##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DFP_1.71.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing DFP ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── DFP session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpk2plBD/file81ff172313d22/DFP
→ BiocVersion: 3.24
→ Package: DFP
→ PackageVersion: 1.71.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DFP.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpk2plBD/file81ff172313d22/DFP
→ installDir: /tmp/Rtmpk2plBD/file81ff14b222ba5
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DFP ────────────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/calculateDiscriminantFuzzyPattern.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/calculateFuzzyPatterns.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/calculateMembershipFunctions.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/DFP-internal.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/discretizeExpressionValues.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/discriminantFuzzyPattern.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/ExpressionLevel-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/HighExpressionLevel-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/LowExpressionLevel-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/MediumExpressionLevel-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/plotDiscriminantFuzzyPattern.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/plotMembershipFunctions.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/readCSV.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/rmadataset.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/show-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/showDiscreteValues.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpk2plBD/file81ff172313d22/DFP/man/showFuzzyPatterns.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: GeneExpression
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 (50%).
* 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:
    • DFP.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • DFP.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DFP...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/DFP.R (line 197, column 9)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • DFP.R (line 29, column 12)
    • ...
    • DFP.R (line 479, column 50)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/DFP.R (line 423, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/DFP.R (line 28, column 20)
    • ...
    • R/DFP.R (line 467, column 29)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • discriminantFuzzyPattern() (R/DFP.R): 84 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/show-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calculateDiscriminantFuzzyPattern.Rd
    • ...
    • showFuzzyPatterns.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; 205 lines (12%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L1 setClass("ExpressionLevel", representati ...
    • ...
    • vignettes/DFP.Rnw#L194 \item F. Diaz, F. Fdez-Riverola, J. M. C ...
ℹ NOTE: Consider 4 spaces instead of tabs; 444 lines (27%) contain tabs.
  First few lines:
    • R/DFP.R#L8 #maxim <- max(values, na.rm=T); maxim ...
    • ...
    • man/readCSV.Rd#L9 \item \sQuote{\code{pData}} with the sa ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 210 lines (13%) are
not.
  First few lines:
    • R/DFP.R#L27 y <- NULL ...
    • ...
    • vignettes/DFP.Rnw#L99 \subsection{Extended Example} ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 14 NOTES
ℹ See the DFP.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.