##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('transcriptogramer_1.35.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing transcriptogramer ────────────────────────────────────────────────
✔ Package installed successfully
── transcriptogramer session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmpzdhYDZ/file14e90226f618a9/transcriptogramer
→ BiocVersion: 3.24
→ Package: transcriptogramer
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/transcriptogramer.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpzdhYDZ/file14e90226f618a9/transcriptogramer
→ installDir: /tmp/RtmpzdhYDZ/file14e9023b5b6509
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on transcriptogramer ──────────────────────────────────────
* 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 3.4 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:
GenomeWideAssociation
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...
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 (24%).
* 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:
    • transcriptogramer.Rmd
* Checking package installation calls in R code...
* Checking for library/require of transcriptogramer...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllMethods.R (line 398, column 15)
    • ...
    • R/AllMethods.R (line 974, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllMethods.R (line 496, column 26)
    • ...
    • AllMethods.R (line 969, column 34)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllConstructors.R (line 40, column 17)
    • ...
    • R/AllMethods.R (line 844, column 19)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/AllMethods.R (line 878, column 56)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 20 times)
  • <<- in R/AllMethods.R (line 399, column 19)
  • ...
  • <<- in R/AllMethods.R (line 975, column 17)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/AllMethods.R (line 987, column 13)
  • ...
  • suppressMessages() in R/AllMethods.R (line 805, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.337() (R/AllMethods.R): 247 lines
    • ...
    • _anonymous_.32() (R/AllMethods.R): 90 lines
* Checking man page documentation...

ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 32% of man
pages use at least one of these tags.
  Found in files:
    • clusterEnrichment-method.Rd
    • ...
    • transcriptogramStep2-method.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • clusterEnrichment-method.Rd
    • ...
    • transcriptogramStep2-method.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; 141 lines (4%) are > 80 characters long.
  First few lines:
    • R/AllChecks.R#L185 stop("NA returned by parallel::d ...
    • ...
    • vignettes/transcriptogramer.Rmd#L286 This is not possible in the current
    tran ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 297 lines (9%) are
not.
  First few lines:
    • R/AllChecks.R#L135 name <- "nTerms" ...
    • ...
    • vignettes/transcriptogramer.Rmd#L256 pValue = 0.00 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the transcriptogramer.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.