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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('omicade4_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing omicade4 ─────────────────────────────────────────────────────────
✔ Package installed successfully
── omicade4 session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpseh4RF/filef98493b8b7481/omicade4
→ BiocVersion: 3.24
→ Package: omicade4
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/omicade4.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpseh4RF/filef98493b8b7481/omicade4
→ installDir: /tmp/Rtmpseh4RF/filef98491c062b8d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on omicade4 ───────────────────────────────────────────────
* 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 3.0.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpseh4RF/filef98493b8b7481/omicade4/man/plotVar.mcia.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpseh4RF/filef98493b8b7481/omicade4/man/selectVar.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpseh4RF/filef98493b8b7481/omicade4/vignettes/omicade4.Rnw'
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* 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 (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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • omicade4.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/omicade4.Rnw
* Checking package installation calls in R code...
* Checking for library/require of omicade4...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getdata.R (line 13, column 45)
    • ...
    • R/selectVar.mcia.R (line 68, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • getdata.R (line 24, column 42)
    • ...
    • topVar.R (line 55, column 48)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/mcia.R (line 107, column 5)
    • print() in R/selectVar.cia.R (line 25, column 7)
    • print() in R/selectVar.mcia.R (line 65, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/array2ade4.R (line 33, column 22)
    • ...
    • R/getdata.R (line 29, column 49)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/getdata.R (line 33, column 25)
    • R/mcia.R (line 17, column 12)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 6 times:
    • T in R/mcia.R (line 1, column 64)
    • ...
    • F in R/splot.sample.mcia.R (line 92, column 77)
* 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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • mcia() (R/mcia.R): 131 lines
    • ...
    • plot.mcia() (R/plot.mcia.R): 71 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; 148 lines (8%) are > 80 characters long.
  First few lines:
    • R/array2ade4.R#L7 # Allows matrix, data.frame, Exp ...
    • ...
    • vignettes/omicade4.Rnw#L203 to know where these genes are projected ...
ℹ NOTE: Consider 4 spaces instead of tabs; 16 lines (1%) contain tabs.
  First few lines:
    • R/array2ade4.R#L14 # COA needs table of positive data, wil ...
    • ...
    • man/topVar.Rd#L43 topVar(mcoin, axis = 1, end = "both", t ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 708 lines (38%) are
not.
  First few lines:
    • R/array2ade4.R#L9 ...
    • ...
    • vignettes/omicade4.Rnw#L98 plot(dend, horiz=TRUE) ...
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 16 NOTES
ℹ See the omicade4.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.