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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('pRolocGUI_2.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing pRolocGUI ────────────────────────────────────────────────────────
✔ Package installed successfully
── pRolocGUI session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2OyNSv/file1036376e7b688b/pRolocGUI
→ BiocVersion: 3.24
→ Package: pRolocGUI
→ PackageVersion: 2.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/pRolocGUI.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp2OyNSv/file1036376e7b688b/pRolocGUI
→ installDir: /tmp/Rtmp2OyNSv/file10363724132e26
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on pRolocGUI ──────────────────────────────────────────────
* 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 3.1.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Spatial,
Classification, Clustering, ShinyApps, MassSpectrometry, ImmunoOncology,
QualityControl
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (9%).
* 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 6 out of 9 code chunks = 66% unevaluated
ℹ 
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/pRolocGUI.Rmd
* Checking package installation calls in R code...
* Checking for library/require of pRolocGUI...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/pRolocVis_aggregation.R (line 110, column 9)
    • ...
    • R/pRolocVis_explore.R (line 595, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • pRolocVis_aggregation.R (line 43, column 41)
    • ...
    • utils.R (line 204, column 26)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/pRolocVis_aggregation.R (line 13, column 16)
    • ...
    • R/utils.R (line 111, column 7)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/pRolocVis_compare.R (line 38, column 33)
    • ...
    • R/utils.R (line 192, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 44 times)
  • <<- in R/pRolocVis_aggregation.R (line 263, column 39)
  • ...
  • <<- in R/pRolocVis_explore.R (line 904, column 22)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
  The longest 5 functions are:
    • pRolocVis_compare() (R/pRolocVis_compare.R): 1136 lines
    • ...
    • server() (R/pRolocVis_explore.R): 456 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/pRolocVis-apps.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 305 lines (8%) are > 80 characters long.
  First few lines:
    • R/css.R#L31 .dataTables_wrapper.no-footer > ...
    • ...
    • vignettes/pRolocGUI.Rmd#L451 proteome*. [Nat Commun. 2016 Jan 12;7:99 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1912 lines (53%) are
not.
  First few lines:
    • R/css.R#L5 /* ------ logo ------ */ ...
    • ...
    • vignettes/pRolocGUI.Rmd#L397 groupBy = "Protein.Group.Acces ...
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 | ⚠ 2 WARNINGS | ℹ 14 NOTES
ℹ See the pRolocGUI.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.