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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BUS_1.69.0.tar.gz','quit-with-status'=TRUE)"
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── Installing BUS ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── BUS session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpqt2UPG/file6061f70a2ef6c/BUS
→ BiocVersion: 3.24
→ Package: BUS
→ PackageVersion: 1.69.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BUS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpqt2UPG/file6061f70a2ef6c/BUS
→ installDir: /tmp/Rtmpqt2UPG/file6061fe7b5221
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BUS ────────────────────────────────────────────────────
* 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 2.3.0 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/Rtmpqt2UPG/file6061f70a2ef6c/BUS/man/copasi.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpqt2UPG/file6061f70a2ef6c/BUS/man/gene.pvalue.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpqt2UPG/file6061f70a2ef6c/BUS/man/gene.trait.pvalue.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpqt2UPG/file6061f70a2ef6c/BUS/man/gene.trait.similarity.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpqt2UPG/file6061f70a2ef6c/BUS/man/pred.network.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
Network, NetworkInference, GraphAndNetwork
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 (33%).
* 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:
    • bus.rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • bus.rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/bus.rnw
* Checking package installation calls in R code...
* Checking for library/require of BUS...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • gene.pvalue.R (line 36, column 27)
    • ...
    • gene.trait.pvalue.R (line 119, column 33)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/BUS.R (line 27, column 5)
    • ...
    • R/pred.network.R (line 6, column 4)
* 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 4
functions greater than 50 lines.
  The longest 5 functions are:
    • `gene.trait.pvalue`() (R/gene.trait.pvalue.R): 126 lines
    • ...
    • `gene.similarity`() (R/gene.similarity.R): 68 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/copasi.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; 141 lines (15%) are > 80 characters long.
  First few lines:
    • R/BUS.R#L2 function(EXP,trait=NULL,measure,method.p ...
    • ...
    • vignettes/bus.rnw#L221 T.~Liu, T.~Papagiannakopoulos, K.~ Puska ...
ℹ NOTE: Consider 4 spaces instead of tabs; 21 lines (2%) contain tabs.
  First few lines:
    • R/BUS.R#L6 message("This is a 'gene-trait' case. I ...
    • ...
    • R/gene.trait.similarity.R#L96 out<-b.similarity(EXP,trait,measure,d ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 257 lines (27%) are
not.
  First few lines:
    • R/BUS.R#L9 ...
    • ...
    • vignettes/bus.rnw#L212 gene expression modules. ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 14 NOTES
ℹ See the BUS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.