brio 0.3.0 (2019-07-22)

Bumped version number to reflect changes in basejump dependencies.

Minor changes

  • Improved naming consistency of internal functions.
  • Updated package dependency versions.

brio 0.3.1 (2019-07-30)

Minor changes

  • import: Bug fix for invalid objects (e.g. S4 objects that inherit SummarizedExperiment) not returning silently. Had to convert the try call to a tryCatch call to avoid errors popping up during name checks.
  • import: Now suppressing partial match of 'OS' to 'OS.type' warning for import of XLS files, which is a bug in gdata package.

brio 0.3.2 (2019-08-06)

Minor changes

  • Now using acidroxygen package to manage shared roxygen documentation params.

brio 0.3.3 (2019-08-13)

Minor changes

  • Added support for url calls to import, localOrRemoteFile, and loadRemoteData.
  • Improved message consistency.
  • Updated basejump dependency versions.

brio 0.3.4 (2019-08-16)

Minor changes

  • Reworked organization and naming of internal importer functions. Now including these in the import documentation, for clarity.
  • import: Added format and setclass arguments.
  • Switched to data.table::fread for import of bcbio count matrix. Previously, was using readr::read_tsv.
  • Import of lines no longer stores brio attributes.
  • Reduced number of package dependencies, no longer requiring readr.

brio 0.3.5 (2019-08-22)

Minor changes

  • No longer warn on MTX import without sidecar rownames and colnames files.
  • import: Don’t attempt to slot attributes for atomic vector return. This applies to source code lines and helps avoid valid name issues when assigning these values to colnames or rownames. I came across this issue while updating the Chromium package to assign names from 10X Genomics sidecar files.

brio 0.3.6 (2019-08-27)

  • Updated R dependency to 3.6.

Major changes

  • export: Reworked internal code to call data.table::fwrite directly, rather than having to pass to brio::export. Added support for bz2 output for matrix and sparseMatrix classes.

brio 0.3.7 (2019-09-03)

Minor changes

brio 0.3.8 (2019-09-11)

Major changes

  • import: Improved metadata stash approach inside S4 (metadata) and S3 (attributes) return objects. Previously, import metadata was stashed inside “brio”, but this has been renamed to “import”. Metadata is no longer stashed inside R data objects loaded via import. Simplified the internal code inside import to only stash the call, whereas importer metadata is now handled by an internal .defineImportMetadata function.

Minor changes

  • export: Improved default extension documentation and internal argument matching via match.arg. For matrix files exported simply with dir argument, this will default to CSV format. For sparse Matrix files exported simply with dir argument, this will default to MTX format.

brio 0.3.9 (2019-10-04)

Minor changes

  • Updated data.table and rio dependencies, based on recent data.table 1.12.4 update, which has a lot of changes.
  • Fixed internal code to no longer show rownames message, even when rownames = FALSE.

brio 0.3.10 (2019-10-12)

Major changes

  • Added back internal support for readr package instead of data.table for import and export functions. We have observed stack imbalance and segfault memory dump issues with the latest data.table release (v1.12.4) on multi-core Azure VMs. The engine can now be changed using global options:

    • import: acid.import.engine (“data.table” or “readr”).
    • export: acid.export.engine (“data.table” or “readr”).

    This new addition is experimental and may be dropped in a future release. We find that readr currently works more reliably for export in some cases for large CSV files, but data.table is generally faster and more robust for data import of CSV and TSV files. We’re intentionally keeping this functions simple and not providing a user-facing argument for selecting the internal engine.

Minor changes

  • Converted unnecessary exported global variables into internal globals: compressExtPattern, extPattern, rdataExtPattern, rdataLoadError.
  • Updated naStrings to include empty whitespace.

brio 0.3.11 (2019-10-13)

  • naStrings: Reverted back to including only “NA” and “NULL”, instead of including empty space strings. This results in unwanted messages regarding strip whitespace from data.table fread function.

brio 0.3.12 (2019-10-18)

New functions

  • getURLDirList: Return a simple character vector of files and subdirectories in a remote directory. Intended for use with FTP servers.
  • Also now reexporting the getURL function from RCurl.

Minor changes

  • import: Default format argument has been renamed from “none” to “auto”.
  • localOrRemoteFile: Improved handling for remote URLs without a file extension.
  • pasteURL: Now smartly strips trailing slashes prior to internal paste call.

brio 0.3.13 (2019-10-22)

Minor changes

  • NAMESPACE updates to support migration of some low-level functions to the new acidbase package.

brio 0.3.14 (2019-11-07)

Minor changes

  • Updated package dependencies to require Bioconductor 3.10 release.

brio 0.3.15 (2019-12-09)

Minor changes

  • export: Removed internal dependencies on as_tibble and as.data.table calls. The tibble package recently changed the default row name handling behavior in as_tibble, which broke the code here. I reworked the internal code to only use base R approaches, so changes in the tidyverse no longer affect the package.