ...
    • F in R/GeneGA.R (line 34, column 67)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/evaluationFunction.R (line 4, column 16)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • GeneGA() (R/GeneGA.R): 214 lines
    • ...
    • _anonymous_.92() (R/GeneGA-internal.R): 69 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plotGeneGA-methods.Rd
* 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; 145 lines (11%) are > 80 characters long.
  First few lines:
    • R/evaluationFunction.R#L41 CAI_=cai(s2c(paste(xx,collapse=""))[(ra ...
    • ...
    • vignettes/GeneGA.Rnw#L119 The {\tt GeneGA} package depends on thre ...
ℹ NOTE: Consider 4 spaces instead of tabs; 797 lines (59%) contain tabs.
  First few lines:
    • R/evaluationFunction.R#L4 fold_r=system(paste("echo ",x,"|RNAfold ...
    • ...
    • vignettes/GeneGA.Rnw#L81 w_value[i]=rscu[[names(rscu)[i]]]/amino ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 60 lines (4%) are not.
  First few lines:
    • R/GeneGA-internal.R#L102 ramp=object@ramp ...
    • ...
    • man/wSet.Rd#L12 A data frame with 200 observations on ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the GeneGA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.