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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('matter_2.15.0.tar.gz','quit-with-status'=TRUE)"
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── Installing matter ───────────────────────────────────────────────────────────
✔ Package installed successfully
── matter session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpLJtmVg/filed08e97cb1088d/matter
→ BiocVersion: 3.24
→ Package: matter
→ PackageVersion: 2.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/matter.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpLJtmVg/filed08e97cb1088d/matter
→ installDir: /tmp/RtmpLJtmVg/filed08e951323bc2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on matter ─────────────────────────────────────────────────
* 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 4.4 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...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (23%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of matter...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/matter_list.R (line 142, column 18)
    • R/matter_list.R (line 151, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • fastmap.R (line 52, column 53)
    • ...
    • utils.R (line 796, column 22)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/nnmf.R (line 201, column 23)
    • R/nnmf.R (line 202, column 23)
    • R/signal2.R (line 192, column 11)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/vizi.R (line 1005, column 41)
! WARNING: .Deprecated / .Defunct usage (found 11 times)
  • .Deprecated() in R/apply.R (line 64, column 17)
  • ...
  • .Defunct() in R/utils.R (line 1248, column 9)
* 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 54
functions greater than 50 lines.
  The longest 5 functions are:
    • sgmix_int() (R/sgmix.R): 253 lines
    • ...
    • plot_signal() (R/plot.R): 161 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/deprecated.Rd
    • ...
    • man/vizi-methods.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • deprecated.Rd
  • ...
  • vizi-par.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; 868 lines (3%) are > 80 characters long.
  First few lines:
    • R/drle.R#L15 lens <- c(length(object@values), leng ...
    • ...
    • vignettes/matter2-signal.Rmd#L683 Note that the number of observed peaks
    a ...
ℹ NOTE: Consider 4 spaces instead of tabs; 14006 lines (56%) contain tabs.
  First few lines:
    • R/altrep.R#L5 wrap = getOption("matter.wrap.altrep")) ...
    • ...
    • man/warp2.Rd#L26 \item{x, y}{Images to be aligned by war ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4 lines (0%) are not.
  First few lines:
    • man/matter_arr-class.Rd#L154 \code{\linkS4class{matter}} ...
    • ...
    • man/sparse_arr-class.rd#L176 \code{\linkS4class{matter}} ...
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 | ⚠ 3 WARNINGS | ℹ 11 NOTES
ℹ See the matter.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.