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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ddPCRclust_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ddPCRclust ───────────────────────────────────────────────────────
✔ Package installed successfully
── ddPCRclust session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp83JbYb/file7e5692e5ffd77/ddPCRclust
→ BiocVersion: 3.24
→ Package: ddPCRclust
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ddPCRclust.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp83JbYb/file7e5692e5ffd77/ddPCRclust
→ installDir: /tmp/Rtmp83JbYb/file7e56973a7e60d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ddPCRclust ─────────────────────────────────────────────
* 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 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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (40%).
* 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:
    • ddPCRclust.Rnw
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • utils
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ddPCRclust.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ddPCRclust.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ddPCRclust...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/ddPCRclust.R (line 449, column 73)
    • ...
    • print() in R/ddPCRclust.R (line 483, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cluster_functions.R (line 1128, column 41)
    • ...
    • R/functions.R (line 30, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/cluster_functions.R (line 343, column 29)
    • ...
    • R/ddPCRclust.R (line 1313, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/cluster_functions.R (line 343, column 36)
    • R/cluster_functions.R (line 363, column 36)
* 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 13
functions greater than 50 lines.
  The longest 5 functions are:
    • assignRain() (R/cluster_functions.R): 403 lines
    • ...
    • findPrimaryClusters() (R/cluster_functions.R): 205 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; 638 lines (18%) are > 80 characters long.
  First few lines:
    • R/cluster_functions.R#L24 leftPrim <- deGate(f_remNeg_temp ...
    • ...
    • vignettes/ddPCRclust.Rnw#L227 https://bibiserv.cebitec.uni-bielefeld.d
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 419 lines (12%) are
not.
  First few lines:
    • R/cluster_functions.R#L31 f_leftPrim)[,1], width = 1000) ...
    • ...
    • vignettes/ddPCRclust.Rnw#L123 ggtitle('B01 example')+theme_bw() + ...
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 14 NOTES
ℹ See the ddPCRclust.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.