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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('mobileRNA_1.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing mobileRNA ────────────────────────────────────────────────────────
✔ Package installed successfully
── mobileRNA session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpMblqxe/filedd0654e0dace8/mobileRNA
→ BiocVersion: 3.24
→ Package: mobileRNA
→ PackageVersion: 1.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/mobileRNA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpMblqxe/filedd0654e0dace8/mobileRNA
→ installDir: /tmp/RtmpMblqxe/filedd065529025f1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mobileRNA ──────────────────────────────────────────────
* 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 4.3.0 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 (34%).
* 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:
    • mobileRNA.Rmd
* Checking package installation calls in R code...
* Checking for library/require of mobileRNA...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/invisible.functions.mobileRNA.R (line 106, column 13)
    • R/invisible.functions.mobileRNA.R (line 123, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • RNAdistribution.R (line 256, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/RNApopulation.R (line 167, column 17)
    • cat() in R/RNAsummary.R (line 99, column 3)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/RNAfeatures.R (line 116, column 75)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/invisible.functions.mobileRNA.R (line 135, column 10)
    • ...
    • system() in R/invisible.functions.mobileRNA.R (line 1050, column 10)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressMessages() in R/plotSamplePCA.R (line 179, column 9)
  • ...
  • suppressWarnings() in R/RNAfeatures.R (line 119, column 15)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 19
functions greater than 50 lines.
  The longest 5 functions are:
    • RNAdistribution() (R/RNAdistribution.R): 335 lines
    • ...
    • core_map() (R/invisible.functions.mobileRNA.R): 209 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/mRNA_data.Rd
    • man/sRNA_data.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • mapRNA.Rd
  • RNAimport.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
  Found in files:
    • mapRNA.Rd
    • RNAimport.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • mapRNA.Rd
    • RNAimport.Rd
* 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; 186 lines (3%) are > 80 characters long.
  First few lines:
    • R/invisible.functions.mobileRNA.R#L170 charCols <-
    vapply(S4Vectors::elementM ...
    • ...
    • vignettes/mobileRNA.Rmd#L1233 samtools view -Sb [outputfile_uniqueRead
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • vignettes/mobileRNA.Rmd#L104 * High dependency on arbitrary threshold ...
    • vignettes/mobileRNA.Rmd#L105 * Use of additional statistical tests to ...
    • vignettes/mobileRNA.Rmd#L106 * High false positive rates.  ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1808 lines (29%) are
not.
  First few lines:
    • R/invisible.functions.mobileRNA.R#L8 class_colnames <- data %>%
    dplyr::sel ...
    • ...
    • vignettes/mobileRNA.Rmd#L1164 ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 18 NOTES
ℹ See the mobileRNA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.