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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('TargetSearch_2.15.0.tar.gz','quit-with-status'=TRUE)"
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── Installing TargetSearch ─────────────────────────────────────────────────────
✔ Package installed successfully
── TargetSearch session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmppzYvCv/file14a5e02eda61a1/TargetSearch
→ BiocVersion: 3.24
→ Package: TargetSearch
→ PackageVersion: 2.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/TargetSearch.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmppzYvCv/file14a5e02eda61a1/TargetSearch
→ installDir: /tmp/RtmppzYvCv/file14a5e0198c24b8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TargetSearch ───────────────────────────────────────────
* 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...
* 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...
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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • RICorrection.Rnw
    • TargetSearch.Rnw
* Checking package installation calls in R code...
* Checking for library/require of TargetSearch...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/baseline.R (line 46, column 23)
    • ...
    • R/writeLibText.R (line 14, column 37)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • baseline.R (line 44, column 29)
    • ...
    • Write.Results.R (line 95, column 67)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/FAMEoutliers.R (line 63, column 17)
    • ...
    • cat() in R/Write.Results.R (line 98, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/netCDF.R (line 39, column 22)
    • R/updateRI.R (line 87, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/file.R (line 32, column 22)
    • ...
    • R/ProfileCleanUp.R (line 64, column 29)
! WARNING: .Deprecated / .Defunct usage (found 3 times)
  • .Defunct() in R/fixRI.R (line 5, column 4)
  • .Deprecated() in R/methods-tsLib.R (line 24, column 5)
  • .Defunct() in R/TargetSearchGUI.R (line 7, column 5)
* 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 22
functions greater than 50 lines.
  The longest 5 functions are:
    • `ProfileCleanUp`() (R/ProfileCleanUp.R): 153 lines
    • ...
    • RIcorrect() (R/RIcorrect.R): 100 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plotFAME.Rd
    • ...
    • man/writeMSP.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • TargetSearch-defunct.Rd
  • tsUpdate-method.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
  Found in files:
    • checkRimLim.Rd
    • ...
    • tsUpdate-method.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • checkRimLim.Rd
    • ...
    • tsUpdate-method.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; 1041 lines (10%) are > 80 characters long.
  First few lines:
    • R/baseline.R#L3 baseline <- function(ncdf, bsline_method ...
    • ...
    • vignettes/TargetSearch.Rnw#L588 evenly distributed ``metabolites'' in ti
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1283 lines (12%) contain tabs.
  First few lines:
    • R/checkRimLim.R#L72 return(invisible(se(dat))) ...
    • ...
    • vignettes/TargetSearch.Rnw#L629 function(x) as.numeric(unlist(strsplit(
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 980 lines (9%) are
not.
  First few lines:
    • R/FAMEoutliers.R#L3 threshold=3, group.threshold=0. ...
    • ...
    • vignettes/TargetSearch.Rnw#L631 selMass = metMZ, RIdev = c(1500, 75 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 15 NOTES
ℹ See the TargetSearch.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.