##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GlobalAncova_4.31.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing GlobalAncova ─────────────────────────────────────────────────────
✔ Package installed successfully
── GlobalAncova session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpSxIv9p/filea72b77170ff43/GlobalAncova
→ BiocVersion: 3.24
→ Package: GlobalAncova
→ PackageVersion: 4.31.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GlobalAncova.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpSxIv9p/filea72b77170ff43/GlobalAncova
→ installDir: /tmp/RtmpSxIv9p/filea72b764b73ce1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GlobalAncova ───────────────────────────────────────────
* 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...
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, GO
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 (56%).
* 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:
    • GlobalAncova.rnw
    • GlobalAncovaDecomp.rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GlobalAncova.rnw
    • GlobalAncovaDecomp.rnw
* Checking package installation calls in R code...
* Checking for library/require of GlobalAncova...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/genesettesting.R (line 43, column 15)
    • ...
    • R/Plot.all.R (line 46, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • approximation.R (line 35, column 25)
    • ...
    • Plot.subjects.R (line 231, column 34)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/gGlobalAncova.hierarchical.R (line 120, column 3)
    • ...
    • print() in R/permutation.R (line 38, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/GlobalAncova.decomp.R (line 167, column 12)
    • R/GlobalAncova.decomp.R (line 168, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/gGlobalAncova.R (line 263, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 38 times:
    • F in R/genesettesting.R (line 309, column 55)
    • ...
    • F in R/Plot.subjects.R (line 143, column 63)
* 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 18
functions greater than 50 lines.
  The longest 5 functions are:
    • gGAteststats() (R/gGlobalAncova.R): 186 lines
    • ...
    • gGlobalAncova.hierarchical() (R/gGlobalAncova.hierarchical.R): 105 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/GAhier-class.Rd
  • man/gGlobalAncova.hierarchical.Rd
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/bindata.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/GAhier-class.Rd
    • ...
    • man/Plot.subjects.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • genesettesting.Rd
  • GlobalAncova.closed.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...
Warning in grepl("\t", lines) :
  unable to translate '########################## 'alte' Fkt. f<fc>r 2 Gruppen ###########################' to a wide string
Warning in grepl("\t", lines) : input string 38 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '########################## 'alte' Fkt. f<fc>r 2 Gruppen ###########################' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 38 is invalid
ℹ NOTE: Consider shorter lines; 1017 lines (18%) are > 80 characters long.
  First few lines:
    • R/approximation.R#L2 # calculates the asymptotic p-value usin ...
    • ...
    • vignettes/GlobalAncovaDecomp.rnw#L322
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ...
ℹ NOTE: Consider 4 spaces instead of tabs; 43 lines (1%) contain tabs.
  First few lines:
    • R/GlobalAncova.closed.R#L126 if(tested == FALSE && prev.tested ...
    • ...
    • vignettes/GlobalAncovaDecomp.rnw#L94 data(pathways) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1865 lines (32%) are
not.
  First few lines:
    • R/approximation.R#L9 lams <- .weed(lams = lams, accuracy = ...
    • ...
    • vignettes/GlobalAncova.rnw#L954 model ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the GlobalAncova.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.