brio 0.2.2 (2019-06-08)
loadRemoteData now support overwrite argument. The default behavior of these functions has changed to allow overwriting into the environment by default, matching the base
load function conventions. If this behavior is undesired, set
options(acid.overwrite = FALSE) and this will be inherited in all calls.
acid.save.overwrite to simply use
acid.overwrite global for IO functions. This was modified now that
loadData also supports the
brio 0.2.1 (2019-05-08)
import: Removed Google Sheets support. The
googlesheets R package is currently too buggy, and the replacement
googlesheets4 package isn’t stable. This functionality may be added back in a future update.
brio 0.2.0 (2019-05-06)
Introducing breaking changes to
export method. Now using
object instead of
x as the primary argument, and defaulting to the use of
dir instead of recommending the use of
file, as is the convention in the brio package. This makes interactive file export quicker and more intuitive, involving less repetitive variable declarations.
brio 0.1.20 (2019-04-25)
- S4 generic reexport documentation fixes.
brio 0.1.19 (2019-04-22)
- Backward compatibility fixes/updates to support R 3.4.
brio 0.1.18 (2019-04-01)
- Bug fix release. Re-importing rio package to ensure
export() always works on
brio 0.1.17 (2019-03-31)
import: Added GRP file support for GSEA.
import: Improved Google Sheet import support, using new googlesheets4 package from tidyverse.
- Improved code coverage, getting closer to 100%.
brio 0.1.16 (2019-03-28)
sanitizePercent here from basejump package.
- Switched to using “acid” prefix instead of “basejump” for global
options. This applies in particular to the
saveData functions, where the
dir argument can be set globally for an interactive session using this parameter.
brio 0.1.15 (2019-03-27)
sanitizeNA from basejump here, so these functions can be imported in freeranges package.
brio 0.1.13 (2019-03-20)
localOrRemoteFile: Improved error message for Windows users when tempfile can’t be removed successfully. This can happen on systems when the user is not running as Administrator, but doesn’t happen on macOS or Linux.
brio 0.1.12 (2019-03-17)
import: Added initial
colnames parameter support for
data.frame import. I strongly recommend leaving these enabled by default. However, these are useful in some edge cases when loading data from remote servers (e.g. WormBase).
... passthrough for
brio 0.1.11 (2019-03-13)
import: Switched to using
gdata::read.xls to import legacy XLS binary files.
readxl::read_excel doesn’t work consistently for some files and returns
libxls error. In the meantime, use gdata package, which is slow but works.
validObject check in
brio 0.1.10 (2019-03-11)
localOrRemoteFile: Binary file extension pattern matching bug fix. Applies to files downloaded on Windows. If
download.file is not called with mode
wb (write binary) for files on Windows, decompression will fail.
brio 0.1.9 (2019-03-08)
saveData now support
list argument, supporting a character vector of object names. This allows for programmatic use of the functions with standard evaluation. For reference, this approach is inspired by the method defined in
import: Data provenance metadata is now slotted into
attributes for S3 return (e.g.
metadata for S4 return (e.g.
brio 0.1.8 (2019-02-25)
export: Tightened up the method support, removing the
ANY method. Now we’re explicitly exporting
GRanges methods. This also has the added benefit of making the documentation more readable.
brio 0.1.7 (2019-02-15)
basenameSansExt: Tightened up this function to return
NA on match failure. This behaves simiarly to the new
- Switching back from defunct to deprecated for
sanitizeRowRanges, since these functions are still in use by bcbioRNASeq v0.2.9.
- Improved NEWS file for previous releases.
brio 0.1.6 (2019-02-12)
- Documentation fixes and website improvements.
brio 0.1.5 (2019-02-11)
This release helps ensure backward compatibility with R 3.4.
- Bug fix for assert in
transmit: Need to wrap
all for backward compatibility with R 3.4.
- Miscellaneous CI fixes to Travis CI and AppVeyor CI.
brio 0.1.4 (2019-01-21)
These functions have been migrated from basejump here to brio, since they deal specifically with file input/output:
sanitizeRowData. May need to add back in a future release, but removed for time being.
realpath: Removed unnecessary assert check using
normalizePath already checks for this when
mustWork = TRUE.
- Added initial code coverage support using testthat.
brio 0.1.3 (2019-12-13)
- Updated imports to reflect renaming of S4Transformer package to simply transformer.
brio 0.1.2 (2019-12-12)
extPattern to inherit
- Improved documentation in
import regarding compressed file handling.
- Split out NAMESPACE imports into
sanitizeRowData to take advantage of exported
- Improved Travis CI and AppVeyor CI configuration.
brio 0.1.1 (2019-01-05)
- Added Travis CI and AppVeyor CI support.
- Improved documention in
import regarding supported file formats.
- Split out internal importers into separate R files.
- Fixed return value for
- Disabled working examples for transmit, since they are failing on Travis CI.
- Documentation fixes and miscellaneous tweaks to pass build checks.
brio 0.1.0 (2018-12-24)
Initial release. Migrated input-output (IO) functions from basejump.