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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CAMERA_1.69.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CAMERA ───────────────────────────────────────────────────────────
✔ Package installed successfully
── CAMERA session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp18tHP6/file610b073436b15/CAMERA
→ BiocVersion: 3.24
→ Package: CAMERA
→ PackageVersion: 1.69.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CAMERA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp18tHP6/file610b073436b15/CAMERA
→ installDir: /tmp/Rtmp18tHP6/file610b01877b477
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CAMERA ─────────────────────────────────────────────────
* 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 3.5.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/calcCaS-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/calcCiS-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/cleanParallel.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/findAdducts-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/findKendrickMasses.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/findNeutralLoss.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/findNeutralLossSpecs.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/getAllPeakEICs-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/getpspectra.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/groupDen-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp18tHP6/file610b073436b15/CAMERA/man/psDist-methods.Rd'
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (23%).
* 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:
    • CAMERA.Rnw
    • compoundQuantilesVignette.Rnw
    • IsotopeDetectionVignette.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 28 out of 30 code chunks = 93% unevaluated
ℹ 
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/CAMERA.Rnw
    • vignettes/compoundQuantilesVignette.Rnw
    • vignettes/IsotopeDetectionVignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of CAMERA...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/fct_findAdducts.R (line 4, column 3)
    • ...
    • require() in R/zzz.R (line 2, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/compoundQuantiles.R (line 268, column 22)
    • ...
    • R/xsVisualise.R (line 415, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • compoundQuantiles.R (line 134, column 21)
    • ...
    • xsVisualise.R (line 435, column 39)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/fct_findIsotopes.R (line 328, column 9)
    • ...
    • cat() in R/xsAnnotate.R (line 2277, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/compoundQuantiles.R (line 102, column 10)
    • ...
    • R/xsAnnotate.R (line 921, column 16)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/compoundQuantiles.R (line 96, column 10)
    • ...
    • R/fct_groupCorr.R (line 54, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/ruleSet.R (line 469, column 24)
    • R/xsAnnotate.R (line 259, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 6 times:
    • T in R/fastMatch.R (line 33, column 88)
    • ...
    • F in R/xsAnnotate.R (line 1262, column 44)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • fct_findIsotopes.R (line 283, column 26)
    • ...
    • xsAnnotate.R (line 2241, column 18)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/findNeutralLoss.Rd
ℹ Found @ in man/getAllPeakEICs-methods.Rd
ℹ Found @ in man/ruleSet-class.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 21 times)
  • <<- in R/fct_findAdducts.R (line 212, column 20)
  • ...
  • <<- in R/xsVisualise.R (line 201, column 29)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 37
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.130() (R/ruleSet.R): 345 lines
    • ...
    • _anonymous_.540() (R/xsAnnotate.R): 230 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/calcPC-methods.Rd
    • ...
    • man/groupFWHM-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calcCiS-methods.Rd
    • ...
    • plotPsSpectrum.xsAnnotate.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • cleanParallel.Rd
    • combinexsAnnos.Rd
    • getIsotopeCluster.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • cleanParallel.Rd
    • combinexsAnnos.Rd
    • getIsotopeCluster.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • inst/NEWS
    • inst/ONEWS
* 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; 602 lines (8%) are > 80 characters long.
  First few lines:
    • R/compoundQuantiles.R#L1 ######################################## ...
    • ...
    • vignettes/IsotopeDetectionVignette.Rnw#L95 [4] Tautenhahn, R.; Böttcher,
    C.; Neuman ...
ℹ NOTE: Consider 4 spaces instead of tabs; 27 lines (0%) contain tabs.
  First few lines:
    • R/pspec2metfrag.R#L50 which(object@annoID[, "grpID"]==annoid ...
    • ...
    • vignettes/IsotopeDetectionVignette.Rnw#L72 maxcharge = 3) # annotate isot
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3453 lines (45%) are
not.
  First few lines:
    • R/00xsAnnotate.R#L18 contains=c("Versioned"), ...
    • ...
    • vignettes/IsotopeDetectionVignette.Rnw#L75 peakTable <- getPeaklist(an) #
    extra ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 6 WARNINGS | ℹ 19 NOTES
ℹ See the CAMERA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.