diff -Nru r-bioc-delayedmatrixstats-1.12.2+ds/debian/changelog r-bioc-delayedmatrixstats-1.12.3+ds/debian/changelog --- r-bioc-delayedmatrixstats-1.12.2+ds/debian/changelog 2021-01-17 09:14:20.000000000 +0000 +++ r-bioc-delayedmatrixstats-1.12.3+ds/debian/changelog 2021-02-06 14:45:48.000000000 +0000 @@ -1,3 +1,11 @@ +r-bioc-delayedmatrixstats (1.12.3+ds-1) unstable; urgency=medium + + [ Andreas Tille ] + * Team upload. + * New upstream version + + -- Michael R. Crusoe Sat, 06 Feb 2021 15:45:48 +0100 + r-bioc-delayedmatrixstats (1.12.2+ds-1) unstable; urgency=medium * Team upload. diff -Nru r-bioc-delayedmatrixstats-1.12.2+ds/debian/patches/matrix-1.3-2-dep r-bioc-delayedmatrixstats-1.12.3+ds/debian/patches/matrix-1.3-2-dep --- r-bioc-delayedmatrixstats-1.12.2+ds/debian/patches/matrix-1.3-2-dep 2021-01-09 10:23:46.000000000 +0000 +++ r-bioc-delayedmatrixstats-1.12.3+ds/debian/patches/matrix-1.3-2-dep 2021-02-06 14:45:48.000000000 +0000 @@ -1,5 +1,6 @@ From: Michael R. Crusoe Subject: Require newer Matrix version +Forwarded: not-needed --- r-bioc-delayedmatrixstats.orig/DESCRIPTION +++ r-bioc-delayedmatrixstats/DESCRIPTION @@ -20,7 +20,7 @@ diff -Nru r-bioc-delayedmatrixstats-1.12.2+ds/DESCRIPTION r-bioc-delayedmatrixstats-1.12.3+ds/DESCRIPTION --- r-bioc-delayedmatrixstats-1.12.2+ds/DESCRIPTION 2021-01-12 23:51:15.000000000 +0000 +++ r-bioc-delayedmatrixstats-1.12.3+ds/DESCRIPTION 2021-02-03 23:49:26.000000000 +0000 @@ -2,8 +2,8 @@ Type: Package Title: Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects -Version: 1.12.2 -Date: 2021-01-12 +Version: 1.12.3 +Date: 2020-02-02 Authors@R: c(person("Peter", "Hickey", role = c("aut", "cre"), email = "peter.hickey@gmail.com"), person("Hervé", "Pagès", role = "ctb", email = "hpages.on.github@gmail.com"), @@ -31,11 +31,11 @@ biocViews: Infrastructure, DataRepresentation, Software git_url: https://git.bioconductor.org/packages/DelayedMatrixStats git_branch: RELEASE_3_12 -git_last_commit: e2b0acb -git_last_commit_date: 2021-01-11 -Date/Publication: 2021-01-12 +git_last_commit: 81b5218 +git_last_commit_date: 2021-02-02 +Date/Publication: 2021-02-03 NeedsCompilation: no -Packaged: 2021-01-12 23:51:15 UTC; biocbuild +Packaged: 2021-02-03 23:49:26 UTC; biocbuild Author: Peter Hickey [aut, cre], Hervé Pagès [ctb], Aaron Lun [ctb] diff -Nru r-bioc-delayedmatrixstats-1.12.2+ds/man/colAvgsPerRowSet.Rd r-bioc-delayedmatrixstats-1.12.3+ds/man/colAvgsPerRowSet.Rd --- r-bioc-delayedmatrixstats-1.12.2+ds/man/colAvgsPerRowSet.Rd 2020-10-27 18:09:36.000000000 +0000 +++ r-bioc-delayedmatrixstats-1.12.3+ds/man/colAvgsPerRowSet.Rd 2021-02-03 19:52:28.000000000 +0000 @@ -14,6 +14,7 @@ FUN = colMeans, ..., force_block_processing = FALSE, + na.rm = NA, tFUN = FALSE ) @@ -25,6 +26,7 @@ FUN = rowMeans, ..., force_block_processing = FALSE, + na.rm = NA, tFUN = FALSE ) } @@ -53,6 +55,10 @@ (depending on \verb{\link[DelayedArray]\{getAutoBlockSize\}()}) columns (\code{colFoo()}) or rows (\code{rowFoo()}) into memory as an ordinary \link[base:array]{base::array}.} +\item{na.rm}{(logical) Argument passed to \code{FUN()} as \code{na.rm = na.rm}. +If \code{NA} (default), then \code{na.rm = TRUE} is used if \code{X} or \code{S} holds missing values, +otherwise \code{na.rm = FALSE}.} + \item{tFUN}{If \code{TRUE}, \code{X} is transposed before it is passed to \code{FUN}.} \item{rows}{A \code{\link{vector}} indicating the subset (and/or diff -Nru r-bioc-delayedmatrixstats-1.12.2+ds/R/colAvgsPerRowSet.R r-bioc-delayedmatrixstats-1.12.3+ds/R/colAvgsPerRowSet.R --- r-bioc-delayedmatrixstats-1.12.2+ds/R/colAvgsPerRowSet.R 2020-10-27 18:09:36.000000000 +0000 +++ r-bioc-delayedmatrixstats-1.12.3+ds/R/colAvgsPerRowSet.R 2021-02-03 19:52:28.000000000 +0000 @@ -8,6 +8,7 @@ .DelayedMatrix_block_colAvgsPerRowSet <- function(X, W = NULL, cols = NULL, S, FUN = colMeans, ..., + na.rm = NA, tFUN = FALSE) { # Check input type stopifnot(is(X, "DelayedMatrix")) @@ -35,6 +36,7 @@ W = W, S = matrix(seq_len(nrow(S))), FUN = FUN, + na.rm = na.rm, tFUN = tFUN) }) if (length(val) == 0L) { @@ -64,7 +66,7 @@ #' colAvgsPerRowSet(dm_DF, S = matrix(1:2, ncol = 2)) setMethod("colAvgsPerRowSet", "DelayedMatrix", function(X, W = NULL, cols = NULL, S, FUN = colMeans, ..., - force_block_processing = FALSE, tFUN = FALSE) { + force_block_processing = FALSE, na.rm = NA, tFUN = FALSE) { .smart_seed_dispatcher(X, generic = MatrixGenerics::colAvgsPerRowSet, blockfun = .DelayedMatrix_block_colAvgsPerRowSet, force_block_processing = force_block_processing, @@ -73,6 +75,7 @@ S = S, FUN = FUN, ..., + na.rm = na.rm, tFUN = tFUN) } ) diff -Nru r-bioc-delayedmatrixstats-1.12.2+ds/R/rowAvgsPerColSet.R r-bioc-delayedmatrixstats-1.12.3+ds/R/rowAvgsPerColSet.R --- r-bioc-delayedmatrixstats-1.12.2+ds/R/rowAvgsPerColSet.R 2020-10-27 18:09:36.000000000 +0000 +++ r-bioc-delayedmatrixstats-1.12.3+ds/R/rowAvgsPerColSet.R 2021-02-03 19:52:28.000000000 +0000 @@ -8,6 +8,7 @@ .DelayedMatrix_block_rowAvgsPerColSet <- function(X, W = NULL, rows = NULL, S, FUN = rowMeans, ..., + na.rm = NA, tFUN = FALSE) { # Check input type stopifnot(is(X, "DelayedMatrix")) @@ -36,6 +37,7 @@ W = W, S = matrix(seq_len(nrow(S))), FUN = FUN, + na.rm = na.rm, tFUN = tFUN) }) if (length(val) == 0L) { @@ -62,7 +64,7 @@ #' rowAvgsPerColSet(dm_DF, S = matrix(1:2, ncol = 1)) setMethod("rowAvgsPerColSet", "DelayedMatrix", function(X, W = NULL, rows = NULL, S, FUN = rowMeans, ..., - force_block_processing = FALSE, tFUN = FALSE) { + force_block_processing = FALSE, na.rm = NA, tFUN = FALSE) { .smart_seed_dispatcher(X, generic = MatrixGenerics::rowAvgsPerColSet, blockfun = .DelayedMatrix_block_rowAvgsPerColSet, force_block_processing = force_block_processing, @@ -71,6 +73,7 @@ S = S, FUN = FUN, ..., + na.rm = na.rm, tFUN = tFUN) } )