##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BeadDataPackR_1.65.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing BeadDataPackR ────────────────────────────────────────────────────
✔ Package installed successfully
── BeadDataPackR session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmpjFF4jE/file5a1372a85366a/BeadDataPackR
→ BiocVersion: 3.24
→ Package: BeadDataPackR
→ PackageVersion: 1.65.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BeadDataPackR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpjFF4jE/file5a1372a85366a/BeadDataPackR
→ installDir: /tmp/RtmpjFF4jE/file5a13751facd49
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BeadDataPackR ──────────────────────────────────────────
* 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...
* 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: OneChannel,
TwoChannel
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: 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:
    • BeadDataPackR.rnw
! WARNING: Evaluate more vignette chunks.
ℹ 4 out of 7 code chunks = 57% unevaluated
ℹ 
* Checking package installation calls in R code...
* Checking for library/require of BeadDataPackR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/compressBeadData.R (line 83, column 66)
    • R/readBabFile.R (line 88, column 39)
    • R/writeBabFile.R (line 67, column 42)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • combineFiles.R (line 6, column 19)
    • ...
    • writeBabFile.R (line 117, column 14)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/compressBeadData.R (line 27, column 29)
    • ...
    • R/writeBabFile.R (line 63, column 26)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/compressBeadData.R (line 3, column 13)
    • ...
    • R/readRawData.R (line 37, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/locsFileIndexing.R (line 18, column 89)
* 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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • decompressBeadData() (R/decompressBeadData.R): 139 lines
    • ...
    • combineFiles() (R/combineFiles.R): 80 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/example.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; 160 lines (12%) are > 80 characters long.
  First few lines:
    • R/combineFiles.R#L1 combineFiles <- function(txt, locsGrn, l ...
    • ...
    • vignettes/BeadDataPackR.rnw#L110 Using coordinates in the grid order prov
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7 lines (1%) contain tabs.
  First few lines:
    • R/scanBabFile.R#L49 storeTmp <- readBin(con, integer(), siz ...
    • ...
    • R/scanBabFile.R#L116 ## tell the user if no probe IDs matche ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 65 lines (5%) are not.
  First few lines:
    • R/combineFiles.R#L2 ...
    • ...
    • vignettes/BeadDataPackR.rnw#L107 locs <- extractLocsFile(inputFile = "e
    ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 13 NOTES
ℹ See the BeadDataPackR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.