##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('NoRCE_1.25.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing NoRCE ────────────────────────────────────────────────────────────
✔ Package installed successfully
── NoRCE session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKdMnfT/filef81d03a74b85e/NoRCE
→ BiocVersion: 3.24
→ Package: NoRCE
→ PackageVersion: 1.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/NoRCE.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpKdMnfT/filef81d03a74b85e/NoRCE
→ installDir: /tmp/RtmpKdMnfT/filef81d057db36f8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on NoRCE ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.4.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, FunctionalPrediction, GenePrediction
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' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (37%).
* 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: Evaluate more vignette chunks.
ℹ 28 out of 29 code chunks = 96% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • NoRCE.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/NoRCE.Rmd
* Checking package installation calls in R code...
* Checking for library/require of NoRCE...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/biotypeOperations.R (line 24, column 8)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • getNearest.R (line 680, column 13)
    • reverse.R (line 73, column 12)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotate.R (line 42, column 9)
    • ...
    • R/reverse.R (line 75, column 30)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • expressionBased.R (line 167, column 26)
    • expressionBased.R (line 171, column 26)
* 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 28
functions greater than 50 lines.
  The longest 5 functions are:
    • mirnaPathwayEnricher() (R/mirnaEnrichment.R): 249 lines
    • ...
    • genePathwayEnricher() (R/geneEnrichment.R): 216 lines
* Checking man page documentation...

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • assembly.Rd
    • ...
    • writeEnrichment.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 57% of man
pages use at least one of these tags.
  Found in files:
    • assembly.Rd
    • ...
    • writeEnrichment.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • assembly.Rd
    • ...
    • writeEnrichment.Rd
* Checking package 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; 76 lines (1%) are > 80 characters long.
  First few lines:
    • R/biotypeOperations.R#L34 return(unique(data.frame(gene = gsub(" ...
    • ...
    • vignettes/NoRCE.Rmd#L383 Citation : Olgun G, Nabi A, Tastan O (20 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2093 lines (36%) are
not.
  First few lines:
    • R/annotate.R#L17 GOtype = c("BP", "CC", ...
    • ...
    • vignettes/NoRCE.Rmd#L324 org_assembly = 'hg1 ...
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.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the NoRCE.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.