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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('affy_1.91.0.tar.gz','quit-with-status'=TRUE)"
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── Installing affy ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── affy session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpBWeU3u/file2beee34c56d223/affy
→ BiocVersion: 3.24
→ Package: affy
→ PackageVersion: 1.91.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/affy.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpBWeU3u/file2beee34c56d223/affy
→ installDir: /tmp/RtmpBWeU3u/file2beee39fa3f91
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on affy ───────────────────────────────────────────────────
* 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 2.8.0 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 (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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • affy.Rnw
    • ...
    • vim.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • affy.Rnw
    • ...
    • vim.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/affy.Rnw
    • ...
    • vignettes/vim.Rnw
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/getCDFenv.R (line 100, column 13)
* Checking for library/require of affy...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/read.affybatch.R (line 67, column 43)
    • ...
    • require() in R/xy2indices.R (line 46, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AffyBatch.R (line 442, column 30)
    • ...
    • R/read.affybatch.R (line 347, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AffyBatch.R (line 788, column 23)
    • ...
    • read.affybatch.R (line 54, column 32)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AffyBatch.R (line 51, column 20)
    • ...
    • cat() in R/zzz.R (line 34, column 22)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AffyBatch.R (line 149, column 33)
    • ...
    • R/ProgressBarText.R (line 12, column 31)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AffyBatch.R (line 611, column 20)
    • ...
    • R/xy2indices.R (line 47, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/read.affybatch.R (line 248, column 26)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • zzz.R (line 45, column 25)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/loess.normalize.R (line 5, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/affy.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 11 times)
  • <<- in R/expresso.R (line 63, column 34)
  • ...
  • <<- in R/zzz.R (line 101, column 21)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 24
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.160() (R/mva.pairs.R): 238 lines
    • ...
    • normalize.qspline() (R/normalize.qspline.R): 119 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/affy-deprecated.Rd
    • ...
    • man/summary.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • affy-deprecated.Rd
    • ...
    • whatcdf.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:
    • ppsetApply.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • ppsetApply.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; 312 lines (3%) are > 80 characters long.
  First few lines:
    • R/AffyBatch.R#L68 ## provide a signature consist ...
    • ...
    • vignettes/vim.Rnw#L107 The function \verb+read.affybatch+ shoul ...
ℹ NOTE: Consider 4 spaces instead of tabs; 141 lines (2%) contain tabs.
  First few lines:
    • R/bg.R#L56 pm(object) <- rma.background.correct(pm ...
    • ...
    • man/ProbeSet-class.Rd#L35 statistic to the probe set.} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3041 lines (34%) are
not.
  First few lines:
    • R/AffyBatch.R#L3 normalize.AffyBatch.methods <- function ...
    • ...
    • vignettes/vim.Rnw#L99 \subsection{AffyBatch objects} ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 5 WARNINGS | ℹ 20 NOTES
ℹ See the affy.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.