Bioconductor/DelayedArray issues and pull requests

#118 - Failed to install geneLenDataBase

Issue - State: open - Opened by fhao2 7 months ago - 5 comments

#117 - the problem "the supplied seed must support extract_array() "

Issue - State: closed - Opened by tomyputw 8 months ago - 3 comments

#117 - the problem "the supplied seed must support extract_array() "

Issue - State: closed - Opened by tomyputw 8 months ago - 3 comments

#116 - `base::cbind()`

Issue - State: open - Opened by multimeric 9 months ago

#116 - `base::cbind()`

Issue - State: open - Opened by multimeric 9 months ago

#115 - DelayedMatrixStats no longer supports scalar `center=` arguments

Issue - State: closed - Opened by LTLA 10 months ago - 6 comments

#115 - DelayedMatrixStats no longer supports scalar `center=` arguments

Issue - State: closed - Opened by LTLA 10 months ago - 6 comments

#111 - Feature request: make `seedApply` as a generic function

Issue - State: open - Opened by Yunuuuu about 1 year ago - 5 comments

#111 - Feature request: make `seedApply` as a generic function

Issue - State: open - Opened by Yunuuuu about 1 year ago - 5 comments

#105 - Thoughts on migrating from `read_sparse_block()` to SVTs

Issue - State: closed - Opened by LTLA over 1 year ago - 3 comments

#105 - Thoughts on migrating from `read_sparse_block()` to SVTs

Issue - State: closed - Opened by LTLA over 1 year ago - 3 comments

#103 - Install error

Issue - State: closed - Opened by LliliansCalvo almost 2 years ago - 2 comments

#103 - Install error

Issue - State: closed - Opened by LliliansCalvo almost 2 years ago - 2 comments

#102 - Bioconductor devel / multiple methods tables found for ‘aperm’

Issue - State: closed - Opened by bbimber over 2 years ago - 1 comment

#101 - More elements in the method signature (2) than in the generic signature (1) for function ‘type<-’

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

#100 - Can't `cbind` DelayedArray instances with other matrix-likes

Issue - State: open - Opened by LTLA almost 3 years ago

#99 - Where can i find the old version

Issue - State: closed - Opened by penglu2004 almost 3 years ago - 1 comment

#98 - Have extract_array() accept non-integer dim() outputs

Issue - State: open - Opened by MalteThodberg about 3 years ago - 1 comment

#97 - DelayedArray subsetting via lapply doesn't work

Issue - State: open - Opened by LTLA over 3 years ago

#96 - Benchmarking grouped matrix averaging methods

Issue - State: closed - Opened by bschilder almost 4 years ago - 2 comments

#95 - DelayedArray crossprod with first vector argument doesn't work properly

Issue - State: closed - Opened by LTLA almost 4 years ago - 1 comment

#94 - DelayedArray vector multiplication reports unnecessary column name

Issue - State: closed - Opened by LTLA almost 4 years ago - 1 comment

#93 - Move chunking utilities from HDF5Array to DelayedArray?

Issue - State: open - Opened by LTLA almost 4 years ago

#92 - DelayedArray's log() doesn't respond to argument 'base'

Issue - State: closed - Opened by LTLA almost 4 years ago - 2 comments

#91 - Allowing extract_array calls to use pre-indexed grid information?

Issue - State: open - Opened by LTLA almost 4 years ago - 5 comments

#90 - Is there a way to get `cor` to work?

Issue - State: open - Opened by ekernf01 almost 4 years ago

#89 - Filling large DelayedArray with iid standard normals

Issue - State: closed - Opened by ekernf01 almost 4 years ago - 5 comments

#88 - Coercion from SparseArraySeed to sparse matrix fails with duplicates

Issue - State: closed - Opened by LTLA almost 4 years ago - 2 comments

#87 - Adding a ConstantArray class

Pull Request - State: closed - Opened by LTLA about 4 years ago - 7 comments

#86 - drop() doesn't preserve dimnames in release?

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

#85 - DelayedArray Install Failed in R4.0.2

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

#84 - 0.16.0 on Debian: Tests no longer passing

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

#83 - Install Errors

Issue - State: closed - Opened by Samantha-Czn about 4 years ago - 6 comments

#82 - Preserve sparsity in IsoOpWithArgs.

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

#81 - Support extract_sparse_array for DelayedAbind objects.

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

#80 - extract_sparse_array on DelayedAbind with sparse backends is not yet implement

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

#79 - scale() not working on TENxBrainData

Issue - State: closed - Opened by pablo-rodr-bio2 about 4 years ago - 4 comments

#78 - DelayedArray subsetting by single row/column does not retain names

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

#77 - Combining DelayedArrays coerces later objects to the first backend

Issue - State: closed - Opened by LTLA about 4 years ago - 2 comments

#76 - Parallel matrix multiplication with HDF5Array realization and BiocParallel::SnowParam() fails

Issue - State: closed - Opened by hpages over 4 years ago - 5 comments

#75 - Remove leftover 'block' passing in currentBlockId

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

#74 - Unnecessary (?) warnings from DelayedArray:::.backward_compat

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

#73 - Division by a vector does not preserve sparsity

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

#72 - Unnamed arguments in blockApply breaks in BatchtoolsParam

Issue - State: closed - Opened by LTLA over 4 years ago - 9 comments

#71 - Handling current_block_id and effective_grid for tooling on top of blockApply

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

#70 - Stripped out unnecessary BiocParallel loads.

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

#69 - Alternative to assigning attributes in blockApply?

Issue - State: closed - Opened by LTLA over 4 years ago - 2 comments

#68 - More unit tests and streamlined matrix multiplication

Pull Request - State: closed - Opened by LTLA over 4 years ago - 2 comments

#67 - Respect sparsity in matrix multiplication

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

#66 - Prettier showtree formatting

Issue - State: closed - Opened by PeteHaitch over 4 years ago - 1 comment

#65 - Subsetting with "missing" arguments

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

#64 - Support native matrix multiplication (among other operations)

Pull Request - State: closed - Opened by LTLA over 4 years ago - 18 comments

#63 - is_sparse doesn't work for lgCMatrix objects

Issue - State: closed - Opened by LTLA almost 5 years ago - 3 comments

#62 - Support for RleListMatrix (?)

Issue - State: open - Opened by jonocarroll almost 5 years ago - 1 comment

#61 - Coercion from DelayedArray to dgCMatrix discards dimnames

Issue - State: closed - Opened by LTLA almost 5 years ago - 1 comment

#60 - Summing DelayedArray and Matrix

Issue - State: closed - Opened by const-ae about 5 years ago - 2 comments

#59 - colsum does not respect factor level ordering

Issue - State: closed - Opened by LTLA about 5 years ago - 1 comment

#58 - Get/set AutoBPPARAM in matrix multiplication functions.

Pull Request - State: closed - Opened by LTLA about 5 years ago - 6 comments

#57 - Add row/colsum fallbacks for non-DA/base matrix classes.

Pull Request - State: closed - Opened by LTLA about 5 years ago - 5 comments

#56 - mean(), anyNA(), and members of "Summary" group generic should "untranspose"

Issue - State: open - Opened by hpages about 5 years ago

#55 - `is_pristine()` error

Issue - State: closed - Opened by mjsteinbaugh over 5 years ago - 6 comments

#54 - replacing dimnames with identical values demotes >2-dim DelayedArray derivatives into DelayedArray

Issue - State: closed - Opened by Liubuntu over 5 years ago - 4 comments

#53 - dimnames setting on a DelayedArray should coerce to character

Issue - State: closed - Opened by LTLA over 5 years ago - 3 comments

#52 - Slow matrix multiplication using DelayedArray

Issue - State: closed - Opened by kevinwang09 over 5 years ago - 3 comments

#51 - why does this package depend on BiocParallel

Issue - State: closed - Opened by vjcitn over 5 years ago - 3 comments

#50 - sub-assignment for DelayedArrays doesn't follow base API

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

#49 - Feature Request/Help on Applying Linear Models

Issue - State: closed - Opened by avalcarcel9 over 5 years ago - 6 comments

#48 - type accessor not found, when DelayedArray and Biostrings package are loaded

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

#47 - Reshaping Array

Issue - State: open - Opened by muschellij2 over 5 years ago - 18 comments

#46 - Block-processed methods for DelayedArray objects should try to take advantage of the backend-specific methods whenever they can

Issue - State: open - Opened by hpages over 5 years ago

#45 - multiple methods tables found for ‘splitAsList’ when loading DelayedArray

Issue - State: closed - Opened by ngolan1 over 5 years ago - 14 comments

#44 - NA subscripting

Issue - State: open - Opened by lawremi over 5 years ago

#43 - names on dimnames

Issue - State: closed - Opened by lawremi over 5 years ago - 3 comments

#42 - Linear indexing causes trouble when an index is larger than .Machine$integer.max

Issue - State: closed - Opened by hpages almost 6 years ago - 1 comment

#41 - Re-implementing rowsum/colsum for HDF5Matrix

Issue - State: open - Opened by PeteHaitch almost 6 years ago - 3 comments

#40 - Type-preserving alternative to read_block

Issue - State: closed - Opened by LTLA about 6 years ago - 9 comments

#38 - Initial support for (t)crossprod methods.

Pull Request - State: closed - Opened by LTLA over 6 years ago - 1 comment

#37 - How to implement a realization backend

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

#36 - Memory issue with subassignment

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

#35 - Calling TFSBTools

Issue - State: closed - Opened by akhst7 over 6 years ago - 6 comments

#34 - Bug in makeCappedVolumeBox() results in zero-column volumn box

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

#33 - Implementing crossprod and dual-DA %*%

Issue - State: closed - Opened by LTLA over 6 years ago - 9 comments

#32 - replacement method [<- support the same subassignment as regular array

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

#31 - generic for deep copying

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

#30 - unable to change dim

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

#29 - DelayedArray backend fails on repeated invocation of devtools::test

Issue - State: closed - Opened by sampoll over 6 years ago - 8 comments

#28 - registering `SerialParam()` sets a global preference, but package-specific preference required

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

#27 - possble DelayedArray constructor over `IntegerList` (or other `List`)

Issue - State: open - Opened by Liubuntu over 6 years ago - 3 comments
Labels: enhancement

#26 - Subsetting on DelayedArray objects with list elements fails

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

#25 - show method for >2D arrays load the whole 2d slices (than necessary) in the middle steps

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

#24 - Please consider adding RUnit to Suggests

Issue - State: closed - Opened by HenrikBengtsson over 6 years ago - 2 comments

#23 - Strange behaviour when subsetting and coercing to vector

Issue - State: closed - Opened by kdkorthauer over 6 years ago - 1 comment

#22 - Error when calling as.matrix() on DelayedMatrix with length > .Machine$integer.max

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

#21 - Error in extract_array when print the extended backend

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

#20 - Help implementing 'parallel' writing to a RealizationSink with BiocParallel

Issue - State: open - Opened by PeteHaitch almost 7 years ago - 4 comments

#19 - What about using a seed with "dual layout" i.e. row- and col- oriented?

Issue - State: closed - Opened by hpages almost 7 years ago - 2 comments

#18 - Support `finite` argument in `range,DelayedArray-method`

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

GitHub / Bioconductor/DelayedArray issues and pull requests