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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('IPO_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing IPO ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── IPO session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8P3PKV/filec4c4b4909806a/IPO
→ BiocVersion: 3.24
→ Package: IPO
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/IPO.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp8P3PKV/filec4c4b4909806a/IPO
→ installDir: /tmp/Rtmp8P3PKV/filec4c4b2ec38dee
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on IPO ────────────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp8P3PKV/filec4c4b4909806a/IPO/man/createModel.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 (12%).
* 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:
    • IPO.Rmd
* Checking package installation calls in R code...
* Checking for library/require of IPO...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/optimizeRetCorGroupParameters.R (line 391, column 34)
    • library() in R/optimizeXcmsSetParameters.R (line 791, column 34)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/optimizeRetCorGroupParameters.R (line 118, column 9)
    • ...
    • R/utils.R (line 296, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • optimizeRetCorGroupParameters.R (line 31, column 12)
    • ...
    • utils.R (line 402, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/optimizeRetCorGroupParameters.R (line 173, column 19)
    • ...
    • R/utils.R (line 364, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/optimizeRetCorGroupParameters.R (line 207, column 13)
    • ...
    • R/utils.R (line 520, column 11)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/optimizeRetCorGroupParameters.R (line 389, column 15)
    • R/optimizeXcmsSetParameters.R (line 789, column 15)
    • R/utils.R (line 375, column 13)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • utils.R (line 374, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressMessages() in R/optimizeXcmsSetParameters.R (line 410, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • optimizeXcmsSet() (R/optimizeXcmsSetParameters.R): 197 lines
    • ...
    • xcmsSetExperimentsCluster() (R/optimizeXcmsSetParameters.R): 86 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • getRGTVValues.Rd
  • optimizeRetGroup.Rd
  • optimizeXcmsSet.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 23% of man
pages use at least one of these tags.
  Found in files:
    • getNormalizedResponse.Rd
    • ...
    • optimizeXcmsSet.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • IPO-package.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; 17 lines (1%) are > 80 characters long.
  First few lines:
    • R/optimizeRetCorGroupParameters.R#L146 peaks_IPO(xset)[grou ...
    • ...
    • vignettes/IPO.Rmd#L253 time.RetGroup # time for optimizing rete ...
ℹ NOTE: Consider 4 spaces instead of tabs; 141 lines (6%) contain tabs.
  First few lines:
    • R/optimizeRetCorGroupParameters.R#L52 if(distfunc=="cor_opt") ...
    • ...
    • R/utils.R#L521 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1058 lines (44%) are
not.
  First few lines:
    • R/optimizeRetCorGroupParameters.R#L3 if(params$retcorMethod == "obiwarp")
    { ...
    • ...
    • vignettes/IPO.Rmd#L243 resultRetcorGroup$best_sett ...
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 | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the IPO.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.