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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('gpls_1.85.0.tar.gz','quit-with-status'=TRUE)"
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── Installing gpls ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── gpls session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYhFCtN/file1b22366e5c7a90/gpls
→ BiocVersion: 3.24
→ Package: gpls
→ PackageVersion: 1.85.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/gpls.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpYhFCtN/file1b22366e5c7a90/gpls
→ installDir: /tmp/RtmpYhFCtN/file1b2236697533d8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on gpls ───────────────────────────────────────────────────
* 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: Provide 'URL', '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:
    • gpls.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/gpls.Rnw
* Checking package installation calls in R code...
* Checking for library/require of gpls...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • glm.fun.R (line 94, column 14)
    • ...
    • glpls1a.R (line 227, column 24)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/glm.fun.R (line 6, column 12)
    • ...
    • print() in R/glpls1a.mlogit.R (line 6, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/glpls1a.R (line 19, column 12)
    • ...
    • R/glpls1a.R (line 341, column 9)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 15 times:
    • T in R/glpls1a.error.R (line 3, column 74)
    • ...
    • F in R/glpls1a.R (line 66, 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 3
functions greater than 50 lines.
  The longest 5 functions are:
    • glpls1a.mlogit() (R/glpls1a.mlogit.R): 282 lines
    • glpls1a() (R/glpls1a.R): 238 lines
    • predict.gpls() (R/glpls1a.R): 58 lines
* Checking man page documentation...
* 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; 37 lines (2%) are > 80 characters long.
  First few lines:
    • R/glm.fun.R#L6 else cat("link function not recogn ...
    • ...
    • man/glpls1a.train.test.error.Rd#L49
    \code{\link{glpls1a.mlogit.cv.error}}, ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • R/glpls1a.mlogit.R#L214 for ( j in seq(n)) ...
    • R/my.ginv.R#L15 if (all(Positive)) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 656 lines (41%) are
not.
  First few lines:
    • R/glm.fun.R#L2 function(x,family="normal",link="ident ...
    • ...
    • vignettes/gpls.Rnw#L171 predict(z, Iris[-train, ])$class ...
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 email is ok.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 13 NOTES
ℹ See the gpls.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.