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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scanMiRApp_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scanMiRApp ───────────────────────────────────────────────────────
✔ Package installed successfully
── scanMiRApp session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpIDpZvL/file128fe57ec42e8/scanMiRApp
→ BiocVersion: 3.24
→ Package: scanMiRApp
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scanMiRApp.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpIDpZvL/file128fe57ec42e8/scanMiRApp
→ installDir: /tmp/RtmpIDpZvL/file128fe532c6c717
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scanMiRApp ─────────────────────────────────────────────
* 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 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Alignment
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...
* 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 (44%).
* 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:
    • IndexedFST.Rmd
    • scanMiRApp.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scanMiRApp...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/scanMiRserver.R (line 246, column 14)
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/scanMiRAnno.R (line 105, column 3)
    • ...
    • print() in R/scanMiRserver.R (line 163, column 40)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/scanMiRserver.R (line 492, column 20)
    • R/scanMiRserver.R (line 677, column 46)
    • R/scanMiRserver.R (line 678, column 46)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/getTranscriptSequence.R (line 58, column 13)
  • ...
  • suppressMessages() in R/scanMiRserver.R (line 87, column 11)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
  The longest 5 functions are:
    • scanMiRserver() (R/scanMiRserver.R): 856 lines
    • ...
    • .getHelpModal() (R/appHelp.R): 88 lines
* Checking man page documentation...
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 37 lines (1%) are > 80 characters long.
  First few lines:
    • R/appHelp.R#L141 ", tags$a(href="http://bioconduc ...
    • ...
    • vignettes/scanMiRApp.Rmd#L11 affiliation: Lab of Systems Neuroscien ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 999 lines (37%) are
not.
  First few lines:
    • R/appHelp.R#L2 data.frame( ...
    • ...
    • vignettes/scanMiRApp.Rmd#L148 file.prefix="out_path/agg ...
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 | ⚠ 1 WARNINGS | ℹ 13 NOTES
ℹ See the scanMiRApp.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.