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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('circRNAprofiler_1.27.0.tar.gz','quit-with-status'=TRUE)"
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── Installing circRNAprofiler ──────────────────────────────────────────────────
✔ Package installed successfully
── circRNAprofiler session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpkCR3RH/file6b5754de5aaa2/circRNAprofiler
→ BiocVersion: 3.24
→ Package: circRNAprofiler
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/circRNAprofiler.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpkCR3RH/file6b5754de5aaa2/circRNAprofiler
→ installDir: /tmp/RtmpkCR3RH/file6b5751d5e2445
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on circRNAprofiler ────────────────────────────────────────
* 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 4.5.0 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...
✖ 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 (46%).
* 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:
    • circRNAprofiler.Rmd
✖ ERROR: Package installation calls found in vignette(s)
  Found in files:
    • vignettes/circRNAprofiler.Rmd (chunk no. 39, line 980, column 16)
* Checking package installation calls in R code...
* Checking for library/require of circRNAprofiler...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/annotateBSJs.R (line 55, column 9)
    • ...
    • cat() in R/importFilesPredictionTool.R (line 272, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getMotifs.R (line 656, column 8)
    • ...
    • R/getRandomBSJunctions.R (line 36, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/initCircRNAprofiler.R (line 42, column 17)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/getRandomBSJunctions.R (line 96, column 13)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/annotateRepeats.R (line 240, column 9)
  • ...
  • suppressWarnings() in R/supportFunctions.R (line 390, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 31
functions greater than 50 lines.
  The longest 5 functions are:
    • .fixCoordsWithGTF() (R/supportFunctions.R): 115 lines
    • ...
    • .grCoordsForNegative() (R/getSeqsFromGRs.R): 77 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • initCircRNAprofiler.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • initCircRNAprofiler.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • initCircRNAprofiler.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; 244 lines (3%) are > 80 characters long.
  First few lines:
    • R/annotateBSJs.R#L83 annotatedBSJs$allTranscripts ...
    • ...
    • vignettes/circRNAprofiler.Rmd#L1600 We thank Engr. Dario Zarro and the
    membe ...
ℹ NOTE: Consider 4 spaces instead of tabs; 12 lines (0%) contain tabs.
  First few lines:
    • vignettes/circRNAprofiler.Rmd#L1015 - id: unique identifier.  ...
    • ...
    • vignettes/circRNAprofiler.Rmd#L1139 - chrom: is the chromosome from which
    th ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 173 lines (2%) are
not.
  First few lines:
    • R/annotateRepeats.R#L68 annotationHubID = "AH5122", ...
    • ...
    • vignettes/circRNAprofiler.Rmd#L1557 ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the circRNAprofiler.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.