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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CexoR_1.51.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CexoR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── CexoR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYucOtd/file641bd5a328a0a/CexoR
→ BiocVersion: 3.24
→ Package: CexoR
→ PackageVersion: 1.51.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CexoR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpYucOtd/file641bd5a328a0a/CexoR
→ installDir: /tmp/RtmpYucOtd/file641bd4d4112f1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CexoR ──────────────────────────────────────────────────
* 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 4.2.0 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (78%).
* 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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • CexoR.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • CexoR.Rnw
* Checking package installation calls in R code...
* Checking for library/require of CexoR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cexor.R (line 29, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cexor.R (line 22, column 17)
    • ...
    • pskellam.R (line 28, column 28)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cexor.R (line 190, column 52)
    • R/cexor.R (line 290, column 11)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 5 times:
    • F in R/plotcexor.R (line 18, column 128)
    • ...
    • F in R/plotcexor.R (line 54, column 92)
* 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 2
functions greater than 50 lines.
  The longest 5 functions are:
    • cexor() (R/cexor.R): 345 lines
    • plotcexor() (R/plotcexor.R): 60 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • CexoR-internal.Rd
* 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; 117 lines (15%) are > 80 characters long.
  First few lines:
    • R/cexor.R#L2 cexor <- function( bam, chrN, chrL, p=1e ...
    • ...
    • vignettes/CexoR.Rnw#L103 The author wishes to acknowledge Christo ...
ℹ NOTE: Consider 4 spaces instead of tabs; 87 lines (11%) contain tabs.
  First few lines:
    • R/cexor.R#L115 chrLwithPeaksCount <- 0 ...
    • ...
    • R/cexor.R#L323 Fisher[i] <- Fisher.test(p=PVALMATRIX[i ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 279 lines (35%) are
not.
  First few lines:
    • R/cexor.R#L4 options(digits=10) ...
    • ...
    • man/plotcexor.Rd#L45 setwd(owd) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 12 NOTES
ℹ See the CexoR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.