##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('dagLogo_1.51.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing dagLogo ──────────────────────────────────────────────────────────
✔ Package installed successfully
── dagLogo session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpjw1toM/file7d8597e8719fb/dagLogo
→ BiocVersion: 3.24
→ Package: dagLogo
→ PackageVersion: 1.51.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/dagLogo.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpjw1toM/file7d8597e8719fb/dagLogo
→ installDir: /tmp/Rtmpjw1toM/file7d8596cab55a0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on dagLogo ────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.0.1 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: KEGG
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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • dagLogo.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/dagLogo.Rmd (chunk no. 7, line 155, column 34)
* Checking package installation calls in R code...
* Checking for library/require of dagLogo...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/dagLogo.R (line 251, column 26)
    • ...
    • R/fetchSequence.R (line 218, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dagLogo.R (line 533, column 50)
    • ...
    • testDAU.R (line 333, column 29)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/prepareProteomeByFTP.R (line 79, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/dagLogo.R (line 420, column 18)
    • R/dagLogo.R (line 423, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/prepareProteomeByFTP.R (line 100, column 13)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • buildBackgroundModel.R (line 157, column 50)
    • ...
    • testDAU.R (line 153, column 56)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/buildBackgroundModel.R (line 50, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/dagLogo.Rd
ℹ Found @ in man/ecoli.proteome.Rd
ℹ Found @ in man/fetchSequence.Rd
ℹ Found @ in man/proteome.example.Rd
ℹ Found @ in man/seq.example.Rd
ℹ Found @ in vignettes/dagLogo.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
  The longest 5 functions are:
    • dagLogo() (R/dagLogo.R): 327 lines
    • ...
    • prepareProteomeByFTP() (R/prepareProteomeByFTP.R): 120 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • availableSchemes.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • prepareProteomeByFTP.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • prepareProteomeByFTP.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 154 lines (5%) are > 80 characters long.
  First few lines:
    • R/allclass.R#L7 #' \code{new("dagPeptides", data, pepti ...
    • ...
    • vignettes/dagLogo.Rmd#L230 We can use a heatmap or logo to display ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 809 lines (24%) are
not.
  First few lines:
    • R/allclass.R#L119 representation(background = "li ...
    • ...
    • vignettes/dagLogo.Rmd#L226 groupingScheme = "custom_g ...
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 | ⚠ 3 WARNINGS | ℹ 19 NOTES
ℹ See the dagLogo.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.