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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('EBSeq_2.11.0.tar.gz','quit-with-status'=TRUE)"
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── Installing EBSeq ────────────────────────────────────────────────────────────
✔ Package installed successfully
── EBSeq session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpjT9Azi/file8645438d9a1ff/EBSeq
→ BiocVersion: 3.24
→ Package: EBSeq
→ PackageVersion: 2.11.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/EBSeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpjT9Azi/file8645438d9a1ff/EBSeq
→ installDir: /tmp/RtmpjT9Azi/file86454318b0a74
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EBSeq ──────────────────────────────────────────────────
* 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 3.0.0 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:
GeneExpression, DNASeq
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: 'Date:' field format is not 'YYYY-MM-DD': 2015-12-8
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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • EBSeq_Vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • EBSeq_Vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/EBSeq_Vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of EBSeq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/EBMultiTest.R (line 100, column 27)
    • ...
    • R/RankNorm.R (line 9, column 20)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • crit_fun.R (line 3, column 30)
    • ...
    • RankNorm.R (line 9, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/EBMultiTest.R (line 31, column 45)
    • cat() in R/EBTest.R (line 37, column 45)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/DenNHist.R (line 6, column 14)
    • ...
    • R/RankNorm.R (line 10, column 34)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/EBMultiTest.R (line 283, column 29)
    • ...
    • R/EBTest.R (line 597, column 25)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/EBSeqTest.R (line 58, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 94 times:
    • T in R/DenNHist.R (line 17, column 27)
    • ...
    • F in R/QQP.R (line 43, column 31)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/EBMultiTest.R (line 351, column 26)
  • suppressWarnings() in R/EBTest.R (line 583, column 30)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
  The longest 5 functions are:
    • EBTest() (R/EBTest.R): 723 lines
    • ...
    • EBSeqTest() (R/EBSeqTest.R): 77 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/GeneMat.Rd
    • ...
    • man/MultiGeneMat.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/LogN.Rd
    • man/LogNMulti.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • beta.mom.Rd
    • ...
    • LogNMulti.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; 370 lines (11%) are > 80 characters long.
  First few lines:
    • R/DenNHist.R#L4 if(!"Alpha"%in%names(EBOut))stop("The i ...
    • ...
    • vignettes/EBSeq_Vignette.Rnw#L1171 approximation by setting
    \verb+ApproxVal ...
ℹ NOTE: Consider 4 spaces instead of tabs; 406 lines (12%) contain tabs.
  First few lines:
    • R/beta.mom.R#L3 xbar<-mean(qs.in) ...
    • ...
    • vignettes/EBSeq_Vignette.Rnw#L1102 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 91 lines (3%) are not.
  First few lines:
    • R/EBMultiTest.R#L5 expect_is(sizeFactors, c("numeric","int ...
    • ...
    • vignettes/EBSeq_Vignette.Rnw#L709 PolyFitValue[[i]]=PolyFitPlot(IsoEBOut
    ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 21 NOTES
ℹ See the EBSeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.