NEWS

---

SCArray 1.21.2

• register the native routines (src/init.c) and stop searching symbols dynamically; .Call() now checks the number of arguments
• bug fix: 'colWeightedMeans()' ignored the weights on a non-transposed SC_GDSMatrix (it called the unweighted C kernel instead of c_colWMeans)
• bug fix: 'rowProds()' and 'colProds()' failed on a GDS-backed matrix because the parent method was called with the unsupported 'method=' argument; both now use the native kernels in either orientation
• bug fix: 'rowWeightedVars()', 'colWeightedVars()', 'rowWeightedSds()' and 'colWeightedSds()' returned an incorrect weighted variance (the sum-of-squares term used the weight squared and a non-standard normalization); now matches matrixStats: sum_w(x-mu)^2 / (sum_w - 1)
• bug fix: 'colWeightedMeans(., na.rm=TRUE)' on a sparse matrix used a wrong denominator (the full weight sum was not initialized)
• bug fix: memory protection leak in the C kernel 'c_colProds'
• 'rowLogSumExps()' and 'colLogSumExps()' are now numerically stable (max-subtraction) and no longer overflow for large values
• 'useNames=TRUE' is now the default for the row*/col* statistics, matching DelayedMatrixStats; names are kept unless 'useNames=FALSE'. 'rowRanges()' and 'colRanges()' gain a 'useNames' argument and set the row names
• 'rowCollapse()' and 'colCollapse()' no longer keep state in C file-scope globals (which were not reentrant and shared a column cursor between the two); the row map is held in an external pointer and the column offset is passed per block. This also removes a dangling-pointer hazard in the old colCollapse code
• new unit tests checking every overridden row*/col* statistic against matrixStats for both matrix orientations, with and without NAs, plus tests for log-sum-exp overflow, name handling, and rowCollapse/colCollapse

SCArray 1.20.0

• fix the package anchors for all Rd \link{}

SCArray 1.16.0

• update according to the SparseArray package

SCArray 1.14.0

• update according to DelayedArray(>= 0.31.5)

SCArray 1.12.0

• update according to DelayedArray (>= v0.29.0)

SCArray 1.10.0

• update for DelayedArray (>= v0.27.2)

SCArray 1.8.4

• 'rowMeans()', 'rowSums()', 'colMeans()', 'colSums()' with row or column names
• override S4 functions rowDiffs(), colDiffs(), rowSdDiffs(), colSdDiffs(), rowVarDiffs(), colVarDiffs(), rowLogSumExps(), colLogSumExps()

SCArray 1.8.3

• progress bar in 'scHDF2GDS()'
• update '%*%' with SC_GDSMatrix
• update 'rbind()' and 'cbind()' with SC_GDSMatrix
• 'runPCA()' on SC_GDSMatrix

SCArray 1.8.0

• new functions 'scNumSplit()', 'scRowAutoGrid()', 'scColAutoGrid()'
• update the vignettes
• override S4 functions colsum(), rowsum(), scale(), pmin2(), pmax2() for SC_GDSMatrix
• new S4 generic functions 'row_nnzero()', 'col_nnzero()', 'scGetFiles()', 'scMemory()', 'scRowMeanVar()', 'scColMeanVar()'
• new functions 'scSetMax()', 'scSetMin()', 'scSetBounds()', 'scReplaceNA()'
• update S4 functions '[', '[[', 'names<-', 'dimnames<-', aperm, Ops, Math, crossprod(), tcrossprod() for SC_GDSArray
• override S4 functions rowSums(), colSums(), rowSums2(), colSums2(), rowProds(), colProds(), rowMeans(), colMeans(), rowMeans2(), colMeans2(), rowVars(), colVars(), rowSds(), colSds(), rowMins(), colMins(), rowMaxs(), colMaxs(), rowRanges(), colRanges(), rowAnyNAs(), colAnyNAs(), rowCollapse(), colCollapse() for SC_GDSMatrix

SCArray 1.4.0

• new functions 'scMEX2GDS()' and 'scHDF2GDS()'

SCArray 1.2.1

• new Overview.Rmd in the vignettes

SCArray 1.0.0

• initial version of SCArray