##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('flowVS_1.45.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing flowVS ───────────────────────────────────────────────────────────
✔ Package installed successfully
── flowVS session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKyXjVb/file9d7101170bd7c/flowVS
→ BiocVersion: 3.24
→ Package: flowVS
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/flowVS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpKyXjVb/file9d7101170bd7c/flowVS
→ installDir: /tmp/RtmpKyXjVb/file9d71030c2f5ee
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowVS ─────────────────────────────────────────────────
* 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 3.2 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/RtmpKyXjVb/file9d7101170bd7c/flowVS/man/estParamFlowVS.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpKyXjVb/file9d7101170bd7c/flowVS/man/lymphs.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpKyXjVb/file9d7101170bd7c/flowVS/man/microVS.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpKyXjVb/file9d7101170bd7c/flowVS/man/transFlowVS.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: OneChannel
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 (75%).
* 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:
    • flowVS.Rnw
* Checking package installation calls in R code...
* Checking for library/require of flowVS...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cluster1d.R (line 280, column 18)
    • R/microVS.R (line 115, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cluster1d.R (line 105, column 12)
    • ...
    • flowVS.R (line 285, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/flowVS.R (line 24, column 5)
    • ...
    • print() in R/microVS.R (line 19, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cluster1d.R (line 26, column 5)
    • ...
    • R/microVS.R (line 117, column 19)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/flowVS.R (line 260, column 11)
* 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:
    • densityPeaks() (R/cluster1d.R): 197 lines
    • ...
    • microVS() (R/microVS.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/HD.Rd
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 29% of man
pages use at least one of these tags.
  Found in files:
    • estParamFlowVS.Rd
    • transFlowVS.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; 162 lines (12%) are > 80 characters long.
  First few lines:
    • R/cluster1d.R#L9 ## each row of the matrix indicate ...
    • ...
    • vignettes/flowVS.Rnw#L197 Here is the output of sessionInfo on the ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 387 lines (30%) are
not.
  First few lines:
    • R/cluster1d.R#L15 peak.density.thr=0 ...
    • ...
    • man/transFlowVS.Rd#L40 \code{\link{estParamFlowVS}} ...
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 16 NOTES
ℹ See the flowVS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.