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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('mogsa_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing mogsa ────────────────────────────────────────────────────────────
✔ Package installed successfully
── mogsa session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpxOLV0M/fileddb397954e3b2/mogsa
→ BiocVersion: 3.24
→ Package: mogsa
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/mogsa.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpxOLV0M/fileddb397954e3b2/mogsa
→ installDir: /tmp/RtmpxOLV0M/fileddb39378c3038
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mogsa ──────────────────────────────────────────────────
* 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 3.4.0 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/RtmpxOLV0M/fileddb397954e3b2/mogsa/man/biSoftK.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpxOLV0M/fileddb397954e3b2/mogsa/man/bootMoa.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpxOLV0M/fileddb397954e3b2/mogsa/man/moa.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpxOLV0M/fileddb397954e3b2/mogsa/man/nipalsSoftK.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpxOLV0M/fileddb397954e3b2/mogsa/man/softK.Rd'
* 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 (33%).
* 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:
    • moCluster-knitr.Rnw
    • mogsa-knitr.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • moCluster-knitr.Rnw
    • mogsa-knitr.Rnw
* Checking package installation calls in R code...
* Checking for library/require of mogsa...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllMethods.R (line 114, column 13)
    • ...
    • R/toMoa.R (line 9, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllMethods.R (line 70, column 15)
    • ...
    • toMoa.R (line 20, column 36)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/biSoftK.R (line 36, column 7)
    • ...
    • cat() in R/sup.moa.R (line 78, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllMethods.R (line 117, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/bootMoa.R (line 23, column 17)
    • R/bootMoa.R (line 26, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • bootMoa.R (line 22, column 20)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/preGeneSet.R (line 19, column 5)
  • suppressMessages() in R/preGeneSet.R (line 36, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
  The longest 5 functions are:
    • biSoftK() (R/biSoftK.R): 102 lines
    • ...
    • moa() (R/moa.R): 77 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/moa-class.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plot-methods.Rd
    • ...
    • man/summary-methods.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • bootMbpca.Rd
  • ...
  • summary-methods.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; 421 lines (8%) are > 80 characters long.
  First few lines:
    • R/AllMethods.R#L9 # tol=1e-5 - the tolerance of eige ...
    • ...
    • vignettes/mogsa-knitr.Rnw#L294 inputs, first is the multiple omics data
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 165 lines (3%) contain tabs.
  First few lines:
    • R/pairwise.rv.R#L2 if (match %in% "row") ...
    • ...
    • man/summary-methods.Rd#L17 summary "moa" class ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1879 lines (34%) are
not.
  First few lines:
    • R/AllClasses.R#L2 slots = c("eig","tau", "partial ...
    • ...
    • vignettes/mogsa-knitr.Rnw#L302 proc.row = "center_ssq1", ...
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 | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the mogsa.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.