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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('illuminaio_0.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing illuminaio ───────────────────────────────────────────────────────
✔ Package installed successfully
── illuminaio session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmptkt2iL/file3d7ebd2c2c2b17/illuminaio
→ BiocVersion: 3.24
→ Package: illuminaio
→ PackageVersion: 0.55.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/illuminaio.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/Rtmptkt2iL/file3d7ebd2c2c2b17/illuminaio
→ installDir: /tmp/Rtmptkt2iL/file3d7ebd78043dc1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on illuminaio ─────────────────────────────────────────────
* 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...
ℹ Package version 0.55.0; pre-release
* Checking R version dependency...
* 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...
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 NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • EncryptedFormat.Rnw
    • illuminaio.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/EncryptedFormat.Rnw
* Checking package installation calls in R code...
* Checking for library/require of illuminaio...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • readBPM.R (line 88, column 19)
    • ...
    • readIDAT_nonenc.R (line 211, column 16)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/readIDAT_enc.R (line 19, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/readBPM.R (line 57, column 13)
    • ...
    • R/readIDAT.R (line 25, column 14)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/readBPM.R (line 2, column 5)
* 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:
    • readIDAT_nonenc() (R/readIDAT_nonenc.R): 269 lines
    • readBPM() (R/readBPM.R): 123 lines
    • readIDAT_enc() (R/readIDAT_enc.R): 108 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • readBGX.Rd
    • readBPM.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; 66 lines (7%) are > 80 characters long.
  First few lines:
    • R/readBGX.R#L3 ## read the [Heading] section of the ...
    • ...
    • vignettes/illuminaio.Rnw#L109 The first plot shows the summarized bead
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 169 lines (17%) are
not.
  First few lines:
    • R/readBGX.R#L2 ...
    • ...
    • vignettes/illuminaio.Rnw#L105 breaks = 100, main = "", xlab = "Di ...
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 v1.49.6 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 11 NOTES
ℹ See the illuminaio.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.