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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RankProd_3.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RankProd ─────────────────────────────────────────────────────────
✔ Package installed successfully
── RankProd session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd
→ BiocVersion: 3.24
→ Package: RankProd
→ PackageVersion: 3.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RankProd.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd
→ installDir: /tmp/RtmpgH3x6Y/file1075fa1725d758
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RankProd ───────────────────────────────────────────────
* 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 3.2.1 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/RtmpgH3x6Y/file1075fa536326e3/RankProd/man/Apples.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd/man/arab.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd/man/lymphoma.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd/man/plotRP.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd/man/RP.advance.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd/man/RP.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd/man/RPadvance.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd/man/RSadvance.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpgH3x6Y/file1075fa536326e3/RankProd/man/topGene.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...
ℹ NOTE: License 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • RankProd.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • RankProd.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/RankProd.Rnw
* Checking package installation calls in R code...
* Checking for library/require of RankProd...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/RankProducts_francesco_2.R (line 227, column 17)
    • ...
    • R/RankProducts_francesco_advance.R (line 395, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • computeOrirank.R (line 7, column 15)
    • ...
    • topGene.R (line 66, column 53)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/OriginxyCall.R (line 7, column 1)
    • ...
    • cat() in R/xyCall.R (line 29, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/computeOrirank.R (line 2, column 7)
    • ...
    • R/xyCall.R (line 9, column 11)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/OriginxyCall.R (line 40, column 6)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/RankProducts_francesco_advance.R (line 13, column 43)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/RankProducts_francesco_2.R (line 7, column 21)
  • set.seed() in R/RankProducts_francesco_advance.R (line 7, column 27)
* 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 6
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.1() (R/RankProducts_francesco_advance.R): 489 lines
    • ...
    • _anonymous_.1() (R/plotRP_2.R): 76 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/Apples.Rd
    • man/arab.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; 66 lines (2%) are > 80 characters long.
  First few lines:
    • R/rankprodbounds.R#L13 # rho a vector of integers correspon ...
    • ...
    • vignettes/RankProd.Rnw#L662 different laboratories. Specifically, we ...
ℹ NOTE: Consider 4 spaces instead of tabs; 13 lines (0%) contain tabs.
  First few lines:
    • R/OriginxyCall.R#L31 cl[which(cl == min(lev))] <- 0 ##small ...
    • ...
    • R/topGene.R#L71 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 236 lines (7%) are
not.
  First few lines:
    • R/plotRP_2.R#L62 cat("No genes found using t ...
    • ...
    • vignettes/RankProd.Rnw#L451 name sample ...
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 | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the RankProd.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.