##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('FamAgg_1.41.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing FamAgg ───────────────────────────────────────────────────────────
✔ Package installed successfully
── FamAgg session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsbaGZp/file989c63f08c3d3/FamAgg
→ BiocVersion: 3.24
→ Package: FamAgg
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/FamAgg.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpsbaGZp/file989c63f08c3d3/FamAgg
→ installDir: /tmp/RtmpsbaGZp/file989c66074fcdb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on FamAgg ─────────────────────────────────────────────────
* 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...
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (12%).
* 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...
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/FamAgg.Rmd
* Checking package installation calls in R code...
* Checking for library/require of FamAgg...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Methods-FAGenIndexResults.R (line 277, column 28)
    • R/Methods-FAGenIndexResults.R (line 287, column 28)
    • R/utils.R (line 676, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Methods-FAData.R (line 488, column 14)
    • ...
    • utils.R (line 481, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Methods-FAKinGroupResults.R (line 477, column 5)
    • cat() in R/plotting-functions.R (line 462, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Methods-FAData.R (line 907, column 34)
    • ...
    • R/Methods-FAKinSumResults.R (line 291, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/Constructors.R (line 26, column 17)
    • ...
    • R/utils.R (line 507, column 31)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/Deprecated.R (line 220, column 17)
    • ...
    • R/plotting-functions.R (line 478, column 23)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Methods-FAStdIncidenceRateResults.R (line 345, column 16)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/plotting-functions.R (line 303, column 25)
    • system() in R/zzz.R (line 29, column 21)
! WARNING: .Deprecated / .Defunct usage (found 10 times)
  • .Deprecated() in R/Deprecated.R (line 92, column 5)
  • ...
  • .Deprecated() in R/utils.R (line 861, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 14 times)
  • suppressMessages() in R/Deprecated.R (line 58, column 15)
  • ...
  • suppressMessages() in R/zzz.R (line 16, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 30
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.64() (R/Methods-FAKinGroupResults.R): 254 lines
    • ...
    • buildHaplopaintDataframe() (R/plotting-functions.R): 149 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • FAProbResults.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; 74 lines (1%) are > 80 characters long.
  First few lines:
    • R/import-export.R#L94 ## Check if we've got case/control o ...
    • ...
    • vignettes/FamAgg.Rmd#L996 perform this type of test using the `bin ...
ℹ NOTE: Consider 4 spaces instead of tabs; 32 lines (0%) contain tabs.
  First few lines:
    • vignettes/FamAgg.Rmd#L410 b = c("193"))) ...
    • ...
    • vignettes/FamAgg.Rmd#L985 prune = TRUE, label1 = fr) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1687 lines (20%) are
not.
  First few lines:
    • R/Classes.R#L14 slots=c( ...
    • ...
    • vignettes/FamAgg.Rmd#L775 main = "Per family averaged familia ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the FamAgg.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.