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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('affycomp_1.89.0.tar.gz','quit-with-status'=TRUE)"
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── Installing affycomp ─────────────────────────────────────────────────────────
✔ Package installed successfully
── affycomp session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpux9hws/file4b49e15a7f674/affycomp
→ BiocVersion: 3.24
→ Package: affycomp
→ PackageVersion: 1.89.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/affycomp.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpux9hws/file4b49e15a7f674/affycomp
→ installDir: /tmp/Rtmpux9hws/file4b49e1a4f2d6a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on affycomp ───────────────────────────────────────────────
* 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 2.13.0 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 (50%).
* 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:
    • affycomp.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • affycomp.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/affycomp.Rnw
* Checking package installation calls in R code...
* Checking for library/require of affycomp...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/assess.R (line 37, column 3)
    • require() in R/figures.R (line 211, column 3)
    • require() in R/newfuncs.R (line 32, column 3)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/newfuncs.R (line 153, column 15)
    • ...
    • R/newfuncs.R (line 507, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • assess.R (line 43, column 12)
    • ...
    • table.R (line 149, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/assess.R (line 13, column 15)
    • ...
    • cat() in R/newfuncs.R (line 26, column 15)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/newfuncs.R (line 131, column 10)
    • ...
    • R/newfuncs.R (line 187, column 11)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/newfuncs.R (line 131, column 58)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/figures.R (line 222, column 3)
  • set.seed() in R/newfuncs.R (line 130, 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 6
functions greater than 50 lines.
  The longest 5 functions are:
    • assessFC() (R/assess.R): 135 lines
    • ...
    • assessFC2() (R/assess.R): 54 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • assessAll.Rd
    • ...
    • remove.hgu133a.xhyb.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...
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; 49 lines (2%) are > 80 characters long.
  First few lines:
    • R/assess.R#L27 if(verbose) cat("Performing 9 assessme ...
    • ...
    • vignettes/affycomp.Rnw#L25 \title{Bioconductor Expression Assessmen ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
  First few lines:
    • R/figures.R#L112 text(xx[o1],yy[o1],expression(infinit ...
    • ...
    • R/newfuncs.R#L378 text(xxx[o2],yyy[o2],expression(- ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1100 lines (39%) are
not.
  First few lines:
    • R/assess.R#L2 if(is.null(method.name)) method.name < ...
    • ...
    • vignettes/affycomp.Rnw#L454 against mean log expression. ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 15 NOTES
ℹ See the affycomp.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.