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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Oscope_1.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Oscope ───────────────────────────────────────────────────────────
✔ Package installed successfully
── Oscope session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpO5SXVr/filefbd571549db16/Oscope
→ BiocVersion: 3.24
→ Package: Oscope
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Oscope.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpO5SXVr/filefbd571549db16/Oscope
→ installDir: /tmp/RtmpO5SXVr/filefbd572e9afaee
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Oscope ─────────────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: SingleCell,
Clustering, DifferentialExpression, MultipleComparison
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: 'Date:' field format is not 'YYYY-MM-DD': 2015-7-28
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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:
    • Oscope_vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Oscope_vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of Oscope...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/FlagCluster.R (line 40, column 14)
    • ...
    • R/SineFun.R (line 25, column 35)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • CalcMV.R (line 69, column 18)
    • ...
    • scanK.R (line 110, column 38)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/FlagCluster.R (line 61, column 9)
    • print() in R/FlagCluster.R (line 63, column 9)
    • print() in R/FlagCluster.R (line 80, column 1)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/FormatSineOut.R (line 42, column 24)
    • ...
    • R/scanK.R (line 82, column 19)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • SineOptim.R (line 17, column 22)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/FlagCluster.R (line 36, column 1)
* 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:
    • CalcMV() (R/CalcMV.R): 73 lines
    • scanK() (R/scanK.R): 73 lines
    • FlagCluster() (R/FlagCluster.R): 57 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; 305 lines (15%) are > 80 characters long.
  First few lines:
    • R/CalcMV.R#L2 #' @usage CalcMV(Data, Sizes=NULL, NormD ...
    • ...
    • vignettes/Oscope_vignette.Rnw#L360 Here is the output of sessionInfo on
    the ...
ℹ NOTE: Consider 4 spaces instead of tabs; 328 lines (16%) contain tabs.
  First few lines:
    • R/AbsCor.R#L11 MatCor <- cor(scale(t(DataIn))) ...
    • ...
    • man/OscopeExampleData.Rd#L12 GeneExampleData is a matrix with 600 ge ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 10 lines (0%) are not.
  First few lines:
    • R/FlagCluster.R#L67 #P[i] <- suppressWarnings(ks.test(Inpe ...
    • ...
    • man/SineOptim.Rd#L16 -2X_{g1,s}X_{g ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the Oscope.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.