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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('annaffy_1.85.0.tar.gz','quit-with-status'=TRUE)"
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── Installing annaffy ──────────────────────────────────────────────────────────
✔ Package installed successfully
── annaffy session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpHDH9Rb/file5471a608832fa/annaffy
→ BiocVersion: 3.24
→ Package: annaffy
→ PackageVersion: 1.85.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/annaffy.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpHDH9Rb/file5471a608832fa/annaffy
→ installDir: /tmp/RtmpHDH9Rb/file5471a413ca539
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on annaffy ────────────────────────────────────────────────
* 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 2.5.0 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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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:
    • annaffy.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • annaffy.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/annaffy.Rnw
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install() in R/chkPkgs.R (line 17, column 22)
* Checking for library/require of annaffy...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/annotation.R (line 30, column 38)
    • ...
    • require() in R/zzz.R (line 1, column 31)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • annotation.R (line 63, column 14)
    • ...
    • table.R (line 394, column 52)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/chkPkgs.R (line 8, column 5)
    • print() in R/chkPkgs.R (line 20, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotation.R (line 501, column 8)
    • ...
    • R/table.R (line 354, column 26)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/annotation.R (line 51, column 14)
    • ...
    • R/search.R (line 32, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/annotation.R (line 281, column 57)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • table.R (line 90, column 33)
    • table.R (line 352, column 45)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/annaffy.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/widget.R (line 23, column 18)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/annotation.R (line 30, column 21)
  • suppressWarnings() in R/annotation.R (line 86, column 20)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • selectorWidget() (R/widget.R): 83 lines
    • ...
    • _anonymous_.335() (R/table.R): 55 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/aafExpr.Rd
    • ...
    • man/getURL-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • aaf.handler.Rd
    • ...
    • selectorWidget.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; 41 lines (1%) are > 80 characters long.
  First few lines:
    • R/annotation.R#L86 tmp <- suppressWarnings(as.i ...
    • ...
    • vignettes/annaffy.Rnw#L188 \href{http://godatabase.org/cgi-bin/go.c ...
ℹ NOTE: Consider 4 spaces instead of tabs; 22 lines (1%) contain tabs.
  First few lines:
    • R/search.R#L2 ...
    • ...
    • man/is.annpkg.Rd#L18 are searched before the libraries. ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 642 lines (17%) are
not.
  First few lines:
    • R/annotation.R#L17 "ENTREZID", "MAP", "PA ...
    • ...
    • man/selectorWidget.Rd#L24 coerced back to the correct type. ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the annaffy.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.