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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('r3Cseq_1.59.0.tar.gz','quit-with-status'=TRUE)"
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── Installing r3Cseq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── r3Cseq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq
→ BiocVersion: 3.24
→ Package: r3Cseq
→ PackageVersion: 1.59.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/r3Cseq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq
→ installDir: /tmp/Rtmp5Xuq2f/file106d673311f5ae
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on r3Cseq ─────────────────────────────────────────────────
* 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/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/contrCoverage.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/enzymeDb.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/expCoverage.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/getCoverage.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/hg18refGene.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/hg19refGene.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/mm10refGene.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/mm9refGene.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/Myb_prom_FB.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/Myb_prom_FL.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/plot3Cecdf.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5Xuq2f/file106d67114b9bbc/r3Cseq/man/rn5refGene.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: LongRead,
Coverage, Alignment, Normalization, QualityControl, DataImport
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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (58%).
* 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...
ℹ NOTE: Potential intermediate files found:
  • vignettes/r3cseq.html
  • vignettes/r3cseq.html
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • r3Cseq.Rnw
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/r3Cseq.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • knitr
* Checking package installation calls in R code...
* Checking for library/require of r3Cseq...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/FunctionInCommon.R (line 36, column 17)
    • ...
    • library() in R/RestrictionEnzymeFunctions.R (line 120, column 25)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • FunctionInCommon.R (line 777, column 37)
    • ...
    • Visualize3Cseq.R (line 1428, column 74)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/FunctionInCommon.R (line 924, column 9)
    • ...
    • print() in R/Report.R (line 69, column 33)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/FunctionInCommon.R (line 406, column 52)
    • ...
    • R/Visualize3Cseq.R (line 1467, column 40)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/FunctionInCommon.R (line 43, column 30)
    • ...
    • R/FunctionsForNoReplicationAnalysis.R (line 85, column 54)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 31 times:
    • T in R/Annotation.R (line 33, column 70)
    • ...
    • T in R/Visualize3Cseq.R (line 1469, column 59)
* 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 22
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.1075() (R/Visualize3Cseq.R): 404 lines
    • ...
    • plotInteractionsPerChromosome() (R/Visualize3Cseq.R): 332 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/calculateBatchRPM.Rd
    • ...
    • man/rn5refGene.Rd
No methods found in package ‘Biostrings’ for request: ‘DNAString’ when loading ‘r3Cseq’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calculateBatchRPM.Rd
    • ...
    • plotOverviewInteractions.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; 778 lines (10%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L36 return( "This version of r3Cseq supp ...
    • ...
    • vignettes/r3Cseq.Rnw#L339 \Rfunction{getExpInteractionsInRefseq} a ...
ℹ NOTE: Consider 4 spaces instead of tabs; 5015 lines (67%) contain tabs.
  First few lines:
    • R/AllClasses.R#L2 Class="r3CseqCommon", ...
    • ...
    • vignettes/r3Cseq.Rnw#L359 #generate3CseqReport(my3Cseq.obj) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 231 lines (3%) are
not.
  First few lines:
    • man/calculateBatchRPM.Rd#L7 Normalize 3C-Seq data by transforming ...
    • ...
    • man/r3CseqInBatch-class.Rd#L98 \link{r3CseqInBatch} ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 14 NOTES
ℹ See the r3Cseq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.