NEWS.md

In acidgenomics/bb8: Acid Genomics Developer Tools

Release notes

AcidDevTools 0.7.4 (2023-12-13)

New functions:

• inspectRow: Quickly examine nested values in a data.frame row. Supports any object that can be coerced to a data.frame.

AcidDevTools 0.7.3 (2023-10-24)

New functions:

• rebuildBinary: New function for updating problematic binary file in drat repo. Added this after I hit S4 subclass caching issues related to the change in AcidGenomes from HumanToMouse to JaxHumanToMouse. This affected AcidSingleCell and DESeqAnalysis. Function is vectorized, supporting multiple packageName in a single call.

AcidDevTools 0.7.2 (2023-10-06)

Minor changes:

• view2: Need to set optional = TRUE for as.data.frame coercion.

AcidDevTools 0.7.1 (2023-10-03)

Minor changes:

• No longer reexporting functions from remotes.

AcidDevTools 0.7.0 (2023-09-28)

New functions:

• cacheTestFiles: New utility function used in other packages to quickly cache files for testthat build checks.
• longtest: Variant of test that runs optional tests defined in longtests. This is useful for matching recommended Bioconductor conventions. These tests are run in a temporary directory.
• nonCamelArgs: Check for documented arguments that are not correctly formatted in strict camel case.
• nonCamelExports: Check for exported functions that are not correctly formatted in strict camel case.

Minor changes:

• check: Now returns the amount of time required to run checks.
• Enforcing strict camel case in function names. As a result, we have renamed pkgdownDeployToAWS to pkgdownDeployToAws.

AcidDevTools: 0.6.18 (2023-09-21)

Minor changes:

• check: Don't check as CRAN by default. Can have issues with requireNamespace not finding packages as expected.

AcidDevTools 0.6.17 (2023-09-21)

Minor changes:

• check: Check as CRAN by default. Also added tweaks to BiocCheck settings.

AcidDevTools 0.6.16 (2023-09-14)

Minor changes:

• packageDependencies: Can now disable recursion using recursive = FALSE. Still recommended by default for true evaluation of package heaviness.

AcidDevTools 0.6.15 (2023-09-07)

Minor changes:

• catVec: Now handles return of named vectors. This addition was very useful for improving code coverage against Sanger CellModelPassports in the recent Cellosaurus package update.

AcidDevTools 0.6.14 (2023-08-15)

Minor changes:

• check: Ensure that testthat test does not return successful if any errors or warnings are detected. This requires coercion of testthat_results to a data.frame.

AcidDevTools 0.6.13 (2023-08-15)

Minor changes:

• NAMESPACE fix for accidental is call.

AcidDevTools 0.6.12 (2023-08-15)

Minor changes:

• check: Rework assert check for testthat results return.

AcidDevTools 0.6.11 (2023-08-15)

Minor changes:

• check: Need to pass package location to style_pkg.

AcidDevTools 0.6.10 (2023-08-10)

New functions:

• size: Returns object size in a human readable format. Calls object.size and format internally.

Minor changes:

• test: Now using test_local instead of test_dir internally, which plays nicer with testthat tests run in parallel.

AcidDevTools 0.6.9 (2023-05-31)

• check: Now checking that all required and suggested packages are installed before proceeding. Otherwise we can run into NAMESPACE linter errors.

AcidDevTools 0.6.8 (2023-05-22)

• valid: Improved checking of binary/source packages when pkgType is set to "both" mode. This applies primarily to macOS.
• findAndReplace now uses parallel instead of BiocParallel internally.

AcidDevTools 0.6.7 (2023-05-17)

• Disabling error on warning during install and uninstall steps, to avoid current issues with Bioconductor 3.17 repos.

AcidDevTools 0.6.6 (2023-05-02)

• devinstall: Improved install support of Bioconductor dependencies when dependencies = TRUE is set.

AcidDevTools 0.6.5 (2023-02-09)

• Renamed drat function to publish, which is a better verb.

AcidDevTools 0.6.4 (2023-01-10)

• valid: Bug fix for incorrect quoting of package names.

AcidDevTools 0.6.3 (2023-01-09)

• valid: Improved singular/plural handling of package names.

AcidDevTools 0.6.2 (2022-11-22)

• valid: Restricted internal old.packages call to specifically check .Library.site and ignore .Library, so that we don't return unwanted messages about outdated system packages.

AcidDevTools 0.6.1 (2022-10-25)

• check: Don't error on URL check failures. This is often too strict, and currently problematic when checking AcidGenomes package.

AcidDevTools 0.6.0 (2022-10-20)

• install: Added back type argument, to install from source when required on macOS, as a lot of binaries are still not being built in a timely manner.
• Removed unused dev function.
• Reworked internal functions to rely less upon goalie package when possible. Switched back to using stopifnot instead of assert, and message instead of alert.
• Added a simplified internal variant of requireNamespaces, which makes conditional loading of packages easier. Follows the conventions of the function defined in AcidBase, with the exception that our internal version here always returns a logical, instead of erroring on failure. This is intended to be called within stopifnot.
• updatePackages: Simplified validity check after packages are installed.
• Using styler instead of formatR for code formatting.
• Removed formatR, gh, and reticulate, rmarkdown, tibble as suggested packages.
• Removed pipette and syntactic functions (e.g. loadData, saveData; camelCase, snakeCase, etc.) as reexports, to avoid unwanted NAMESPACE collision message when loading pipette package.

AcidDevTools 0.5.11 (2022-09-13)

• installRecommendedPackages: Added base R recommended packages that are normally included with binary installs: KernSmooth, MASS, Matrix, boot, class, cluster, codetools, foreign, lattice, mgcv, nlme, nnet, rpart, spatial, survival.

AcidDevTools 0.5.10 (2022-09-13)

• migrateRecommendedPackages: Fixed function export and final assert check that assesses whether migration was successful.

AcidDevTools 0.5.9 (2022-09-06)

• migrateRecommendedPackages: Added new function to migrate recommended packages installed by default in system library for R CRAN binaries.

AcidDevTools 0.5.8 (2022-08-01)

• installRecommendedPackages: Increased the priority of data.table package, to ensure it builds from source to enable multiple cores with OpenMP support on macOS. The binary package of data.table is currently compiled with support for single core mode only on macOS.

AcidDevTools 0.5.7 (2022-07-29)

• valid: Improved checks for old built system packages, by calling old.packages internally. Currently, BiocManager valid variant doesn't check if built system packages are out of date.
• Removed internal usage of custom Makevars.
• Removed reexports from lobstr package.

AcidDevTools 0.5.6 (2022-06-20)

• installRecommendedPackages: No longer recommending RDAVIDWebService, which was removed in Bioconductor 3.14 update.

AcidDevTools 0.5.5 (2022-06-10)

• check: Hardened URL checker to error on failure.

AcidDevTools 0.5.4 (2022-06-09)

• installRecommendedPackages: Simplified this function. No longer allowing selection of specific optional packages to install, as this is too confusing.

AcidDevTools 0.5.3 (2022-05-31)

• Improved file path normalization consistency using .realpath internally, matching our conventions defined in AcidBase. This helps improve file path message consistency on Windows.

AcidDevTools 0.5.2 (2022-05-24)

• drat: Bug fix for default branch handling in drat repo.

AcidDevTools 0.5.1 (2022-05-23)

• check: Added automatic package style checking using styler.
• install: Now using koopa GCC for gfortran by default.
• Updated lintr and testthat checks.

AcidDevTools 0.5.0 (2022-05-02)

• Updated minimum R dependency to 4.2.
• Migrated drat and pkgdownDeployToAWS from r-koopa package to here.
• Improved drat engine to use R CMD build and R CMD INSTALL --build instead of devtools, which handles vignettes inside of binary packages properly.

AcidDevTools 0.4.9 (2022-04-13)

• Simplified R package configuration on macOS, enforcing binary installs for difficult to build packages, when possible.

AcidDevTools 0.4.8 (2022-03-21)

• Added support for custom styler theme defined as acid_style.
• Added wrapper support for style_dir, style_file, and style_pkg, which uses our acid_style styler theme by default, instead of tidyverse conventions. In particular, this enforces 4 spaces instead of 2.

AcidDevTools 0.4.7 (2022-03-11)

Minor changes:

• Renamed installGitHub to installFromGitHub.
• installFromGitHub: Added branch argument support.
• valid: Updated recommended install call to use AcidDevTools. This helps avoid compilation issues with tricky packages, such as sf.

AcidDevTools 0.4.6 (2022-02-28)

Major changes:

• valid: Reworked to separately return install calls for outdated and pre-release packages. This now extracts return from BiocManager::valid.

Minor changes:

• installRecommendedPackages: Added GGally.

AcidDevTools 0.4.5 (2022-02-04)

Minor changes:

• install: Switched back to dependencies = NA by default, matching base R conventions.
• install: Bug fix for incorrect handling of geospatial library checks on Linux machines using system GDAL, GEOS, and PROJ.
• install: No longer checking for ~/.R/Makevars.

AcidDevTools 0.4.4 (2021-11-09)

Minor changes:

• Updated R dependency to 4.1, matching Bioconductor 3.14.
• install: Now ensures that sf, and other r-spatial packages install from source, with specific pinning to GEOS, GDAL, and PROJ.

AcidDevTools 0.4.3 (2021-09-22)

Minor changes:

• Bug fix for autoconfiguration detection of Homebrew install prefix on Linux, when HOMEBREW_PREFIX variable is defined, but the directory doesn't exist. This is currently the case with our updated koopa Renviron config.

AcidDevTools 0.4.2 (2021-09-14)

Minor changes:

• installRecommendedPackages: Need to remove parallel from this list.

AcidDevTools 0.4.1 (2021-09-08)

Minor changes:

• coverage: Default coverage threshold bumped from 80% to 95%.
• installRecommendedPackages: Added spatialreg package.
• test: Improved error message on unit test failure. Now using named argument in stopifnot call, which is supported in R 4.0.

AcidDevTools 0.4.0 (2021-08-23)

Major changes:

• Finally added code coverage for the package, using testthat.
• Added working examples when feasible for all functions.
• install, installGitHub, installedPackages, updatePackages now support a lib argument.
• installGitHub: Switched release argument to tag argument. User must now declare a specific tag instead of supporting install from default branch.

Minor changes:

• Consolidated alias functions: cd, clear, d, la.
• check: Added support for lints and urls overrides. Still enabled by default (non-breaking change), and calls lintr, urlchecker packages internally.
• dev: Reduced the number of packages loaded. Now calls magrittr, testthat, goalie, and basejump.
• findAndReplace: Reworked internal code using BiocParallel instead of parallel package, and switched from readr to base R for line import/export.
• getCurrentGitHubVersion: Now supports multiple version checks in a single call, defined by the repo argument.
• installRecommendedPackages: Updated default list.
• Bioconductor validity with valid now passes lib argument (see above).
• Default path in formal arguments has been changed from "." to getwd().
• load_all: Simplified default alias.

AcidDevTools 0.3.16 (2021-07-19)

• Reworked check, dev, and test functions.
• Tweaked test to call testthat::test_dir directly again.
• Reworked default handling of code coverage. Disabled automatic code coverage report checking when calling test.
• Simplified the number of default packages loaded in dev.
• Cleaned up internal comments for load_all.

AcidDevTools 0.3.15 (2021-07-06)

• Reorganized internal functions.
• check: Now always runs test internally, since rcmdcheck in some cases doesn't run unit tests in R 4.1.
• Migrated from using pryr to lobstr.
• Removed unused memfree function.

AcidDevTools 0.3.14 (2021-06-04)

• check: Added biocCheck and coverage arguments. Now checking package coverage for at least 80% coverage by default.

AcidDevTools 0.3.13 (2021-05-19)

• installRecommendedPackages: Added GRmetrics and dr4pl, for IC50 calculations.

AcidDevTools 0.3.12 (2021-05-18)

• Fix for BiocManager / install.packages handling in R 4.1

AcidDevTools 0.3.11 (2021-05-18)

• Removed magrittr as an import, now that base R supports pipe in 4.1.

AcidDevTools 0.3.10 (2021-05-18)

• check: Made lintr, urlchecker, and BiocCheck checks optional if these packages are not installed. This can be the case inside Docker images.

AcidDevTools 0.3.9 (2021-05-18)

• Removed clearWarnings from exports, which doesn't seem to be compatible with R 4.1 due to inability to assign last.warning to base environment.
• memfree: Now using %s instead of %d internally in sprintf call, due to hardened change in R 4.1.

AcidDevTools 0.3.8 (2021-05-12)

• installRecommendedPackages: Made this function more modular, allowing for the user to specify which types of extra packages should be installed. Applies primarily to Bioconductor (i.e. next-generation sequencing) analysis packages, which can often be quite large and inappropriate for a compact virtual machine instance.

AcidDevTools 0.3.7 (2021-05-10)

• install: Bug fix for stopifnot check on makevarsFile.
• Updated references to available and urlchecker packages.

AcidDevTools 0.3.6 (2021-05-03)

• install: Improved autoconf handling for data.table, now using ~/.R/Makevars dynamically to define gfortran GCC compiler options used to enable OpenMP support for parallel threads on macOS.

AcidDevTools 0.3.5 (2021-04-30)

• install: Improved autoconf handling for data.table, geos, rgl, and sf packages. Refer to internal .autoconf code for details.

AcidDevTools 0.3.4 (2021-04-27)

• install now ensures data.table gets built from source automatically. Currently on macOS, the prebuilt CRAN binaries don't enable parallel threading by default due to improper OpenMP configuration, which is annoying. Since we install the fxcoudert GCC compiler by default, let's use this instead to enable OpenMP and parallel processing support. May want to consider a similar approach in the future for Rcpp, etc.

AcidDevtools 0.3.3 (2021-04-27)

• Increased verbosity of dyn.load calls during load_all, which is very useful for debugging package load time and dependency chain.

AcidDevTools 0.3.2 (2021-04-23)

• install: Added new autoconf option, which will automatically set internal configuration overrides automatically for some problematic packages (e.g. rgl on macOS).

AcidDevTools 0.3.1 (2021-03-04)

• load_all alias now has helpers = FALSE set by default, to speed up package loads significantly.

AcidDevTools 0.3.0 (2021-02-04)

• Renamed package from "bb8" to "AcidDevTools".

bb8 0.2.50 (2021-01-31)

• Added veloviz and liger to recommended packages.

bb8 0.2.49 (2021-01-15)

• check: Improved package name detection, which doesn't always correspond to the directory name. Using desc package to harden this. Also a couple of bug fixes related to checking outside of package working directory.
• printComment: Bug fix to better set the width.
• Removed pc alias, which can get masked by Bioconductor.

bb8 0.2.48 (2020-12-16)

• Added pc alias for printComment, to reduce the amount of typing required during an interactive scripting session.

bb8 0.2.47 (2020-12-09)

• check: Hardened against lintr check failure.

bb8 0.2.46 (2020-12-07)

• Fix for packages with dependency issues: Seurat and dendsort.

bb8 0.2.45 (2020-12-03)

• install: Improved automatic definition of type internally for manual local package installs.

bb8 0.2.44 (2020-11-25)

• updatePackages: Improved error message handling when internal BiocManager validity checks fail. Wrapped using tryCatch call to better show which packages are responsible for the check failure.

bb8 0.2.43 (2020-11-24)

• installRecommendedPackages: Install all packages by default.

bb8 0.2.42 (2020-11-11)

• Added currentBiocVersion, which checks for current Bioconductor release version.
• updatePackages now automatically upgrades the Bioconductor release, when applicable.

bb8 0.2.41 (2020-11-06)

• Renamed installDefaultPackages to installRecommendedPackages.
• Fixed internal Bioconductor installation code.

bb8 0.2.40 (2020-11-05)

• install: Attempt to improve internal repository handling.
• updatePackages: Attempt to improve internal repository handling.

bb8 0.2.39 (2020-11-04)

• Migrated installBioconductor code into koopa package.
• Hardened uninstall and updatePackages against warnings.

bb8 0.2.38 (2020-11-04)

• installBioconductor: Also include automatic installation of BiocCheck.

bb8 0.2.37 (2020-11-04)

• install: Set dependencies argument to TRUE by default instead of NA, which will automatically install suggested packages.

bb8 0.2.36 (2020-11-03)

Migrated some install functions from koopa R package:

• installAcidverse: Install all Acid Genomics packages.
• installBioconductor: Wrapper for BiocManager::install.
• installDefaultPackages: Install default recommended R packages.

bb8 0.2.35 (2020-10-29)

• install: Improve support for direct installation from a local file.

bb8 0.2.34 (2020-10-29)

• install: Added support for automatic installation from a Git repository. Calls remotes::install_git internally.

bb8 0.2.33 (2020-10-28)

• Bug fix, ensuring tibble view is reexported.

bb8 0.2.32 (2020-10-23)

• Draft update adding view as a reexport, from tibble package.

bb8 0.2.31 (2020-10-20)

• updateDeps: Hardened against missing packages.

bb8 0.2.30 (2020-10-12)

• updatePackages: Only attempt to update GitHub packages if GITHUB_PAT environment variable is set.

bb8 0.2.29 (2020-10-07)

• Renamed acidbase package to AcidBase, and updated import here.
• Removed GitHub remotes to Acid Genomics packages.

bb8 0.2.28 (2020-08-25)

• updatePackages: Don't attempt to remove brio, as it's now on CRAN.

bb8 0.2.27 (2020-08-18)

• Bug fix for Bioconductor and CRAN/RSPM package detection.

bb8 0.2.26 (2020-08-18)

• installedPackages: Improved detection of Acid Genomics packages installed from r.acidgenomics.com instead of GitHub.

bb8 0.2.25 (2020-08-17)

• install: Don't attempt to update old packages by default.

bb8 0.2.24 (2020-08-11)

• updatePackages: Migrated automatic CRAN and GitHub removals here from code previously defined in koopa.
• Migrated isCleanSystemLibrary to goalie package.

bb8 0.2.23 (2020-08-11)

Minor changes:

• Renamed cleanSystemLibrary to isCleanSystemLibrary.

bb8 0.2.22 (2020-08-11)

Minor changes:

• install: Bug fix for skipping install from tarball URLs if the package is already installed. Can override with reinstall = TRUE.

bb8 0.2.21 (2020-08-05)

Minor changes:

• install now supports direct installation of package tarballs from URLs.

bb8 0.2.20 (2020-08-05)

Minor changes:

• install now internally treats all warnings as errors.

bb8 0.2.19 (2020-08-03)

Minor changes:

• Removed reexport of export and import from pipette package. The export function doesn't detect sym class correctly.
• Switched magrittr from Depends to Imports.

bb8 0.2.18 (2020-07-28)

Minor changes:

• Removed internal references to patrick package, which provides parameterized unit testing. Now falling back to simply using for or mapply loops instead inside of packages.

bb8 0.2.17 (2020-07-23)

Minor changes:

• updateDeps: Now calling install internally rather than handing off to BiocManager::install call.

bb8 0.2.16 (2020-07-22)

Major changes:

• install and installGitHub now default to reinstall = TRUE.

bb8 0.2.15 (2020-07-01)

Minor changes:

• Renamed getCurrentVersion function to getCurrentGitHubVersion.

bb8 0.2.14 (2020-06-21)

bb8 0.2.13 (2020-05-12)

Minor changes:

• printComment: Added width parameter. This allows for improved automatic return of comments at a desired width. Currently defaults to 80 characters.

bb8 0.2.12 (2020-04-13)

Minor changes:

• install: Another bug fix. Switching from vapply to lapply internally to capture return from BiocManager, as this output can vary.

bb8 0.2.11 (2020-04-13)

Minor changes:

• install: Bug fix for systems lacking BiocManager or remotes packages. These dependencies are now installed in the fly if missing.

bb8 0.2.10 (2020-04-12)

Minor changes:

• installGitHub: Bug fix for JSON parsing compability across Linux and macOS.

bb8 0.2.9 (2020-04-12)

Major changes:

• Revert back to approach where package doesn't import any dependencies via Imports, instead only using Suggests. This allows for package update calls inside Travis CI checks and Docker images to work more consistently.

bb8 0.2.8 (2020-04-12)

New functions:

• installGitHub: Install function that allows for versioned package installs without requiring GITHUB_PAT variable to be set. Intended for use inside Docker images. Otherwise, use remotes::install_github for interactive installs.

Major changes:

• Attempted to rework and simplify internal code, using acidbase and goalie as dependnecies. May revert back to no import approach.

bb8 0.2.7 (2020-01-31)

• rcmdcheck now uses --as-cran flag automatically.
• Updated import to use pipette instead of brio.

bb8 0.2.6 (2020-01-18)

• Updated BiocCheck reexport to not require biocViews in DESCRIPTION by default. This makes CI checks on non-Bioconductor packages destined for CRAN not error.

bb8 0.2.5 (2020-01-07)

• Removed lookup package from reexports, to avoid accidental installation of GitHub versions that cause BiocManager::valid() check to fail.

bb8 0.2.4 (2019-12-04)

• install and updatePackages no longer attempt to install and/or update suggested packages by default. I ran into some dependency issues with Seurat (SDMTools and adehabitat). See Seurat issue #2377.

bb8 0.2.3 (2019-11-19)

• Updated package documentation to support roxygen2 7.0 update.
• Added useful gh, locate, and remotes reexports.

bb8 0.2.2 (2019-10-30)

• Added more useful interactive reexports, including pipes.

bb8 0.2.1 (2019-10-23)

• Added killAll function, which calls pkill rsession internally.
• updateDeps: Now attempts to update "Enhances", "LinkingTo", and "Suggests" by default.
• Consistently using system2 instead of system internally.
• Added getPackageVersion, which gets current version of a GitHub package.
• Added isInstalled, which checks against installed.packages return.

bb8 0.2.0 (2019-10-20)

• Added install, which wraps BiocManager::install with some improved defaults for Mike's usage.
• Added updatePackages, which wraps BiocManager::install and remotes::update_packages with some improved defaults.
• Rexporting additional useful functions that get loaded by default in an interactive R session. See Mike's corresponding Rprofile dotfile.
• Package doesn't load any other additional packages as dependencies, to keep loading super fast in a new R session.

bb8 0.1.4 (2019-10-17)

• Removed lint_dir, which is now exported in lintr package.
• Added installedPackages, which returns a camelCase formatted data.frame containing a "source" column. This column includes whether the package was installed from CRAN, Biocondcutor, GitHub, GitLab, or NA (if system, or is a local build).

bb8 0.1.3 (2019-08-27)

• Updated R dependency to 3.6.

bb8 0.1.2 (2019-08-22)

• Improved updateDeps handling for Rcheck on Travis CI.

bb8 0.1.1 (2019-08-13)

• Removed goalie dependency.
• Fixed updateDeps so it can run on Travis CI.

bb8 0.1.0 (2019-08-13)

Initial stable release.

acidgenomics/bb8 documentation built on Feb. 1, 2024, 11:38 a.m.