export: Reworked internal methods to use new
decompressfunctions defined in acidbase package.
localOrRemoteFile: Reworked to use new
decompressdefined in acidbase internally, with improved
coercemethod is reexported – thanks @dpryan79 for catching this issue in basejump.
droplevels: Ensuring S4 generic variant defined in S4Vectors package gets reexported and masks base S3 generic. This helps avoid a
C stack usageissue that has popped up in the latest version of R.
import: Fix for importing JSON files without extension. Can now declare using the
formatargument. This fix was needed to import GitHub JSON URLs inside new
installGitHubfunction defined in bb8 package.
exportfunctions now default to using vroom engine instead of data.table. Internally, these now call
vroom_write. We noticed that the data.table
fwritefunction in particular can have issues writing many files on AWS EC2 instances, resulting in a stack imbalance. The vroom package seems to be more stable currently.
importHardened Excel input to intentionally error on any warnings returned by internal
read_excelcall, which is too liberal in coercing data types, in my opinion.
import: Switched XLS parser from gdata (no longer updated) back to readxl, which is more actively developed.
makeNamesargument, to override default internal handling. This allows the user to apply snake case and/or camel case formatting automatically with this argument.
cacheURL: Utility function for easy package file caching using BiocFileCache package internally.
getURLDirList: Migrated this function from previous definition in basejump, so we can inherit inside new AcidGenomes package.