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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ExpressionAtlas_2.5.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ExpressionAtlas ──────────────────────────────────────────────────
✔ Package installed successfully
── ExpressionAtlas session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp69SlOR/file987c62609cc0b/ExpressionAtlas
→ BiocVersion: 3.24
→ Package: ExpressionAtlas
→ PackageVersion: 2.5.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ExpressionAtlas.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp69SlOR/file987c62609cc0b/ExpressionAtlas
→ installDir: /tmp/Rtmp69SlOR/file987c6334d1d75
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ExpressionAtlas ────────────────────────────────────────
* 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 4.2.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ ExperimentData
* 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...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 2025/09/01
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (42%).
* 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: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/ExpressionAtlas.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • knitr
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ExpressionAtlas.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ExpressionAtlas.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ExpressionAtlas...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/functions.R (line 122, column 13)
    • R/functions.R (line 150, column 55)
    • R/functions.R (line 203, column 19)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • functions.R (line 306, column 27)
    • functions.R (line 333, column 18)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/functions.R (line 246, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/functions.R (line 31, column 9)
    • ...
    • R/functions.R (line 332, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/functions.R (line 51, column 21)
    • ...
    • R/functions.R (line 389, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • functions.R (line 44, column 29)
    • functions.R (line 81, column 28)
* Checking parsed R code in R directory, examples, vignettes...
* 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:
    • searchAtlasExperiments() (R/functions.R): 209 lines
    • getAtlasExperiment() (R/functions.R): 97 lines
* Checking man page documentation...
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • inst/NEWS
    • ExpressionAtlas/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; 47 lines (6%) are > 80 characters long.
  First few lines:
    • R/functions.R#L13 urlBase <- "ftp://ftp.ebi.ac.uk/pub/ ...
    • ...
    • vignettes/ExpressionAtlas.Rmd#L210 #
    ftp://ftp.ebi.ac.uk/pub/databases/mic ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1 lines (0%) are not.
  First few lines:
    • R/functions.R#L392 ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the ExpressionAtlas.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.