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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MethTargetedNGS_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MethTargetedNGS ──────────────────────────────────────────────────
✔ Package installed successfully
── MethTargetedNGS session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpI0Wc77/filed59934933e269/MethTargetedNGS
→ BiocVersion: 3.24
→ Package: MethTargetedNGS
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MethTargetedNGS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpI0Wc77/filed59934933e269/MethTargetedNGS
→ installDir: /tmp/RtmpI0Wc77/filed599319c3ac7f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MethTargetedNGS ────────────────────────────────────────
* 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 3.1.2 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/RtmpI0Wc77/filed59934933e269/MethTargetedNGS/man/bconv.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpI0Wc77/filed59934933e269/MethTargetedNGS/man/compare_samples.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpI0Wc77/filed59934933e269/MethTargetedNGS/man/methEntropy.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpI0Wc77/filed59934933e269/MethTargetedNGS/man/methHeatmap.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpI0Wc77/filed59934933e269/MethTargetedNGS/man/odd_ratio.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpI0Wc77/filed59934933e269/MethTargetedNGS/vignettes/MethTargetedNGS.Rnw'
* 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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (25%).
* 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:
    • MethTargetedNGS.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • MethTargetedNGS.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/MethTargetedNGS.Rnw
* Checking package installation calls in R code...
* Checking for library/require of MethTargetedNGS...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bisulfiteConversion.R (line 4, column 13)
    • ...
    • sequenceAlignment.R (line 139, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/hmmer.R (line 5, column 5)
    • ...
    • print() in R/sequenceAlignment.R (line 107, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bisulfiteConversion.R (line 18, column 16)
    • ...
    • R/sequenceAlignment.R (line 148, column 17)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/hmmer.R (line 8, column 5)
    • system() in R/hmmer.R (line 20, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/sequenceAlignment.R (line 58, column 3)
* Checking function lengths...
* Checking man page documentation...
* 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; 84 lines (9%) are > 80 characters long.
  First few lines:
    • R/bisulfiteConversion.R#L19 write.fasta(final_seq,names(ref_se ...
    • ...
    • vignettes/MethTargetedNGS.Rnw#L149 \newblock Journal of the Royal
    Statistic ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 182 lines (20%) are
not.
  First few lines:
    • R/bisulfiteConversion.R#L3 ref_seq <- read.fasta(fasta_file,as.st ...
    • ...
    • vignettes/MethTargetedNGS.Rnw#L67 average = N_C/(N_C + N_T) ...
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 | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the MethTargetedNGS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.