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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MSstatsBioNet_1.5.1.tar.gz','quit-with-status'=TRUE)"
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── Installing MSstatsBioNet ────────────────────────────────────────────────────
✔ Package installed successfully
── MSstatsBioNet session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmpC2OrUX/filee9212156a7ee8/MSstatsBioNet
→ BiocVersion: 3.24
→ Package: MSstatsBioNet
→ PackageVersion: 1.5.1
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MSstatsBioNet.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpC2OrUX/filee9212156a7ee8/MSstatsBioNet
→ installDir: /tmp/RtmpC2OrUX/filee9212790fae7a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MSstatsBioNet ──────────────────────────────────────────
* 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 4.4.0 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: Transcription,
Normalization, TimeCourse
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...
ℹ NOTE: License 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (8%).
* 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:
    • Cytoscape-Visualization.Rmd
    • ...
    • PTM-Analysis.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Cytoscape-Visualization.Rmd
! WARNING: Vignette set global option 'eval=FALSE'
  Found in files:
    • vignettes/Filter-By-Context.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MSstatsBioNet...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/filterSubnetworkByContext.R (line 182, column 5)
    • ...
    • R/utils_annotateProteinInfoFromIndra.R (line 270, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/exportNetworkToHTML.R (line 64, column 9)
    • ...
    • cat in R/utils_cytoscapeNetwork.R (line 212, column 30)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotateProteinInfoFromIndra.R (line 59, column 25)
    • ...
    • R/utils_getSubnetworkFromIndra.R (line 424, column 30)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/utils_getSubnetworkFromIndra.R (line 51, column 22)
    • R/utils_getSubnetworkFromIndra.R (line 87, column 21)
    • R/utils_getSubnetworkFromIndra.R (line 92, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/filterSubnetworkByContext.R (line 377, column 25)
    • ...
    • R/utils_getSubnetworkFromIndra.R (line 92, column 23)
* 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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • .buildElements() (R/utils_cytoscapeNetwork.R): 130 lines
    • ...
    • .extract_evidence_text() (R/filterSubnetworkByContext.R): 58 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • cytoscapeNetwork.Rd
    • ...
    • renderCytoscapeNetwork.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 25% of man
pages use at least one of these tags.
  Found in files:
    • cytoscapeNetwork.Rd
    • ...
    • renderCytoscapeNetwork.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • cytoscapeNetwork.Rd
    • ...
    • renderCytoscapeNetwork.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; 121 lines (4%) are > 80 characters long.
  First few lines:
    • R/annotateProteinInfoFromIndra.R#L17 #'
    \item{IsTranscriptionFactor}{Logica ...
    • ...
    • vignettes/PTM-Analysis.Rmd#L70 previewNetworkInBrowser(subnetwork$nodes
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 72 lines (2%) are not.
  First few lines:
    • R/annotateProteinInfoFromIndra.R#L63 gsub("_ ...
    • ...
    • vignettes/Cytoscape-Visualization.Rmd#L155 ) ...
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 | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the MSstatsBioNet.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.