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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MouseFM_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MouseFM ──────────────────────────────────────────────────────────
✔ Package installed successfully
── MouseFM session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9OJ308/filee0c2a298a594c/MouseFM
→ BiocVersion: 3.24
→ Package: MouseFM
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MouseFM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp9OJ308/filee0c2a298a594c/MouseFM
→ installDir: /tmp/Rtmp9OJ308/filee0c2a284448f9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MouseFM ────────────────────────────────────────────────
* 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 4.0.0 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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (24%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • fetch.Rmd
    • finemap.Rmd
    • prio.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MouseFM...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotation.R (line 35, column 23)
    • ...
    • R/send_request.R (line 85, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/annotation.R (line 46, column 13)
    • ...
    • R/prio.R (line 206, column 15)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/annotation.R (line 252, column 25)
    • R/annotation.R (line 269, column 25)
* 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 11
functions greater than 50 lines.
  The longest 5 functions are:
    • annotate_mouse_genes() (R/annotation.R): 157 lines
    • ...
    • prio() (R/prio.R): 125 lines
* Checking man page documentation...

  ---------
  For example usage please run: vignette('MouseFM')
  
  Support me: https://matthiasmunz.de/en/thanks/

  Citation appreciated:
  Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I (2021) In silico candidate variant and gene identification using inbred mouse strains. PeerJ. doi:10.7717/peerj.11017
  
  Github Repo: https://github.com/matmu/MouseFM
  MouseFM Backend: https://github.com/matmu/MouseFM-Backend
  ---------
* 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; 34 lines (2%) are > 80 characters long.
  First few lines:
    • R/annotation.R#L250 "The selected En ...
    • ...
    • vignettes/prio.Rmd#L44 df = prio("chr1", start=5000000, end=600 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 516 lines (25%) are
not.
  First few lines:
    • R/annotation.R#L36 if ("GRanges" %in% is(geno)) { ...
    • ...
    • vignettes/finemap.Rmd#L48 impact=c("HIGH", "MODERATE ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 11 NOTES
ℹ See the MouseFM.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.