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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DECIPHER_3.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DECIPHER ─────────────────────────────────────────────────────────
✔ Package installed successfully
── DECIPHER session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpw4QA4g/file7e941314428f4/DECIPHER
→ BiocVersion: 3.24
→ Package: DECIPHER
→ PackageVersion: 3.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DECIPHER.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpw4QA4g/file7e941314428f4/DECIPHER
→ installDir: /tmp/Rtmpw4QA4g/file7e9411d66ca8c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DECIPHER ───────────────────────────────────────────────
* 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 3.5.0 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:
Classification, SequenceMatching
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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (57%).
* 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:
    • ArtOfAlignmentInR.Rnw
    • ...
    • SearchForResearch.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • DesignSignatures.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ArtOfAlignmentInR.Rnw
    • ...
    • SearchForResearch.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/DECIPHERing.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DECIPHER...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AlignSeqs.R (line 771, column 44)
    • ...
    • R/Zipline.R (line 31, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AlignDB.R (line 170, column 19)
    • ...
    • Treeline.R (line 3663, column 50)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Add2DB.R (line 50, column 25)
    • ...
    • print() in R/Zipline.R (line 321, column 33)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AlignDB.R (line 237, column 30)
    • ...
    • R/Treeline.R (line 1869, column 30)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/TrimDNA.R (line 73, column 22)
    • R/TrimDNA.R (line 75, column 22)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Genes-class.R (line 2, column 25)
    • ...
    • Taxa-class.R (line 661, column 31)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/CalculateEfficiencyFISH.R (line 139, column 53)
    • ...
    • system() in R/DesignProbes.R (line 766, column 20)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 70 times)
  • <<- in R/AlignSeqs.R (line 508, column 54)
  • ...
  • <<- in R/Treeline.R (line 2973, column 51)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 29 times)
  • suppressWarnings() in R/AlignSeqs.R (line 474, column 17)
  • ...
  • suppressWarnings() in R/Taxa-class.R (line 613, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 111
functions greater than 50 lines.
  The longest 5 functions are:
    • Treeline() (R/Treeline.R): 2157 lines
    • ...
    • FindSynteny() (R/FindSynteny.R): 1463 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/NonCodingRNA.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/AA_REDUCED.Rd
    • ...
    • man/Taxa-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 10% of man
pages use at least one of these tags.
  Found in files:
    • AmplifyDNA.Rd
    • ...
    • PredictDBN.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • AmplifyDNA.Rd
    • ...
    • PredictDBN.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; 2301 lines (5%) are > 80 characters long.
  First few lines:
    • R/AA_REDUCED.R#L1 AA_REDUCED <- list(c("A", "C", "D", "E", ...
    • ...
    • vignettes/SearchForResearch.Rnw#L453 \newblock {Bioinformatics}, 40(12),
    btae ...
ℹ NOTE: Consider 4 spaces instead of tabs; 34528 lines (71%) contain tabs.
  First few lines:
    • R/AA_REDUCED.R#L2 c("AG", "C", "DE", "FY", "H", "ILMV", " ...
    • ...
    • vignettes/SearchForResearch.Rnw#L385 processors=1) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1553 lines (3%) are
not.
  First few lines:
    • man/Add2DB.Rd#L11 dbFile, ...
    • ...
    • vignettes/SearchForResearch.Rnw#L432 \hline ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 23 NOTES
ℹ See the DECIPHER.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.