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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Path2PPI_1.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Path2PPI ─────────────────────────────────────────────────────────
✔ Package installed successfully
── Path2PPI session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplgPBa1/filefd148633932a2/Path2PPI
→ BiocVersion: 3.24
→ Package: Path2PPI
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Path2PPI.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmplgPBa1/filefd148633932a2/Path2PPI
→ installDir: /tmp/RtmplgPBa1/filefd14870f5a490
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Path2PPI ───────────────────────────────────────────────
* 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 3.2.1 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...
* 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...
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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Path2PPI-tutorial.Rmd
* Checking package installation calls in R code...
* Checking for library/require of Path2PPI...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/private_methods.R (line 77, column 45)
    • R/public_methods.R (line 704, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • initialize-methods.R (line 31, column 40)
    • ...
    • show-methods.R (line 114, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/initialize-methods.R (line 184, column 29)
    • ...
    • R/public_methods.R (line 471, column 56)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/private_methods.R (line 55, column 23)
    • R/private_methods.R (line 91, column 27)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • private_methods.R (line 175, column 33)
    • ...
    • private_methods.R (line 288, column 33)
* 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 6
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.456() (R/public_methods.R): 229 lines
    • ...
    • _anonymous_.282() (R/public_methods.R): 66 lines
* Checking man page documentation...
* 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 multiples of 4 spaces for line indents; 874 lines (28%) are
not.
  First few lines:
    • R/AllClasses.R#L53 targetSpecies = NULL, ...
    • ...
    • vignettes/Path2PPI-tutorial.Rmd#L631 ...
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 12 NOTES
ℹ See the Path2PPI.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.