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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('LOBSTAHS_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing LOBSTAHS ─────────────────────────────────────────────────────────
✔ Package installed successfully
── LOBSTAHS session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpF4D8n4/filec991d31ed322e/LOBSTAHS
→ BiocVersion: 3.24
→ Package: LOBSTAHS
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/LOBSTAHS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpF4D8n4/filec991d31ed322e/LOBSTAHS
→ installDir: /tmp/RtmpF4D8n4/filec991d28649b9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on LOBSTAHS ───────────────────────────────────────────────
* 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 3.4 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/RtmpF4D8n4/filec991d31ed322e/LOBSTAHS/man/LOBSet-class.Rd'
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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: Evaluate more vignette chunks.
ℹ 15 out of 16 code chunks = 93% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • LOBSTAHS.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/LOBSTAHS.Rmd
* Checking package installation calls in R code...
* Checking for library/require of LOBSTAHS...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/doLOBscreen.R (line 633, column 70)
    • ...
    • R/generateLOBdbase.R (line 322, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • doLOBscreen.R (line 292, column 14)
    • ...
    • LOBdbase.R (line 275, column 22)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/doLOBscreen.R (line 12, column 3)
    • ...
    • cat() in R/generateLOBdbase.R (line 696, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/doLOBscreen.R (line 6, column 13)
    • ...
    • R/LOBSet.R (line 330, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/doLOBscreen.R (line 702, column 15)
    • ...
    • R/doLOBscreen.R (line 2074, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/doLOBscreen.R (line 2030, column 25)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • doLOBscreen.R (line 19, column 18)
    • ...
    • LOBSet.R (line 174, column 34)
* 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 13
functions greater than 50 lines.
  The longest 5 functions are:
    • screenPSpectrum() (R/doLOBscreen.R): 875 lines
    • ...
    • getLOBpeaklist() (R/doLOBscreen.R): 177 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • generateLOBdbase.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
  Found in files:
    • doLOBscreen.Rd
    • generateLOBdbase.Rd
* Checking package NEWS...
* 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; 142 lines (2%) are > 80 characters long.
  First few lines:
    • R/doLOBscreen.R#L6 doLOBscreen = function(xsA, polarity = N ...
    • ...
    • vignettes/LOBSTAHS.Rmd#L520 1. <span id="note8">See A. Pearson, 2014 ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • man/LOBdbase-class.Rd#L168 } ...
    • man/LOBSet-class.Rd#L89 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2875 lines (46%) are
not.
  First few lines:
    • R/doLOBscreen.R#L7 rt.restrict = TR ...
    • ...
    • vignettes/LOBSTAHS.Rmd#L416 retain.unid ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 20 NOTES
ℹ See the LOBSTAHS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.