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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ABSSeq_1.67.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ABSSeq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── ABSSeq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq
→ BiocVersion: 3.24
→ Package: ABSSeq
→ PackageVersion: 1.67.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ABSSeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq
→ installDir: /tmp/RtmpNnKWB3/file467ee64b5ac64
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ABSSeq ─────────────────────────────────────────────────
* 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 2.10 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq/man/ABSDataSet.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq/man/counts.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq/man/excounts.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq/man/LevelstoNormFC.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq/man/maxRates.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq/man/minimalDispersion.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq/man/minRates.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNnKWB3/file467ee15a32a10/ABSSeq/man/paired.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Normalization
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 (33%).
* 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:
    • ABSSeq.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • ABSSeq.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ABSSeq.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/ABSSeq.Rnw (chunk no. 18, line 148, column 19)
    • vignettes/ABSSeq.Rnw (chunk no. 18, line 158, column 32)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ABSSeq.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ABSSeq...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/functions.R (line 304, column 5)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • complexmodel.R (line 238, column 12)
    • ...
    • methods.R (line 520, column 15)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.R (line 33, column 9)
    • ...
    • R/Plotfuns.R (line 24, column 16)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/methods.R (line 30, column 24)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 9 times:
    • F in R/complexmodel.R (line 53, column 48)
    • ...
    • F in R/functions.R (line 1130, column 102)
* 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 9
functions greater than 50 lines.
  The longest 5 functions are:
    • genAFold() (R/functions.R): 187 lines
    • ...
    • callParameterwithoutReplicates() (R/functions.R): 126 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/counts.Rd
    • ...
    • man/sFactors.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; 258 lines (10%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L1 setClass("SumInfo",representation(begins ...
    • ...
    • vignettes/ABSSeq.Rnw#L229 \bibitem{deseq} Anders S, Huber W \texts ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 996 lines (38%) are
not.
  First few lines:
    • R/AllClasses.R#L3 function(x, i,j,..., value) { ...
    • ...
    • vignettes/ABSSeq.Rnw#L77 obj=callParameter(obj) ...
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 | ⚠ 5 WARNINGS | ℹ 14 NOTES
ℹ See the ABSSeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.