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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Anaquin_2.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Anaquin ──────────────────────────────────────────────────────────
✔ Package installed successfully
── Anaquin session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpX7Y01H/file53df972285e47/Anaquin
→ BiocVersion: 3.24
→ Package: Anaquin
→ PackageVersion: 2.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Anaquin.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpX7Y01H/file53df972285e47/Anaquin
→ installDir: /tmp/RtmpX7Y01H/file53df96931e808
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Anaquin ────────────────────────────────────────────────
* 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 3.3 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/RtmpX7Y01H/file53df972285e47/Anaquin/man/plotConjoint.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX7Y01H/file53df972285e47/Anaquin/man/plotLinear.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX7Y01H/file53df972285e47/Anaquin/man/plotLOD.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX7Y01H/file53df972285e47/Anaquin/man/plotLogistic.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX7Y01H/file53df972285e47/Anaquin/man/plotROC.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX7Y01H/file53df972285e47/Anaquin/man/RnaQuinGeneMixture.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX7Y01H/file53df972285e47/Anaquin/man/RnaQuinIsoformMixture.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX7Y01H/file53df972285e47/Anaquin/man/UserGuideData_5.4.5.1.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX7Y01H/file53df972285e47/Anaquin/man/UserGuideData_5.4.6.3.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX7Y01H/file53df972285e47/Anaquin/man/UserGuideData_5.6.3.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (18%).
* 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: Vignette(s) found with missing chunk labels
  Found in files:
    • Anaquin.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Anaquin.Rmd
* Checking package installation calls in R code...
* Checking for library/require of Anaquin...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • plotLinear.R (line 65, column 19)
    • plotROC.R (line 39, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/LOQ.R (line 151, column 9)
    • ...
    • print() in R/plotROC.R (line 98, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/plotLogistic.R (line 23, column 12)
    • R/plotLogistic.R (line 25, column 17)
    • R/plotROC.R (line 82, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/plotLogistic.R (line 65, column 22)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 11 times)
  • <<- in R/LOQ.R (line 110, column 16)
  • ...
  • <<- in R/plotLogistic.R (line 36, column 17)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/plotConjoint.R (line 31, column 5)
  • suppressWarnings() in R/plotLinear.R (line 233, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
  The longest 5 functions are:
    • plotLinear() (R/plotLinear.R): 232 lines
    • ...
    • .plotLODR() (R/plotLOD.R): 83 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • plotConjoint.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; 11 lines (1%) are > 80 characters long.
  First few lines:
    • R/LOQ.R#L46 data <- data[data$perc < 0.40 | (dat ...
    • ...
    • vignettes/Anaquin.Rmd#L314 plotLOD(mean, pval, abs(ratio), qval=qva ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 196 lines (11%) are
not.
  First few lines:
    • R/graphics.R#L8 list(a = format(co ...
    • ...
    • vignettes/Anaquin.Rmd#L266 showLOQ=FALSE) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 17 NOTES
ℹ See the Anaquin.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.