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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('nethet_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing nethet ───────────────────────────────────────────────────────────
✔ Package installed successfully
── nethet session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPqi8AI/filef6ce53e4b4105/nethet
→ BiocVersion: 3.24
→ Package: nethet
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/nethet.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpPqi8AI/filef6ce53e4b4105/nethet
→ installDir: /tmp/RtmpPqi8AI/filef6ce531608703
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on nethet ─────────────────────────────────────────────────
* 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...
* 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: Network
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (11%).
* 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:
    • nethet.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • nethet.Rnw
* Checking package installation calls in R code...
* Checking for library/require of nethet...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/auxfunc.R (line 2, column 1)
    • ...
    • library() in R/netsim.R (line 5, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/auxfunc.R (line 29, column 16)
    • ...
    • R/netsim.R (line 181, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • auxfunc.R (line 29, column 23)
    • ...
    • netsim.R (line 294, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/diffnet.R (line 231, column 3)
    • ...
    • cat() in R/netsim.R (line 301, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/auxfunc.R (line 87, column 44)
    • ...
    • R/netsim.R (line 270, column 48)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/netsim.R (line 48, column 10)
    • R/netsim.R (line 70, column 28)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • netplot.R (line 237, column 34)
* 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 26
functions greater than 50 lines.
  The longest 5 functions are:
    • mixglasso_init() (R/mixglasso.R): 151 lines
    • ...
    • MStepGlasso() (R/mixglasso.R): 96 lines
* Checking man page documentation...
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘nethet’
Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 1% of man
pages use at least one of these tags.
  Found in files:
    • export_network.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • export_network.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; 517 lines (8%) are > 80 characters long.
  First few lines:
    • R/auxfunc.R#L26 ##' invcov.array = sapply(1:5, function( ...
    • ...
    • vignettes/nethet.Rnw#L703 \texttt{export\_network} can be invoked ...
ℹ NOTE: Consider 4 spaces instead of tabs; 542 lines (8%) contain tabs.
  First few lines:
    • R/auxfunc.R#L14 return(-invcov*tcrossprod(sqrt(1/diag(i ...
    • ...
    • vignettes/nethet.Rnw#L727 # p.corrs.thresh=0.25, quote=FALS ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1665 lines (26%) are
not.
  First few lines:
    • R/cvglasso.R#L55 use.package='h ...
    • ...
    • vignettes/nethet.Rnw#L587 return(tab) ...
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 | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the nethet.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.