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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('annmap_1.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing annmap ───────────────────────────────────────────────────────────
✔ Package installed successfully
── annmap session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpksNqRA/file547b063114f99/annmap
→ BiocVersion: 3.24
→ Package: annmap
→ PackageVersion: 1.55.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/annmap.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpksNqRA/file547b063114f99/annmap
→ installDir: /tmp/RtmpksNqRA/file547b019444e78
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on annmap ─────────────────────────────────────────────────
* 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 2.15.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: ExonArray,
Sequencing, Coverage
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 'BugReports' field(s) in DESCRIPTION
* 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:
    • annmap.Rnw
    • cookbook.Rnw
    • INSTALL.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/annmap.Rnw
    • vignettes/cookbook.Rnw
    • vignettes/INSTALL.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/db.R (line 103, column 9)
* Checking for library/require of annmap...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/db.R (line 99, column 10)
    • require() in R/db.R (line 105, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/plot.ngs.R (line 144, column 3)
    • ...
    • R/ws.R (line 105, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • coords.R (line 22, column 22)
    • ...
    • ws.R (line 196, column 28)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/db.R (line 31, column 7)
    • ...
    • cat() in R/ws.R (line 143, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cache.R (line 1, column 15)
    • ...
    • R/zzz.R (line 1, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/coords.R (line 12, column 14)
    • ...
    • R/ws.R (line 33, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 41 times:
    • T in R/db.R (line 99, column 36)
    • ...
    • F in R/ws.R (line 176, column 111)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • db.R (line 157, column 46)
    • ...
    • utils.R (line 394, column 18)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/utils.R (line 289, column 13)
  • suppressWarnings() in R/ws.R (line 13, column 12)
  • suppressWarnings() in R/ws.R (line 71, column 12)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 21
functions greater than 50 lines.
  The longest 5 functions are:
    • .single.transcript.to.utr.range() (R/utr.R): 188 lines
    • ...
    • .genome.to.single.transcript.coords() (R/coords.R): 88 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/annmap.coords.Rd
    • ...
    • man/plot.ngs.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • plot.genomic.Rd
  • plot.ngs.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; 872 lines (15%) are > 80 characters long.
  First few lines:
    • R/coords.R#L1 # -------------------------------------- ...
    • ...
    • vignettes/INSTALL.Rnw#L146 When you run \code{annmapConnect()} insi ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • man/annmap.all.Rd#L60 annmapConnect() ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2669 lines (46%) are
not.
  First few lines:
    • R/cache.R#L2 paste( file.path( .xmap.internals$cach ...
    • ...
    • vignettes/INSTALL.Rnw#L138 \end{tabular} ...
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 Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 17 NOTES
ℹ See the annmap.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.