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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ChIPexoQual_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ChIPexoQual ──────────────────────────────────────────────────────
✔ Package installed successfully
── ChIPexoQual session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpR2UWJY/file6593621d497a2/ChIPexoQual
→ BiocVersion: 3.24
→ Package: ChIPexoQual
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ChIPexoQual.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpR2UWJY/file6593621d497a2/ChIPexoQual
→ installDir: /tmp/RtmpR2UWJY/file6593667363be0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ChIPexoQual ────────────────────────────────────────────
* 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 3.5.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: RNASeq,
ImmunoOncology, DataImport
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (40%).
* 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...
! WARNING: Vignette(s) still using 'VignetteIndexEntry{Vignette Title}'
  The following files use template defaults:
    • vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ChIPexoQual...
* Checking coding practice...
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • AllClasses.R (line 120, column 24)
    • AllClasses.R (line 121, column 24)
    • base_blacklist.R (line 38, column 24)
* 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 3
functions greater than 50 lines.
  The longest 5 functions are:
    • ExoData() (R/AllClasses.R): 110 lines
    • ExoDataBlacklist() (R/base_blacklist.R): 80 lines
    • ExoDataSubsampling() (R/base_subsampling.R): 54 lines
* Checking man page documentation...
* 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; 63 lines (4%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L46 ##' @param reads a \code{GAlignments} ob ...
    • ...
    • vignettes/vignette.Rmd#L210 We presented a systematic exploration of ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 137 lines (10%) are
not.
  First few lines:
    • R/AllClasses.R#L18 contains = "GRanges", ...
    • ...
    • vignettes/vignette.Rmd#L150 names.input = c("All", ...
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 | ⚠ 2 WARNINGS | ℹ 8 NOTES
ℹ See the ChIPexoQual.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.