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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('casper_2.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing casper ───────────────────────────────────────────────────────────
✔ Package installed successfully
── casper session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpXd0Qws/file6182e7200f49a/casper
→ BiocVersion: 3.24
→ Package: casper
→ PackageVersion: 2.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/casper.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpXd0Qws/file6182e7200f49a/casper
→ installDir: /tmp/RtmpXd0Qws/file6182e634ef84d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on casper ─────────────────────────────────────────────────
* 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 3.6.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: DenovoGenome,
AlternativeSplicing, Coverage, VariantAnnotation
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...
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 (65%).
* 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:
    • casper.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • casper.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • casper.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/casper.Rnw
* Checking package installation calls in R code...
* Checking for library/require of casper...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/calcDenovo.R (line 5, column 1)
    • ...
    • require() in R/procGenome.R (line 1, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/calcDenovo.R (line 49, column 11)
    • ...
    • R/wrapKnown.R (line 191, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • asymmetryCheck.R (line 42, column 19)
    • ...
    • wrapKnown.R (line 188, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/calcDenovo.R (line 103, column 16)
    • ...
    • cat() in R/wrapKnown.R (line 129, column 16)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/calcExp.R (line 91, column 43)
    • ...
    • R/wrapKnown.R (line 176, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/probNonEquiv.R (line 25, column 40)
    • R/probNonEquiv.R (line 94, column 40)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/checks.R (line 17, column 27)
    • R/makeTranscriptDbFromGFF.R (line 245, column 15)
    • R/simPost.R (line 35, column 28)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 31 times:
    • T in R/calcExp.R (line 9, column 41)
    • ...
    • F in R/wrapKnown.R (line 6, column 74)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • ClassDefinitions.R (line 10, column 56)
    • ClassDefinitions.R (line 11, column 55)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/casperVignettes.R (line 7, column 8)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/simReads.Rd
ℹ Found @ in vignettes/casper.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11 times)
  • suppressWarnings() in R/getDistrs.R (line 187, column 11)
  • ...
  • suppressWarnings() in R/wrapKnown.R (line 195, column 21)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 31
functions greater than 50 lines.
  The longest 5 functions are:
    • getNBinomParams() (R/modelPrior.R): 229 lines
    • ...
    • assignExons2GeneF() (R/createDenovoGenome.R): 122 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/getNreads.Rd
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/simMAE.Rd
    • man/simMAEcheck.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plot-methods.Rd
    • ...
    • man/subsetGenome.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calcDenovo.Rd
    • ...
    • wrapKnown.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 1191 lines (12%) are > 80 characters long.
  First few lines:
    • R/asymmetryCheck.R#L2 setMethod("asymmetryCheck", signature(x= ...
    • ...
    • vignettes/casper.Rnw#L669 %fit1 <- calcDenovo(distrs=distrs, genom ...
ℹ NOTE: Consider 4 spaces instead of tabs; 23 lines (0%) contain tabs.
  First few lines:
    • R/procBam.R#L56 uniquifyQname<-function(bam, seed=1){ ...
    • ...
    • man/txLength-methods.Rd#L45 genome \code{genomeDB}. ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4049 lines (40%) are
not.
  First few lines:
    • R/asymmetryCheck.R#L5 m <- rowMeans(x); s <- rowSD(x) ...
    • ...
    • vignettes/casper.Rnw#L480 r_{gi}= 10^9 \frac{ \hat{\pi}_{gi} n_g ...
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 | ⚠ 6 WARNINGS | ℹ 24 NOTES
ℹ See the casper.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.