##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BBCAnalyzer_1.43.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing BBCAnalyzer ──────────────────────────────────────────────────────
✔ Package installed successfully
── BBCAnalyzer session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpb4vnCk/file59c89176d32c9/BBCAnalyzer
→ BiocVersion: 3.24
→ Package: BBCAnalyzer
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BBCAnalyzer.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpb4vnCk/file59c89176d32c9/BBCAnalyzer
→ installDir: /tmp/Rtmpb4vnCk/file59c8964b71120
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BBCAnalyzer ────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpb4vnCk/file59c89176d32c9/BBCAnalyzer/vignettes/BBCAnalyzer.Rnw'
ℹ NOTE: Consider adding these automatically suggested biocViews: WholeGenome,
MultipleSequenceAlignment, 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: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (86%).
* 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:
    • BBCAnalyzer.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • BBCAnalyzer.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • BBCAnalyzer.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/BBCAnalyzer.Rnw
* Checking package installation calls in R code...
* Checking for library/require of BBCAnalyzer...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • BBCAnalyzer.R (line 3, column 18)
    • ...
    • report.R (line 286, column 34)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/determineTarget_analyzeReads.R (line 123, column 46)
    • ...
    • R/plot.R (line 3434, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/BBCAnalyzer.R (line 6, column 25)
    • ...
    • R/BBCAnalyzer.R (line 43, column 38)
* 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 33
functions greater than 50 lines.
  The longest 5 functions are:
    • plotCountsPerTargetVcf_plot() (R/plot.R): 346 lines
    • ...
    • plotCountsPerSampleRelativeVcf_plot() (R/plot.R): 286 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 67% of man
pages use at least one of these tags.
  Found in files:
    • analyzeBases.Rd
    • BBCAnalyzer-package.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; 649 lines (12%) are > 80 characters long.
  First few lines:
    • R/BBCAnalyzer.R#L4 if(file.exists(paste(bam_inp ...
    • ...
    • vignettes/BBCAnalyzer.Rnw#L370 \caption{Output file Example\_IonTorrent
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • vignettes/BBCAnalyzer.Rnw#L332 4 106157698 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1113 lines (21%) are
not.
  First few lines:
    • R/BBCAnalyzer.R#L20 !=sample_names[i,1]){ ...
    • ...
    • man/BBCAnalyzer-package.Rd#L57 ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the BBCAnalyzer.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.