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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scDD_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scDD ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── scDD session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUcdZCi/file12a5e94cd7d4c/scDD
→ BiocVersion: 3.24
→ Package: scDD
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scDD.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUcdZCi/file12a5e94cd7d4c/scDD
→ installDir: /tmp/RtmpUcdZCi/file12a5e97ba7142e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scDD ───────────────────────────────────────────────────
* 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 3.5.0 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...
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (43%).
* 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:
    • scDD.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • scDD.Rnw
* Checking package installation calls in R code...
* Checking for library/require of scDD...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/classify.dd.R (line 98, column 13)
    • ...
    • R/Single_Cell_Simu.R (line 199, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • classify.dd.R (line 25, column 13)
    • ...
    • Single_Cell_Simu.R (line 247, column 6)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat in R/classify.dd.R (line 105, column 5)
    • ...
    • cat in R/classify.dd.R (line 381, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/classify.dd.R (line 266, column 6)
    • ...
    • R/Validation.R (line 33, column 12)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/Find_FC.R (line 79, column 25)
    • ...
    • R/Simulate_set.R (line 274, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/Preprocess.R (line 108, column 10)
    • ...
    • R/Single_Cell_Simu.R (line 209, column 8)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/Simulate_set.R (line 149, column 1)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 10 times)
  • suppressWarnings() in R/classify.dd.R (line 268, column 13)
  • ...
  • suppressWarnings() in R/Test_KS.R (line 64, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • scDD() (R/scDD.R): 386 lines
    • ...
    • simuDP() (R/SimuDP.R): 186 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; 20 lines (0%) are > 80 characters long.
  First few lines:
    • R/scDD.R#L65 #' is below `level`, then the gene is ca ...
    • ...
    • vignettes/scDD.Rnw#L497 Now, apply the \Rfunction{preprocess} fu ...
ℹ NOTE: Consider 4 spaces instead of tabs; 14 lines (0%) contain tabs.
  First few lines:
    • R/classify.dd.R#L126 } ...
    • ...
    • R/Single_Cell_Simu.R#L257 Simulated_Data <- desim[[1]] ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1437 lines (30%) are
not.
  First few lines:
    • R/classify.dd.R#L20 ...
    • ...
    • vignettes/scDD.Rnw#L588 title.gene=rownames(scDatExSi ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the scDD.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.