PeteHaitch/DelayedMatrixStats issues and pull requests

#102 - Resync with recent developments in DelayedArray package

Pull Request - State: closed - Opened by hpages 7 months ago - 1 comment

#101 - Restore scalar center argument for matrix functions

Pull Request - State: closed - Opened by hpages 10 months ago - 3 comments

#100 - Backporting PR #94 to the RELEASE_3_17 branch (current release)

Pull Request - State: closed - Opened by hpages over 1 year ago - 1 comment

#99 - No recent tags

Issue - State: closed - Opened by ryandesign over 1 year ago - 1 comment

#98 - Broken Travis CI image in README

Issue - State: closed - Opened by ryandesign over 1 year ago - 1 comment

#97 - Use BLOCK_colVars/BLOCK_rowVars workhorses for colVars/rowVars methods

Pull Request - State: closed - Opened by PeteHaitch over 1 year ago - 4 comments

#96 - Devel matrix stats 1.0.0 resync

Pull Request - State: closed - Opened by PeteHaitch over 1 year ago - 2 comments

#95 - Deprecate colAnyMissings() and rowAnyMissings()

Issue - State: open - Opened by PeteHaitch over 1 year ago

#94 - Use BLOCK_colVars/BLOCK_rowVars workhorses for colVars/rowVars methods

Pull Request - State: closed - Opened by hpages over 1 year ago - 2 comments

#93 - Release 3 17 matrix stats v1

Pull Request - State: closed - Opened by PeteHaitch over 1 year ago - 2 comments

#92 - Release 3 17 matrix stats v1

Pull Request - State: closed - Opened by PeteHaitch over 1 year ago

#91 - matrixStats 1.0.0: Breaking changes

Issue - State: closed - Opened by HenrikBengtsson over 1 year ago - 5 comments

#90 - One test fails on ppc32: Error: cannot allocate vector of size 305.2 Mb

Issue - State: open - Opened by barracuda156 almost 2 years ago - 8 comments

#89 - ERROR: compilation failed for package 'DelayedArray'

Issue - State: closed - Opened by chen-peng-1874 about 2 years ago - 11 comments

#88 - Please use consistent signing in version numbers

Issue - State: closed - Opened by tillea over 2 years ago - 2 comments

#87 - unable to install version 1.14.0 in R-4.1.0

Issue - State: closed - Opened by rardin over 3 years ago - 1 comment

#86 - Installation of package ‘DelayedMatrixStats’ had non-zero exit status

Issue - State: closed - Opened by stephen-siecinski over 3 years ago - 6 comments

#85 - Installation fails

Issue - State: closed - Opened by christie-ga over 3 years ago - 1 comment

#84 - Implement `useNames` argument

Issue - State: open - Opened by PeteHaitch over 3 years ago - 9 comments

#83 - HEADS UP: New default for `ties.method` of {col,row}Ranks()

Issue - State: open - Opened by HenrikBengtsson over 3 years ago - 1 comment

#82 - Benchmarking grouped matrix averaging methods

Issue - State: closed - Opened by bschilder almost 4 years ago - 11 comments

#81 - `colSums2()` failing on RleMatrix when `rows` supplied in devel

Issue - State: closed - Opened by PeteHaitch almost 4 years ago - 3 comments

#80 - Error while installing

Issue - State: closed - Opened by maxim-h about 4 years ago - 5 comments

#79 - Error : in method for ‘colAvgsPerRowSet’ with signature ‘X="DelayedMatrix"’

Issue - State: closed - Opened by ndusek about 4 years ago - 3 comments

#78 - Failed to download DelayedMatrixStats

Issue - State: closed - Opened by RunhangShu about 4 years ago - 1 comment

#77 - Unable to install the package

Issue - State: closed - Opened by daisyyr about 4 years ago - 1 comment

#76 - Fix for missing na.rm= argument in AvgsPerSet functions.

Pull Request - State: closed - Opened by LTLA about 4 years ago

#75 - Fix na.rm install issue

Pull Request - State: closed - Opened by bbimber about 4 years ago - 2 comments

#74 - Error installing Delayed Matrix Stats

Issue - State: closed - Opened by sanhe374 about 4 years ago - 1 comment

#73 - Fail to install version 1.12.2

Issue - State: closed - Opened by derbalkon about 4 years ago - 11 comments

#72 - Why does this depend on HDF5Array?

Issue - State: closed - Opened by LTLA about 4 years ago - 3 comments

#71 - Correct handling of drop= by quantile functions.

Pull Request - State: closed - Opened by LTLA about 4 years ago - 3 comments

#70 - colQuantiles fails with length-1 probs

Issue - State: closed - Opened by LTLA about 4 years ago - 5 comments

#69 - Fix 2 issues with how the 'center' argument is handled

Pull Request - State: closed - Opened by hpages about 4 years ago - 1 comment

#68 - More issues with how the 'center' argument is handled

Issue - State: closed - Opened by hpages about 4 years ago - 14 comments

#67 - Test fail on arm64 and armhf systems

Issue - State: closed - Opened by mr-c over 4 years ago - 12 comments

#66 - Pass MatGen namespaced generic rather than just its name.

Pull Request - State: closed - Opened by LTLA over 4 years ago - 1 comment

#65 - Assorted fixes

Pull Request - State: closed - Opened by LTLA over 4 years ago - 1 comment

#64 - colVars yields incorrect results with vector center=

Issue - State: closed - Opened by LTLA over 4 years ago - 3 comments

#63 - Seems like a bad idea to coerce a DelayedMatrix to the seed class

Issue - State: closed - Opened by LTLA over 4 years ago

#62 - Replaced all generic definitions with those from MatrixGenerics.

Pull Request - State: closed - Opened by LTLA over 4 years ago - 8 comments

#61 - Why is colVars so slow?

Issue - State: closed - Opened by LTLA over 4 years ago - 7 comments

#60 - matrixStats::{col,row}Quantiles() dropping support for logical input

Issue - State: closed - Opened by HenrikBengtsson about 5 years ago - 4 comments

#59 - Use MatrixGenerics

Pull Request - State: closed - Opened by const-ae about 5 years ago - 9 comments

#58 - Bug due to a change in matrixStats ties.method= ordering

Issue - State: closed - Opened by LTLA over 5 years ago - 2 comments

#57 - Re-disabling one rowsum() test on Windows

Pull Request - State: closed - Opened by hpages about 6 years ago - 2 comments

#56 - Remove rowsum() and colsum() S4 generics and a few methods

Pull Request - State: closed - Opened by hpages about 6 years ago - 2 comments

#55 - Deprecate rowsum in favour of DelayedArray::rowsum

Issue - State: closed - Opened by PeteHaitch about 6 years ago - 1 comment

#54 - new rowsum() on RleMatrix and dgCMatrix produces errors?

Issue - State: closed - Opened by MalteThodberg over 6 years ago - 4 comments

#53 - Conditional use of setMethod()

Issue - State: open - Opened by PeteHaitch over 6 years ago

#52 - Plans for rowsum?

Issue - State: closed - Opened by MalteThodberg over 6 years ago - 2 comments
Labels: enhancement

#51 - Consider adding `withDimnames`-type argument to all generics

Issue - State: open - Opened by PeteHaitch almost 7 years ago

#50 - rowAvgsPerColSet2

Issue - State: open - Opened by PeteHaitch almost 7 years ago

#49 - Test more data_seeds?

Issue - State: open - Opened by PeteHaitch almost 7 years ago

#48 - Update installation instructions in README

Issue - State: open - Opened by PeteHaitch almost 7 years ago

#47 - README benchmarking

Issue - State: open - Opened by PeteHaitch almost 7 years ago
Labels: benchmarking

#46 - Categorise methods and refactor code base

Issue - State: open - Opened by PeteHaitch almost 7 years ago - 1 comment

#45 - DelayedArray:::is_pristine() no longer available

Issue - State: closed - Opened by PeteHaitch almost 7 years ago - 6 comments

#44 - as.data.frame method

Issue - State: open - Opened by PeteHaitch almost 7 years ago
Labels: out_of_scope

#43 - Use implicitGeneric

Issue - State: open - Opened by PeteHaitch about 7 years ago

#42 - Add progress bars

Issue - State: open - Opened by PeteHaitch about 7 years ago
Labels: enhancement

#41 - Re-export matrixStats API rather than DEPEND on it?

Issue - State: closed - Opened by PeteHaitch about 7 years ago - 1 comment
Labels: question

#40 - NEWS.md to NEWS

Issue - State: open - Opened by PeteHaitch about 7 years ago
Labels: enhancement

#39 - REVDEP matrixStats: formals(dms_generic) not identical to formals(ms_fun)

Issue - State: closed - Opened by HenrikBengtsson about 7 years ago - 3 comments

#38 - Fast colRanks implementation in scran

Issue - State: open - Opened by LTLA about 7 years ago

#37 - Wrap arbitrary matrix-like objects in DelayedArray() to allow arbitrary dispatch

Issue - State: open - Opened by PeteHaitch about 7 years ago - 2 comments

#36 - Use debugme

Issue - State: open - Opened by PeteHaitch about 7 years ago
Labels: enhancement

#35 - Priorities

Issue - State: open - Opened by PeteHaitch about 7 years ago

#34 - Remove dependency on unreleased version of matrixStats

Issue - State: closed - Opened by PeteHaitch over 7 years ago
Labels: initial_release

#33 - Generics and methods already in DelayedArray

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: help wanted, initial_release

#32 - Automagic updating of inherited documentation

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: help wanted

#31 - Reconcile README and vignette

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: help wanted

#30 - API table in vignette

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: initial_release

#29 - Update installation instructions in README

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: initial_release

#28 - Explain how delayed ops are realised and use of `force_block_processing`

Issue - State: closed - Opened by PeteHaitch over 7 years ago
Labels: initial_release

#27 - Run BiocCheck::BiocCheck()

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 2 comments
Labels: initial_release

#26 - Compare to just loading data into memory

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: benchmarking

#25 - [Enhancement]: Add examples to docs

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 2 comments
Labels: initial_release

#24 - Additional non-matrixStats methods

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: enhancement

#23 - Additional matrixStats functions

Issue - State: open - Opened by PeteHaitch over 7 years ago - 1 comment
Labels: enhancement, out_of_scope, ongoing

#22 - Use `setNames()` instead of `dimnames<-()` when appropriate

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 1 comment

#21 - Use named args in all function calls

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 2 comments

#20 - Dimensions of returned value vary by method

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 1 comment

#19 - DRY unit tests

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: ongoing

#18 - Check answer type

Issue - State: closed - Opened by PeteHaitch over 7 years ago

#17 - Ensure full range of args of methods are tested

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: ongoing

#16 - Test with small block size

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 2 comments

#15 - [Question]: Ownership of generics

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 1 comment

#14 - Location of dots in generic/method signatures

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 3 comments
Labels: help wanted, initial_release

#13 - What to do with `dim.` arg?

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: help wanted

#12 - colCounts()/rowCounts() subject to (in)equality

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: enhancement

#11 - Provide support for different realization strategies (via BACKEND)

Issue - State: open - Opened by PeteHaitch over 7 years ago - 2 comments
Labels: future_release

#10 - Provide support for multicore (perhaps via BPPARAM)

Issue - State: open - Opened by PeteHaitch over 7 years ago - 1 comment
Labels: future_release

#9 - Unit tests for generic signature

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 2 comments

#8 - Methods for HDF5Matrix objects

Issue - State: open - Opened by PeteHaitch over 7 years ago - 1 comment
Labels: future_release

#7 - Block vs. row. vs. column processing

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 1 comment

#6 - Subset-then-compute vs. compute-then-subset

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: benchmarking

#5 - Optimisation level of implementation

Issue - State: open - Opened by PeteHaitch over 7 years ago
Labels: future_release

#4 - Add checklist of supported API to README

Issue - State: closed - Opened by PeteHaitch over 7 years ago

#3 - DelayedMatrix with a BigWig-derived seed

Issue - State: closed - Opened by PeteHaitch over 7 years ago - 2 comments
Labels: out_of_scope

GitHub / PeteHaitch/DelayedMatrixStats issues and pull requests