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2 years ago BiocCheck PASSED.
Warning message: package ‘BiocCheck’ was built under R version 4.1.3
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``` * Checking Package Dependencies... * Checking if other packages can import this one... * Checking to see if we understand object initialization... * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * Checking version number... * Checking version number validity... * WARNING: y of x.y.z version should be even in release * Checking R Version dependency... * Checking package size... Skipped... only checked on source tarball * Checking individual file sizes... * WARNING: The following files are over 5MB in size: 'check/scater.Rcheck/00_pkg_src/scater/inst/doc/overview.html check/scater.Rcheck/scater/doc/overview.html' * 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... * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * NOTE: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field, and structure it as a full paragraph * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version field... * Checking for valid maintainer... * Checking License: for restrictive use... * Checking DESCRIPTION/NAMESPACE consistency... * Checking .Rbuildignore... * Checking vignette directory... * Checking package installation calls in R code... * Checking for library/require of scater... * Checking coding practice... * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths............................................................................ * NOTE: Recommended function length <= 50 lines. There are 13 functions > 50 lines. The longest 5 functions are: plotHeatmap() (scater/R/plotHeatmap.R, line 85): 161 lines .central_plotter() (scater/R/plot_central.R, line 57): 130 lines plotExpression() (scater/R/plotExpression.R, line 83): 104 lines plotReducedDim() (scater/R/plotReducedDim.R, line 93): 95 lines plotHighestExprs() (scater/R/plotHighestExprs.R, line 47): 85 lines * Checking man page documentation... * NOTE: Consider adding runnable examples to the following man pages which document exported objects: annotateBMFeatures.Rd, reexports.Rd, toSingleCellExperiment.Rd * NOTE: Usage of dontrun{} / donttest{} found in man page examples. 11% of man pages use one of these cases. Found in the following files: annotateBMFeatures.Rd multiplot.Rd plot_reddim.Rd toSingleCellExperiment.Rd * NOTE: Use donttest{} instead of dontrun{}. Found in the following files: annotateBMFeatures.Rd multiplot.Rd plot_reddim.Rd toSingleCellExperiment.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... * NOTE: Consider shorter lines; 1429 lines (16%) are > 80 characters long. First 6 lines: scater/R/AllClasses.R:17 #' \item{\code{logExprsOffset}:}{Scalar of ... scater/R/AllClasses.R:18 #' applied to expression data in the `exprs... scater/R/AllClasses.R:27 #' \item{\code{reducedDimension}:}{Matrix o... scater/R/AllClasses.R:31 #' \item{\code{sc3}:}{List containing resul... scater/R/AllGenerics.R:14 setGeneric("norm_exprs<-", function(object, v... scater/R/AllGenerics.R:29 setGeneric("stand_exprs<-", function(object, ... * NOTE: Consider multiples of 4 spaces for line indents, 419 lines(5%) are not. First 6 lines: scater/R/AllClasses.R:46 contains = "ExpressionSet", scater/R/AllClasses.R:47 slots = c(logExprsOffset = "numeric", scater/R/AllClasses.R:48 lowerDetectionLimit = "nume... scater/R/AllClasses.R:49 cellPairwiseDistances = "di... scater/R/AllClasses.R:50 featurePairwiseDistances = ... scater/R/AllClasses.R:51 reducedDimension = "matrix", See http://bioconductor.org/developers/how-to/coding-style/ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking if package already exists in CRAN... 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://packagemanager.rstudio.com/all/__linux__/focal/latest * Checking for bioc-devel mailing list subscription... * 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... Maintainer is registered at support site. Package name is in support site watched tags. ```Summary:
ERROR count: 0
WARNING count: 2
NOTE count: 8For detailed information about these checks, see the BiocCheck vignette, available at https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
I think there should probably be the equivalent of calculate/computeSumFactors in that one function can just do the embedding and the other adds it to the SCE. However I'd prefer if the names were clear about which does which