##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('bigmelon_1.39.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing bigmelon ─────────────────────────────────────────────────────────
✔ Package installed successfully
── bigmelon session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1NIaPD/file5b28c16af6ada/bigmelon
→ BiocVersion: 3.24
→ Package: bigmelon
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/bigmelon.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp1NIaPD/file5b28c16af6ada/bigmelon
→ installDir: /tmp/Rtmp1NIaPD/file5b28c26dae8f6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on bigmelon ───────────────────────────────────────────────
* 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 3.3 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Epigenetics,
Normalization, MultiChannel, ImmunoOncology, DifferentialMethylation
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • bigmelon.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • bigmelon.Rnw
* Checking package installation calls in R code...
* Checking for library/require of bigmelon...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/ecc.gdsn.R (line 46, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/bumphunterGdsn.R (line 52, column 28)
    • ...
    • R/inout.R (line 265, column 28)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bumphunterGdsn.R (line 108, column 48)
    • ...
    • ranknorm.R (line 136, column 14)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bumphunterGdsn.R (line 87, column 26)
    • ...
    • R/pfilterGds.R (line 30, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/comboGds.R (line 17, column 17)
    • ...
    • R/inout.R (line 80, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 17 times:
    • T in R/gdsnclass_methods.R (line 936, column 36)
    • ...
    • T in R/inout.R (line 343, column 70)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • comboGds.R (line 13, column 24)
    • ...
    • ranknorm.R (line 105, column 22)
* 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 15
functions greater than 50 lines.
  The longest 5 functions are:
    • bumphunterEngine.gdsn() (R/bumphunterGdsn.R): 331 lines
    • ...
    • chainsaw() (R/chainsaw.R): 117 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/bigPepo.Rd
    • ...
    • man/ecc.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • bumphunterGdsn.Rd
    • ...
    • wm-port.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • finalreport2gds.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • finalreport2gds.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 160 lines (4%) are > 80 characters long.
  First few lines:
    • R/bumphunterGdsn.R#L1 .getEstimate2 <- function(mat, design, c ...
    • ...
    • vignettes/bigmelon.Rnw#L488 Often, it will be necessary to make use ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/bumphunterGdsn.R#L189 NullBeta<-as.matrix(permRawBeta) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 430 lines (10%) are
not.
  First few lines:
    • R/bumphunterGdsn.R#L2 # mat = node (i.e betas) ...
    • ...
    • R/ranknorm.R#L30 valdim = c( sum(on ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 5 WARNINGS | ℹ 17 NOTES
ℹ See the bigmelon.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.