##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('flowFP_1.71.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing flowFP ───────────────────────────────────────────────────────────
✔ Package installed successfully
── flowFP session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmphUY5FI/file9bcc67faada2e/flowFP
→ BiocVersion: 3.24
→ Package: flowFP
→ PackageVersion: 1.71.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/flowFP.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmphUY5FI/file9bcc67faada2e/flowFP
→ installDir: /tmp/RtmphUY5FI/file9bcc64c956e71
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowFP ─────────────────────────────────────────────────
* 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 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: ImmunoOncology
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: 'Date:' field format is not 'YYYY-MM-DD': 2009
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (44%).
* 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:
    • flowFP_HowTo.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • flowFP_HowTo.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/flowFP_HowTo.Rnw
* Checking package installation calls in R code...
* Checking for library/require of flowFP...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllGenerics.R (line 80, column 31)
    • ...
    • R/plot-utils.R (line 160, column 29)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllGenerics.R (line 495, column 30)
    • ...
    • plot-utils.R (line 250, column 54)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllGenerics.R (line 521, column 17)
    • cat() in R/AllGenerics.R (line 534, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllGenerics.R (line 45, column 22)
    • ...
    • R/plot-utils.R (line 251, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AllGenerics.R (line 84, column 22)
    • ...
    • R/plot-utils.R (line 252, column 22)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/flowFPModel.R (line 204, column 10)
    • R/flowFPModel.R (line 208, column 10)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/flowFPModel.R (line 29, column 65)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • flowFP.R (line 57, column 28)
    • ...
    • plot-model.R (line 41, column 19)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • plotFancy() (R/plot-fancy.R): 107 lines
    • ...
    • initFPplot() (R/plot-utils.R): 54 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/append-methods.Rd
    • ...
    • man/tags-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • binBoundary-methods.Rd
    • ...
    • tags-methods.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; 451 lines (11%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L28 ## trainingSet - List of sample names fr ...
    • ...
    • vignettes/flowFP_HowTo.Rnw#L600 Pennsylvania Flow Cytometry Resource.  W
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1171 lines (29%) contain tabs.
  First few lines:
    • R/AllClasses.R#L108 return (TRUE) ...
    • ...
    • vignettes/flowFP_HowTo.Rnw#L483 exprs(fs2[[i]]) = exprs(fs2[[i]])[sampl
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 398 lines (10%) are
not.
  First few lines:
    • R/AllClasses.R#L60 n ...
    • ...
    • vignettes/flowFP_HowTo.Rnw#L508 6, 7, 10 and 11 corresponding to green
    ...
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 | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the flowFP.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.