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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ChIPanalyser_1.35.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ChIPanalyser ─────────────────────────────────────────────────────
✔ Package installed successfully
── ChIPanalyser session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZuk5ox/file658c4a19e9ba/ChIPanalyser
→ BiocVersion: 3.24
→ Package: ChIPanalyser
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ChIPanalyser.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZuk5ox/file658c4a19e9ba/ChIPanalyser
→ installDir: /tmp/RtmpZuk5ox/file658c451a9b0b0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ChIPanalyser ───────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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...
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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (41%).
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ChIPanalyser.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/ChIPanalyser.Rmd (chunk no. 8, line 207, column 33)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/GA_ChIPanalyser.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ChIPanalyser...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllShowMethods.R (line 99, column 64)
    • ...
    • R/plotOccupancy.R (line 66, column 32)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllShowMethods.R (line 16, column 38)
    • ...
    • plotOptimalHeatMapDev.R (line 146, column 35)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • GenomicProfileGenericFunctions.R (line 382, column 22)
    • GenomicProfileGenericFunctions.R (line 384, column 45)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/computeChIPProfile.R (line 67, column 7)
    • cat() in R/computeOccupancy.R (line 51, column 7)
    • cat() in R/profileAccuracyEstimateDev.R (line 33, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/DataPreprocessingGenericFunctionsDev.R (line 68, column 80)
    • ...
    • R/GenomicProfileGenericFunctions.R (line 346, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/computeChIPProfile.R (line 26, column 14)
    • ...
    • R/profileAccuracyEstimateDev.R (line 21, column 12)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/2AllS4Class_ProfileParameters.R (line 177, column 17)
    • R/2AllS4Class_ProfileParameters.R (line 181, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 68 times:
    • F in R/DataPreprocessingGenericFunctionsDev.R (line 121, column 62)
    • ...
    • F in R/plotOptimalHeatMapDev.R (line 153, column 47)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • 2AllS4Class_ProfileParameters.R (line 132, column 38)
    • ...
    • profileAccuracyEstimateDev.R (line 19, column 26)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/DataPreprocessingDev.R (line 148, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 26
functions greater than 50 lines.
  The longest 5 functions are:
    • definition() (R/AllInitialize.R): 266 lines
    • ...
    • computeGenomeWideScores() (R/computeGenomeWide.R): 145 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/averageExpPWMScore-methods.Rd
  • ...
  • man/whichstrand-methods.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/averageExpPWMScore-methods.Rd
    • ...
    • man/whichstrand-methods.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • computeGenomeWideScores.Rd
  • profiles-methods.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 10% of man
pages use at least one of these tags.
  Found in files:
    • BPFrequency_-.Rd
    • ...
    • searchSites.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 410 lines (6%) are > 80 characters long.
  First few lines:
    • R/2AllS4Class_ProfileParameters.R#L43 if(all(object@PFMFormat %in%
    c("raw" ...
    • ...
    • vignettes/GA_ChIPanalyser.Rmd#L282 ```{r plotOccup, eval = TRUE, echo =
    TRU ...
ℹ NOTE: Consider 4 spaces instead of tabs; 40 lines (1%) contain tabs.
  First few lines:
    • R/computeChIPProfile.R#L75 names(loci)<-paste0(seqnames(loci), ...
    • ...
    • R/parallelInternalFunctionsDev.R#L72 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1206 lines (17%) are
not.
  First few lines:
    • R/2AllS4Class_ProfileParameters.R#L171 contains="parameterOptions", ...
    • ...
    • vignettes/ChIPanalyser.Rmd#L449 geneRef=geneRef) ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 22 NOTES
ℹ See the ChIPanalyser.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.