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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('flowMerge_2.61.0.tar.gz','quit-with-status'=TRUE)"
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── Installing flowMerge ────────────────────────────────────────────────────────
✔ Package installed successfully
── flowMerge session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp3GPnQX/file9c3f1568aae3f/flowMerge
→ BiocVersion: 3.24
→ Package: flowMerge
→ PackageVersion: 2.61.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/flowMerge.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp3GPnQX/file9c3f1568aae3f/flowMerge
→ installDir: /tmp/Rtmp3GPnQX/file9c3f153cd4c53
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowMerge ──────────────────────────────────────────────
* Checking for deprecated package usage...
✖ ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated
and does not work on Windows.
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
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: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/flowmerge.Rmd (chunk no. 8, line 82, column 49)
    • ...
    • vignettes/flowmerge.Rmd (chunk no. 8, line 86, column 30)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/flowmerge.Rmd
* Checking package installation calls in R code...
* Checking for library/require of flowMerge...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/flowMerge.R (line 36, column 24)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/flowMerge.R (line 10, column 30)
    • ...
    • R/SetMethods.R (line 256, column 30)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • flowMerge.R (line 43, column 36)
    • ...
    • SetMethods.R (line 256, column 37)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/flowMerge.R (line 25, column 9)
    • ...
    • print() in R/SetMethods.R (line 235, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/flowMerge.R (line 119, column 9)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 22 times:
    • T in R/flowMerge.R (line 88, column 75)
    • ...
    • T in R/SetMethods.R (line 9, column 98)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • flowMerge.R (line 3, column 16)
    • flowMerge.R (line 3, column 35)
* 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:
    • _anonymous_.151() (R/SetMethods.R): 79 lines
    • ptree() (R/flowMerge.R): 76 lines
    • mergeClusters2() (R/flowMerge.R): 62 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/fitPiecewiseLinreg-methods.Rd
    • ...
    • man/summary-methods.Rd
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • checkForRemoteErrors.Rd
    • ...
    • ptree.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • pFlowMerge.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • pFlowMerge.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; 226 lines (15%) are > 80 characters long.
  First few lines:
    • R/flowMerge.R#L10 sum(diff(which(tmp$curv)[sapply(tmp$ ...
    • ...
    • vignettes/flowmerge.Rmd#L116 A: pFlowMerge is implemented to parallel ...
ℹ NOTE: Consider 4 spaces instead of tabs; 102 lines (7%) contain tabs.
  First few lines:
    • R/flowMerge.R#L4 x<-as.matrix(x); ...
    • ...
    • man/ptree.Rd#L28 Greg Finak <gfinak@fhcrc.org> ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 198 lines (13%) are
not.
  First few lines:
    • R/flowMerge.R#L39 stop("Some cluster nodes failed to ...
    • ...
    • vignettes/flowmerge.Rmd#L17 ,fig.width=8,fig.height=6 ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 5 WARNINGS | ℹ 17 NOTES
ℹ See the flowMerge.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.