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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BioNet_1.73.0.tar.gz','quit-with-status'=TRUE)"
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── Installing BioNet ───────────────────────────────────────────────────────────
✔ Package installed successfully
── BioNet session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpCbMaPY/file5dfc075bab391/BioNet
→ BiocVersion: 3.24
→ Package: BioNet
→ PackageVersion: 1.73.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BioNet.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpCbMaPY/file5dfc075bab391/BioNet
→ installDir: /tmp/RtmpCbMaPY/file5dfc06206d71
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BioNet ─────────────────────────────────────────────────
* 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 2.10.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/compareNetworks.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/fbumLL.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/fdrThreshold.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/fitBumModel.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/makeNetwork.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/mapByVar.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/piUpper.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/plot.bum.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/plot3dModule.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/plotLLSurface.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/plotModule.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/print.bum.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/resamplingPvalues.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/rmSelfLoops.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/save3dModule.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/scanFDR.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpCbMaPY/file5dfc075bab391/BioNet/man/summary.bum.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...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (80%).
* 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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • Tutorial.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Tutorial.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/Tutorial.Rnw (chunk no. 33, line 247, column 36)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Tutorial.Rnw
* Checking package installation calls in R code...
* Checking for library/require of BioNet...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/MAUtils.R (line 20, column 20)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/HeinzUtils.R (line 484, column 27)
    • ...
    • R/Plots.R (line 18, column 29)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Graph.R (line 220, column 33)
    • ...
    • Statistics.R (line 221, column 29)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/IO.R (line 454, column 3)
    • ...
    • print() in R/IO.R (line 136, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Graph.R (line 68, column 15)
    • ...
    • R/Statistics.R (line 134, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/MAUtils.R (line 24, column 15)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 13 times:
    • F in R/Graph.R (line 250, column 49)
    • ...
    • F in R/IO.R (line 436, column 71)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • IO.R (line 264, column 56)
    • ...
    • Statistics.R (line 80, column 28)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/HeinzUtils.R (line 258, column 5)
* 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:
    • runFastHeinz() (R/HeinzUtils.R): 188 lines
    • ...
    • writeHeinzNodes() (R/HeinzUtils.R): 85 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/pvaluesExample.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/hist.bum.Rd
    • ...
    • man/writeHeinzNodes.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • loadNetwork.sif.Rd
  • ...
  • runHeinz.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 34% of man
pages use at least one of these tags.
  Found in files:
    • consensusScores.Rd
    • ...
    • writeHeinzNodes.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • consensusScores.Rd
    • ...
    • writeHeinzNodes.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...
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; 470 lines (11%) are > 80 characters long.
  First few lines:
    • R/Graph.R#L21 edgelist <- matrix(unlist(strsplit(e ...
    • ...
    • vignettes/Tutorial.Rnw#L677 \textbf{The new version of Heinz v2.0 is ...
ℹ NOTE: Consider 4 spaces instead of tabs; 156 lines (4%) contain tabs.
  First few lines:
    • R/Graph.R#L63 if(is.null(V(network)$name)) ...
    • ...
    • R/Statistics.R#L217 cc <- cc[order(listLen(cc), decreasing ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 900 lines (21%) are
not.
  First few lines:
    • R/Graph.R#L15 if(is(network, "igraph")) ...
    • ...
    • vignettes/Tutorial.Rnw#L595 resampling.scores[[i]] <- scoreNodes(n ...
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 | ⚠ 7 WARNINGS | ℹ 21 NOTES
ℹ See the BioNet.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.