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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('pepStat_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing pepStat ──────────────────────────────────────────────────────────
✔ Package installed successfully
── pepStat session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpqHlQQA/filefe5cd68865e6a/pepStat
→ BiocVersion: 3.24
→ Package: pepStat
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/pepStat.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpqHlQQA/filefe5cd68865e6a/pepStat
→ installDir: /tmp/RtmpqHlQQA/filefe5cd75ab4dbd
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on pepStat ────────────────────────────────────────────────
* 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...
* 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 (40%).
* 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:
    • pepStat.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • pepStat.Rnw
* Checking package installation calls in R code...
* Checking for library/require of pepStat...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllMethods.R (line 268, column 18)
    • ...
    • R/summarizePeptides.R (line 58, column 41)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllMethods.R (line 249, column 14)
    • ...
    • slidingMean.R (line 56, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllMethods.R (line 120, column 7)
    • ...
    • cat() in R/slidingMean.R (line 92, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/internal.R (line 64, column 12)
    • ...
    • R/summarizePeptides.R (line 118, column 29)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/create_db.R (line 51, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/summarizePeptides.R (line 40, column 34)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • create_db.R (line 53, column 28)
    • ...
    • summarizePeptides.R (line 116, column 24)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • makePeptideSet() (R/makePeptideSet.R): 159 lines
    • ...
    • create_db() (R/create_db.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/create_db.Rd
    • ...
    • man/shinyPepStat.Rd
No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’
No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’
Warning: no function found corresponding to methods exports from ‘pepStat’ for: ‘values’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • peptideSet-methods.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; 153 lines (5%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L3 #' This class gathers all information fr ...
    • ...
    • vignettes/pepStat.Rnw#L260 to easily identify binding peaks. It giv ...
ℹ NOTE: Consider 4 spaces instead of tabs; 149 lines (5%) contain tabs.
  First few lines:
    • R/AllMethods.R#L110 ExpressionSet(assayData(from) ...
    • ...
    • R/summarizePeptides.R#L115 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 621 lines (21%) are
not.
  First few lines:
    • R/AllClasses.R#L32 contains=c("ExpressionSet"), ...
    • ...
    • vignettes/pepStat.Rnw#L234 cutoff = .1, method ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the pepStat.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.