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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('yarn_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing yarn ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── yarn session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsH8Kgv/file154f363e0665ce/yarn
→ BiocVersion: 3.24
→ Package: yarn
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/yarn.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpsH8Kgv/file154f363e0665ce/yarn
→ installDir: /tmp/RtmpsH8Kgv/file154f36a98daab
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on yarn ───────────────────────────────────────────────────
* 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...
* 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...
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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (46%).
* 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:
    • yarn.Rmd
* Checking package installation calls in R code...
* Checking for library/require of yarn...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/downloadGTEx.R (line 32, column 10)
    • R/normalizeTissueAware.R (line 45, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • checkMisAnnotation.R (line 33, column 63)
    • ...
    • qsmooth.R (line 79, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotateFromBiomart.R (line 44, column 11)
    • ...
    • R/annotateFromBiomart.R (line 49, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • extractMatrix.R (line 19, column 18)
    • qsmooth.R (line 25, column 23)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/downloadGTEx.R (line 49, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
  The longest 5 functions are:
    • qsmooth() (R/qsmooth.R): 71 lines
    • downloadGTEx() (R/downloadGTEx.R): 69 lines
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • downloadGTEx.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 24% of man
pages use at least one of these tags.
  Found in files:
    • bladder.Rd
    • ...
    • skin.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; 73 lines (8%) are > 80 characters long.
  First few lines:
    • R/annotateFromBiomart.R#L7 #' @param biomart BioMart database name ...
    • ...
    • vignettes/yarn.Rmd#L107 `plotDensity` - Density plots colored by ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 218 lines (24%) are
not.
  First few lines:
    • R/annotateFromBiomart.R#L36 mart <- useMart(biomart=biomart,datase ...
    • ...
    • vignettes/yarn.Rmd#L120 col = heatmapCols,ColSideColors = heatm ...
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 15 NOTES
ℹ See the yarn.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.