Hervé Pagès

Hi, Some of my functions use `capture.output(..., type="message")` but they don't work as expected when called from my unit tests. For example, the following function: ``` hello

Strange behavior of matrixStats functions on factors

1

``` library(matrixStats) x

This is a request for adding `whichRowMaxs`, `whichColMaxs`, `whichRowMins`, `whichColMins` to matrixStats. Arguments would be the same as `rowMaxs` and family (`colMaxs`, `rowMins`, `colMins`) but instead of returning the max...

Double validation of the int_elementMetadata slot

6

Hi, Now that `int_elementMetadata` is [registered as a parallel slot](https://github.com/drisso/SingleCellExperiment/blob/bc220cab41b7112347dda5e094ebb2a9c987fb23/R/internals.R#L101-L103) it will be automatically checked by the validity method for Vector objects so there's no need to [check it again](https://github.com/drisso/SingleCellExperiment/blob/bc220cab41b7112347dda5e094ebb2a9c987fb23/R/validity.R#L4-L6)...

BiocManager::install() not installing package if available version is lower than current

11

I have **SQLDataFrame** 1.9.1: ``` packageVersion("SQLDataFrame") # [1] ‘1.9.1’ ``` and the version of **SQLDataFrame** currently available in BioC 3.15 is 1.9.0: ``` library(BiocManager) available.packages(repos=BiocManager::repositories())["SQLDataFrame", "Version"] # [1] "1.9.0" ```...

Make BiocManager work for a version of Bioconductor that doesn't "officially exist" yet

7

So we have a bunch of failures on the BioC 3.10 report today because BiocManager is complaining with: ``` unknown Bioconductor version '3.10'; see https://bioconductor.org/install` ``` That's because the build...

Turn off column name mangling?

1

`dbGetQuery()` and other `dbFetch`-based operations mangle the column names of the result if some of them are duplicated. This is done in `dbFetch()` by calling `RMariaDB:::set_tidy_names()` on the result. How...

pwalign

16

Update the following URL to point to the GitHub repository of the package you wish to submit to _Bioconductor_ - Repository: https://github.com/Bioconductor/pwalign Confirm the following by editing each check box...

Unit test failure on Mac arm64

1

Similar to https://github.com/LTLA/BiocNeighbors/issues/21, https://github.com/LTLA/csaw/issues/21, and https://github.com/LTLA/metapod/issues/1. See details of the failure on the Mac arm64 semiweekly report: https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/batchelor/kjohnson1-checksrc.html As a consequence, there's no Mac arm64 binary in BioC 3.18: https://bioconductor.org/packages/3.18/batchelor...

Right now `seqinfo()` returns a Seqinfo object with no genome information, even though that information is available in the file (the genome assembly is specified via the `AS` tag found...