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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('NetPathMiner_1.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing NetPathMiner ─────────────────────────────────────────────────────
✔ Package installed successfully
── NetPathMiner session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpDz9daq/filef6ce617b8cb51/NetPathMiner
→ BiocVersion: 3.24
→ Package: NetPathMiner
→ PackageVersion: 1.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/NetPathMiner.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpDz9daq/filef6ce617b8cb51/NetPathMiner
→ installDir: /tmp/RtmpDz9daq/filef6ce61bd475c0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on NetPathMiner ───────────────────────────────────────────
* 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 3.0.2 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:
GeneExpression, Microarray, Coverage
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...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 2014 onwards
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • NPMVignette.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/NPMVignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of NetPathMiner...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/dbExtract.R (line 24, column 23)
    • ...
    • R/plotPath.R (line 744, column 39)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dbExtract.R (line 281, column 36)
    • ...
    • plotPath.R (line 773, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/netWeight.R (line 384, column 9)
    • ...
    • cat() in R/pathCluster.R (line 178, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/dbExtract.R (line 21, column 18)
    • ...
    • R/plotPath.R (line 625, column 29)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/pathClassifier.R (line 160, column 60)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/dbExtract.R (line 76, column 14)
    • ...
    • R/pathRank.R (line 278, column 26)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/netWeight.R (line 700, column 53)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • netProcess.R (line 136, column 46)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/pathRank.R (line 300, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/netWeight.R (line 431, column 25)
  • suppressWarnings() in R/netWeight.R (line 468, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
  The longest 5 functions are:
    • bpMetabolicL3() (R/dbExtract.R): 197 lines
    • ...
    • plotCytoscapeGML() (R/plotPath.R): 122 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/ex_biopax.Rd
    • ...
    • man/ex_sbml.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/registerMemoryErr.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • plotClassifierROC.Rd
  • registerMemoryErr.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 15% of man
pages use at least one of these tags.
  Found in files:
    • assignEdgeWeights.Rd
    • ...
    • reindexNetwork.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • assignEdgeWeights.Rd
    • ...
    • reindexNetwork.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 700 lines (14%) are > 80 characters long.
  First few lines:
    • R/dbExtract.R#L30 #' This function takes KGML files as inp ...
    • ...
    • vignettes/NPMVignette.Rmd#L481 All networks constructed in NetPathMiner
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 424 lines (8%) contain tabs.
  First few lines:
    • R/dbExtract.R#L105 dup.rns <- split( unname(dup ...
    • ...
    • vignettes/NPMVignette.Rmd#L463 vertex.size = 5, vertex.color = v.co ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 74 lines (1%) are not.
  First few lines:
    • R/dbExtract.R#L871 split( ...
    • ...
    • R/pathRank.R#L312 rbind(enodes,"t")), ...
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 | ⚠ 6 WARNINGS | ℹ 23 NOTES
ℹ See the NetPathMiner.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.