Martin Morgan

`readH5AD(..., reader="R")` fails with recent AnnData formats?

1

cellxgene provides H5AD files for each data set. A recent download of [this one][] (sorry, there is no direct url; click on the cloud download button) has content like (from...

Let environment variables override `workers = ` argument

2

Setting an environment variable (e.g., by a server administrator or build system manager ;) ) can be undermined when the user explicitly requests more workers ``` > Sys.setenv(BIOCPARALLEL_WORKER_NUMBER=2) > ##...

handle failed installations due to unwritable directory

21

A user trying to update a package that has been installed under an unwritable (e.g., windows Administrator) account is told that the package could not be updated. This could be...

Don't allow remotes::install_github() to convert warnings to errors on unavailable PACKAGES file

1

remotes::install_github() converts warnings about dependencies that cannot be installed (e.g., because of missing binaries) into errors. This is different from the install.packages() behavior in non-github installations by BiocManager. This can...

BiocManager delegates to remotes::install_github() to install github packages. The remotes package offers to update Bioc-hosted packages to their github version, which is counter to the BiocManager goal of providing a...

matrix dimensions transposed

3

It's confusing, but I think matrix data is read / written transposed from native hdf5 format ``` > create(fl system2("h5ls", fl) col_attrs Group layers Group matrix Dataset {2/Inf, 3/Inf} row_attrs...

When trying to load SharedObject I get ``` > library(SharedObject) Error: package or namespace load failed for 'SharedObject': .onLoad failed in loadNamespace() for 'SharedObject', details: call: C_initialPkgData() error: An error...

Handle worker abort better

1

When a worker aborts (e.g., out of memory?) the result is an error in BiocParallel code, rather than an error understandable by the user. ``` > bplapply(1:2, \(...) q()) Error...

Reported via email ```{r} .libPaths(tempfile()) BiocManager::install('phangorn') # installs phangorn ``` So far so good, but ```{r} > BiocManager::install('phangorn', dependencies = TRUE) Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)...

BiocManager::valid() does not check for 'missing' dependencies

1

Suppose Package A depends on B depends on C. The user installs A (hence B & C) then removes B. BiocManager::valid() does not detect this situation, because A and C...