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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ArrayExpress_1.73.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ArrayExpress ─────────────────────────────────────────────────────
✔ Package installed successfully
── ArrayExpress session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJoFZMt/file56be4158265a0/ArrayExpress
→ BiocVersion: 3.24
→ Package: ArrayExpress
→ PackageVersion: 1.73.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ArrayExpress.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpJoFZMt/file56be4158265a0/ArrayExpress
→ installDir: /tmp/RtmpJoFZMt/file56be47984905
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ArrayExpress ───────────────────────────────────────────
* 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 2.9.0 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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • ArrayExpress.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ArrayExpress.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ArrayExpress...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/extract.zip.r (line 9, column 23)
    • ...
    • R/procset.r (line 134, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • extract.zip.r (line 5, column 12)
    • ...
    • parseMAGE.r (line 489, column 37)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/getAE.r (line 134, column 5)
    • cat() in R/procset.r (line 78, column 5)
    • cat() in R/procset.r (line 110, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ae2bioc.r (line 7, column 9)
    • ...
    • R/queryAE.r (line 26, column 7)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ArrayExpress.r (line 13, column 15)
    • ...
    • R/queryAE.r (line 7, column 7)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/getAE.r (line 7, column 9)
    • R/queryAE.r (line 8, column 9)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • T in R/parseMAGE.r (line 96, column 98)
    • ...
    • T in R/procset.r (line 37, column 88)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • ae2bioc.r (line 125, column 23)
    • ...
    • ae2bioc.r (line 139, column 25)
* 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 9
functions greater than 50 lines.
  The longest 5 functions are:
    • ae2bioc() (R/ae2bioc.r): 171 lines
    • ...
    • procset() (R/procset.r): 73 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/ae2bioc.Rd
    • ...
    • man/queryAE.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • ae2bioc.Rd
    • ...
    • procset.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 168 lines (9%) are > 80 characters long.
  First few lines:
    • R/ae2bioc.r#L1 # A function that takes ArrayExpress MAG ...
    • ...
    • vignettes/ArrayExpress.Rnw#L236 Here we end up with a list of genes that
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 470 lines (26%) contain tabs.
  First few lines:
    • R/ae2bioc.r#L66 # labelCol = getSDRFcolumn("label",var ...
    • ...
    • man/ArrayExpress.Rd#L33 \item{drop}{ if TRUE and only one plat ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 572 lines (31%) are
not.
  First few lines:
    • R/ae2bioc.r#L8 ...
    • ...
    • vignettes/ArrayExpress.Rnw#L209 qanorm = arrayQualityMetrics(AEsetnorm
    ...
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 | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the ArrayExpress.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.