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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('eiR_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing eiR ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── eiR session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpALtTts/file86aa63fd1ec86/eiR
→ BiocVersion: 3.24
→ Package: eiR
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/eiR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpALtTts/file86aa63fd1ec86/eiR
→ installDir: /tmp/RtmpALtTts/file86aa656378c6b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on eiR ────────────────────────────────────────────────────
* 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 2.10.0 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...
* 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 (23%).
* 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...
✖ ERROR: More than one VignetteEngine specified.
  Found in files:
    • vignettes/eiR.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • eiR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of eiR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/core.R (line 2, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/core.R (line 307, column 29)
    • ...
    • R/measures.R (line 149, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • core.R (line 299, column 41)
    • ...
    • measures.R (line 149, column 24)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/core.R (line 683, column 17)
    • ...
    • print() in R/evaluations.R (line 3, column 19)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/core.R (line 4, column 9)
    • ...
    • R/measures.R (line 140, column 41)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/core.R (line 102, column 22)
    • ...
    • R/measures.R (line 114, column 30)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 14 times:
    • F in R/core.R (line 237, column 61)
    • ...
    • F in R/core.R (line 904, column 100)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
  • .Deprecated() in R/core.R (line 21, column 9)
  • .Deprecated() in R/core.R (line 24, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 14 times)
  • <<- in R/core.R (line 153, column 24)
  • ...
  • <<- in R/db.R (line 410, column 39)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/db.R (line 541, column 9)
  • suppressWarnings() in R/evaluations.R (line 15, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
  The longest 5 functions are:
    • eiMakeDb() (R/core.R): 104 lines
    • ...
    • eiQuery() (R/core.R): 80 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/eiQuery.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/eiAdd.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • freeLSHData.Rd
  • loadLSHData.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
  Found in files:
    • freeLSHData.Rd
    • loadLSHData.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • freeLSHData.Rd
    • loadLSHData.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; 279 lines (8%) are > 80 characters long.
  First few lines:
    • R/core.R#L79 cl=NULL,connSource=NULL,priorityF ...
    • ...
    • vignettes/eiR.Rmd#L171 non-reference samples which can later be ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1771 lines (52%) contain tabs.
  First few lines:
    • R/core.R#L20 matrixFile = NULL){ ...
    • ...
    • vignettes/eiR.Rmd#L433 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 295 lines (9%) are
not.
  First few lines:
    • R/core.R#L1044 embedJob = function(ids){ ...
    • ...
    • vignettes/eiR.Rmd#L288 eiPerformanceTest(runId,K=22) ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 20 NOTES
ℹ See the eiR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.