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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BicARE_1.71.0.tar.gz','quit-with-status'=TRUE)"
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── Installing BicARE ───────────────────────────────────────────────────────────
✔ Package installed successfully
── BicARE session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp7mobZi/file5aedc27ccbda0/BicARE
→ BiocVersion: 3.24
→ Package: BicARE
→ PackageVersion: 1.71.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BicARE.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp7mobZi/file5aedc27ccbda0/BicARE
→ installDir: /tmp/Rtmp7mobZi/file5aedc2c5706ea
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BicARE ─────────────────────────────────────────────────
* 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 1.8.0 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/Rtmp7mobZi/file5aedc27ccbda0/BicARE/man/bicluster.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp7mobZi/file5aedc27ccbda0/BicARE/man/makeReport.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp7mobZi/file5aedc27ccbda0/BicARE/man/sample.bicData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp7mobZi/file5aedc27ccbda0/BicARE/man/sample.biclustering.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp7mobZi/file5aedc27ccbda0/BicARE/man/testAnnot.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp7mobZi/file5aedc27ccbda0/BicARE/man/testSet.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: BiocViews,
GeneExpression, DifferentialExpression, GeneSetEnrichment, MultipleComparison,
GO, KEGG, 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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (60%).
* 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:
    • BicARE.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • BicARE.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/BicARE.Rnw
* Checking package installation calls in R code...
* Checking for library/require of BicARE...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/makeReport.R (line 26, column 43)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • FLOC.R (line 23, column 21)
    • ...
    • testSet.R (line 28, column 19)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/makeReport.R (line 8, column 51)
    • T in R/makeReport.R (line 8, column 74)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • bicluster.R (line 3, column 29)
    • ...
    • testAnnot.R (line 3, column 22)
* 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 3
functions greater than 50 lines.
  The longest 5 functions are:
    • makeReport() (R/makeReport.R): 147 lines
    • testAnnot() (R/testAnnot.R): 64 lines
    • FLOC() (R/FLOC.R): 54 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/makeReport.Rd
    • man/residue.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; 93 lines (10%) are > 80 characters long.
  First few lines:
    • R/FLOC.R#L1 FLOC <- function(Data, k=20, pGene=0.5, ...
    • ...
    • vignettes/BicARE.Rnw#L151 The html report is created in the direct ...
ℹ NOTE: Consider 4 spaces instead of tabs; 19 lines (2%) contain tabs.
  First few lines:
    • man/testAnnot.Rd#L12 \item{resBic}{a biclustering result fro ...
    • ...
    • man/testSet.Rd#L18 Due to the amount of results it is ad ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 100 lines (11%) are
not.
  First few lines:
    • man/bicluster.Rd#L10 \item{biclustering}{an object of class ...
    • ...
    • vignettes/BicARE.Rnw#L148 \end{Sinput} ...
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 | ⚠ 5 WARNINGS | ℹ 14 NOTES
ℹ See the BicARE.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.