##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Rnits_1.47.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing Rnits ────────────────────────────────────────────────────────────
✔ Package installed successfully
── Rnits session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZLcs4C/file12337c2b7f6346/Rnits
→ BiocVersion: 3.24
→ Package: Rnits
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Rnits.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZLcs4C/file12337c2b7f6346/Rnits
→ installDir: /tmp/RtmpZLcs4C/file12337c37aaa15a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Rnits ──────────────────────────────────────────────────
* 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 3.6.0 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: Transcription,
Sequencing, OneChannel, TwoChannel, Metabolomics, Proteomics, Epigenetics,
Cheminformatics, Transcriptomics, GeneTarget, ExperimentalDesign,
Preprocessing, Bayesian, Clustering, Regression, ExonArray, RNASeq,
MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms, CellBiology,
BiomedicalInformatics, FunctionalGenomics, SystemsBiology, ImmunoOncology,
AlternativeSplicing, DifferentialSplicing, GeneSetEnrichment, BatchEffect,
MultipleComparison, QualityControl, DataImport
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 (45%).
* 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:
    • Rnits-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of Rnits...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/plotresults.r (line 105, column 24)
    • R/plotresults.r (line 107, column 33)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • build-rnits.r (line 117, column 53)
    • ...
    • timealign.r (line 101, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/build-rnits.r (line 75, column 7)
    • ...
    • cat() in R/misc-functions.r (line 74, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/build-rnits.r (line 93, column 19)
    • ...
    • R/topdata.r (line 41, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/timealign.r (line 92, column 22)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • fit.r (line 61, column 21)
    • ...
    • timealign.r (line 38, column 23)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/fit.r (line 101, column 3)
  • set.seed() in R/timealign.r (line 55, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressWarnings() in R/calculate-gcv.r (line 55, column 15)
  • ...
  • suppressWarnings() in R/timealign.r (line 62, column 20)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • build.Rnits() (R/build-rnits.r): 327 lines
    • ...
    • _anonymous_.30() (R/calculate-gcv.r): 55 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/extract-methods.Rd
    • man/plotResults-methods.Rd
    • man/timeAlign-methods.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • getNormTwoChannel-methods.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 61% of man
pages use at least one of these tags.
  Found in files:
    • calculateGCV-methods.Rd
    • ...
    • topData-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • calculateGCV-methods.Rd
    • ...
    • topData-methods.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; 274 lines (11%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L14 setClass("Rnits", contains = "Expression ...
    • ...
    • vignettes/Rnits-vignette.Rnw#L203 Dynamic changes in transcriptional
    progr ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 334 lines (13%) are
not.
  First few lines:
    • R/build-rnits.r#L66 callData <- list() ...
    • ...
    • man/topData-methods.Rd#L12 sort.by = "p-value") ...
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 | ⚠ 4 WARNINGS | ℹ 19 NOTES
ℹ See the Rnits.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.