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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('fmcsR_1.54.0.tar.gz','quit-with-status'=TRUE)"
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── Installing fmcsR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── fmcsR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKGL3Vy/file7a2f427b51901/fmcsR
→ BiocVersion: 3.23
→ Package: fmcsR
→ PackageVersion: 1.54.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/fmcsR.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpKGL3Vy/file7a2f427b51901/fmcsR
→ installDir: /tmp/RtmpKGL3Vy/file7a2f45fa223a3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on fmcsR ──────────────────────────────────────────────────
* 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 2.10.0 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 that Package field matches directory/tarball name...
* 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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (43%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • fmcsR.Rmd
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/fmcsR.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • %knitr
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • fmcsR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of fmcsR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/fmcsBatch.R (line 35, column 19)
    • library() in R/fmcsBatch.R (line 36, column 19)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • fmcs.R (line 80, column 19)
    • fmcs.R (line 92, column 19)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/fmcs.R (line 20, column 8)
    • ...
    • R/fmcsBatch.R (line 68, column 23)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • fmcs.R (line 9, column 19)
    • ...
    • fmcsBatch.R (line 10, column 23)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/fmcsBatch.R (line 49, column 72)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/fmcs.R (line 155, column 29)
  • suppressWarnings() in R/fmcs.R (line 157, column 29)
  • suppressWarnings() in R/fmcsBatch.R (line 42, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
  The longest 5 functions are:
    • fmcs() (R/fmcs.R): 97 lines
    • fmcsBatch() (R/fmcsBatch.R): 76 lines
* Checking man page documentation...
* Checking package NEWS...
* 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; 39 lines (4%) are > 80 characters long.
  First few lines:
    • R/fmcs.R#L60 stats <- c(Query_Size=querySize, Tar ...
    • ...
    • vignettes/fmcsR.Rmd#L296 d <- sapply(cid(sdf), function(x) fmcsBa ...
ℹ NOTE: Consider 4 spaces instead of tabs; 75 lines (7%) contain tabs.
  First few lines:
    • R/fmcs.R#L8 matching.mode = "static", fast = FALS ...
    • ...
    • man/MCS-class.Rd#L36 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 38 lines (4%) are not.
  First few lines:
    • R/fmcs.R#L44 ...
    • ...
    • vignettes/fmcsR.Rmd#L317 sessionInfo() ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 5 WARNINGS | ℹ 13 NOTES
ℹ See the fmcsR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.