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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('motifStack_1.57.0.tar.gz','quit-with-status'=TRUE)"
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── Installing motifStack ───────────────────────────────────────────────────────
✔ Package installed successfully
── motifStack session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp05AjYE/filee09cb4d4eb801/motifStack
→ BiocVersion: 3.24
→ Package: motifStack
→ PackageVersion: 1.57.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/motifStack.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp05AjYE/filee09cb4d4eb801/motifStack
→ installDir: /tmp/Rtmp05AjYE/filee09cb7d658449
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on motifStack ─────────────────────────────────────────────
* 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 2.15.1 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:
MultipleSequenceAlignment
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...
* 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 (15%).
* 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...
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/privateUtilities.R (line 30, column 5)
    • install.packages() in R/privateUtilities.R (line 72, column 5)
* Checking for library/require of motifStack...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/browseMotifs.R (line 52, column 10)
    • ...
    • R/reorderUPGMAtree.R (line 57, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AAmotifAlignment.R (line 53, column 12)
    • ...
    • publicUtilities.R (line 305, column 26)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getRankedUniqueMotifs.R (line 31, column 11)
    • ...
    • R/publicUtilities.R (line 252, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/motifCircos.R (line 141, column 18)
    • ...
    • R/plotMotifStackWithRadialPhylog.R (line 132, column 52)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/DNAmotifAlignment.R (line 42, column 13)
    • R/matalign.R (line 66, column 13)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/privateUtilities.R (line 67, column 28)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/motifStack_HTML.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 12 times)
  • <<- in R/browseMotifs.R (line 61, column 25)
  • ...
  • <<- in R/motifSignature.R (line 266, column 12)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times)
  • suppressWarnings() in R/plotAffinityLogo.R (line 126, column 5)
  • ...
  • suppressWarnings() in R/privateUtilities.R (line 1944, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 36
functions greater than 50 lines.
  The longest 5 functions are:
    • importSVG() (R/privateUtilities.R): 1484 lines
    • ...
    • motifSignature() (R/motifSignature.R): 307 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/browseMotifs-shiny.Rd
    • ...
    • man/pssm-class.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • browseMotifs-shiny.Rd
  • motifSig-class.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; 222 lines (2%) are > 80 characters long.
  First few lines:
    • R/alignmentByPCC.R#L1 alignmentByPCC <- function(motifs, minim ...
    • ...
    • vignettes/motifStack_HTML.Rmd#L399 df <- data.frame(xmin=c(.25, .25),
    ymin= ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
  First few lines:
    • R/importMatrix.R#L170 # 250.0 118.0 145.0 168.0 ...
    • ...
    • R/importMatrix.R#L176 # 281.0 91.0 113.0 196.0 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3865 lines (40%) are
not.
  First few lines:
    • R/AAmotifAlignment.R#L19 if(length(pcms)<2) stop("less than 2 m ...
    • ...
    • vignettes/motifStack_HTML.Rmd#L414 fontfamily=fontfamily, fo ...
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 | ⚠ 1 WARNINGS | ℹ 19 NOTES
ℹ See the motifStack.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.