##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('TFBSTools_1.50.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing TFBSTools ────────────────────────────────────────────────────────
✔ Package installed successfully
── TFBSTools session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpVpOAlC/file99d771beb5617/TFBSTools
→ BiocVersion: 3.23
→ Package: TFBSTools
→ PackageVersion: 1.50.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/TFBSTools.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpVpOAlC/file99d771beb5617/TFBSTools
→ installDir: /tmp/RtmpVpOAlC/file99d772cf573f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TFBSTools ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.2.2 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVpOAlC/file99d771beb5617/TFBSTools/man/PFMSimilarity-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVpOAlC/file99d771beb5617/TFBSTools/man/PWMSimilarity-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVpOAlC/file99d771beb5617/TFBSTools/man/readJASPARMatrix.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVpOAlC/file99d771beb5617/TFBSTools/man/TFFM-class.Rd'
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (9%).
* 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: Vignette(s) found with missing chunk labels
  Found in files:
    • TFBSTools.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpVpOAlC/file99d771beb5617/TFBSTools/vignettes/TFBSTools.Rmd
* Checking package installation calls in R code...
* Checking for library/require of TFBSTools...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllClasses.r (line 182, column 18)
    • ...
    • R/XMatrixList-methods.r (line 12, column 52)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • DB-methods.r (line 722, column 22)
    • ...
    • util-methods.r (line 42, column 12)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.r (line 113, column 10)
    • ...
    • R/XMatrix-methods.r (line 119, column 27)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/DB-methods.r (line 186, column 13)
    • R/Wrappers-methods.r (line 30, column 12)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Wrappers-methods.r (line 36, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/PairwiseAlignment-methods.r (line 225, column 11)
  • ...
  • suppressWarnings() in R/PairwiseAlignment-methods.r (line 364, column 12)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 16
functions greater than 50 lines.
  The longest 5 functions are:
    • dirichletMixtureEMEstimation() (R/DirichletMixture.r): 99 lines
    • ...
    • do_PairBSgenomeSearchPositive() (R/PairwiseAlignment-methods.r): 71 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/rPWMDmm-methods.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/SiteSet-class.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calConservation-methods.Rd
    • ...
    • writeGFF3-methods.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 19% of man
pages use at least one of these tags.
  Found in files:
    • dmmEM-methods.Rd
    • ...
    • searchPairBSgenome-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • MotifSet-class.Rd
    • runMEME-methods.Rd
    • searchPairBSgenome-methods.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; 113 lines (1%) are > 80 characters long.
  First few lines:
    • R/AllClasses.r#L344 # gapOp ...
    • ...
    • vignettes/TFBSTools.Rmd#L519 In this section, we will introduce wrapp ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3835 lines (44%) are
not.
  First few lines:
    • R/AllClasses.r#L10 slots=c( ...
    • ...
    • vignettes/TFBSTools.Rmd#L530 ) ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the TFBSTools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.