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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('AGDEX_1.61.0.tar.gz','quit-with-status'=TRUE)"
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── Installing AGDEX ────────────────────────────────────────────────────────────
✔ Package installed successfully
── AGDEX session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKIbDOy/file504f1f7ca320/AGDEX
→ BiocVersion: 3.24
→ Package: AGDEX
→ PackageVersion: 1.61.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/AGDEX.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpKIbDOy/file504f1f7ca320/AGDEX
→ installDir: /tmp/RtmpKIbDOy/file504f1423297b5
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on AGDEX ──────────────────────────────────────────────────
* 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 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpKIbDOy/file504f1f7ca320/AGDEX/man/agdex.scatterplot.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpKIbDOy/file504f1f7ca320/AGDEX/man/read.agdex.result.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpKIbDOy/file504f1f7ca320/AGDEX/man/write.agdex.gset.details.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
DifferentialExpression, MultipleComparison, GeneSetEnrichment, GO, KEGG,
GraphAndNetwork
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...
✖ 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 (67%).
* 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:
    • AGDEX.rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • AGDEX.rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/AGDEX.rnw
* Checking package installation calls in R code...
* Checking for library/require of AGDEX...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • agdex.R (line 20, column 73)
    • ...
    • write.gset.list.result.R (line 9, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/agdex.R (line 11, column 4)
    • ...
    • cat() in R/write.agdex.result.R (line 43, column 4)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/all.assign.agdex.R (line 15, column 29)
    • R/all.assign.agdex.R (line 18, column 35)
    • R/all.assign.agdex.R (line 19, column 34)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/agdex.scatterplot.R (line 44, column 18)
    • R/agdex.scatterplot.R (line 46, column 18)
    • R/get.gset.result.details.R (line 14, column 31)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 94 times:
    • T in R/agdex.R (line 87, column 22)
    • ...
    • F in R/write.gset.list.result.R (line 32, column 68)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • agdex() (R/agdex.R): 308 lines
    • ...
    • map.gset.lists() (R/map.gset.lists.R): 55 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/gset.data.Rd
    • man/read.agdex.gset.details.Rd
    • man/write.agdex.result.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • read.agdex.gset.details.Rd
    • read.agdex.result.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 43% of man
pages use at least one of these tags.
  Found in files:
    • gset.data.Rd
    • ...
    • write.agdex.result.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • gset.data.Rd
    • ...
    • write.agdex.result.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 390 lines (20%) are > 80 characters long.
  First few lines:
    • R/agdex.R#L2 function(dex.setA, # differentia ...
    • ...
    • vignettes/AGDEX.rnw#L251 Data using Projection onto the Most Inte ...
ℹ NOTE: Consider 4 spaces instead of tabs; 42 lines (2%) contain tabs.
  First few lines:
    • R/all.assign.agdex.R#L5 if(!is.vector(x)) x<-as.vector(x) ...
    • ...
    • vignettes/AGDEX.rnw#L53 \item characterize and determine the sta ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 868 lines (44%) are
not.
  First few lines:
    • R/agdex.R#L7 ...
    • ...
    • vignettes/AGDEX.rnw#L204 agdex.scatterplot(agdex.res, gset.id=NU ...
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 | ⚠ 3 WARNINGS | ℹ 19 NOTES
ℹ See the AGDEX.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.