v3.1.2

Release Notes

Documentation is now available at https://metrumresearchgroup.github.io/pkgr/docs/, including new documentation on the configuration format and expanded documentation of many subcommands. (#422)

Installation Instructions

Mac

first time:

brew tap metrumresearchgroup/tap
brew install pkgr

upgrade:

brew upgrade pkgr

Linux

sudo wget https://github.com/metrumresearchgroup/pkgr/releases/download/v3.1.2/pkgr_3.1.2_linux_amd64.tar.gz -O /tmp/pkgr.tar.gz
sudo tar xzf /tmp/pkgr.tar.gz pkgr
sudo mv pkgr /usr/local/bin/pkgr
sudo chmod +x /usr/local/bin/pkgr

v3.1.2-rc.1

First release candidate for version 3.1.2

Installation Instructions

Mac

first time:

brew tap metrumresearchgroup/tap
brew install pkgr

upgrade:

brew upgrade pkgr

Linux

sudo wget https://github.com/metrumresearchgroup/pkgr/releases/download/v3.1.2-rc.1/pkgr_3.1.2-rc.1_linux_amd64.tar.gz -O /tmp/pkgr.tar.gz
sudo tar xzf /tmp/pkgr.tar.gz pkgr
sudo mv pkgr /usr/local/bin/pkgr
sudo chmod +x /usr/local/bin/pkgr

v3.1.1

Release notes

Fixed renv detection when other startup code writes to stdout. (#408)

Changelog

• 0cd65fe Merge pull request #415 from metrumresearchgroup/release/3.1.1
• 092c8f5 NEWS.md: add release notes for v3.1.1
• 6c3d40a Merge pull request #411 from metrumresearchgroup/mran-retire
• b77f172 Merge pull request #412 from metrumresearchgroup/readme-reduce-install
• 258fa61 Merge pull request #414 from metrumresearchgroup/dep-update-yaml
• 8b2d053 dep: update yaml.v3
• 35a26e1 README: reduce Linux/macOS install instructions to pointer
• f6e2cfe tests: replace some Microsoft CRAN URLs to MPN URLs
• 4b4d9cd ci: run gpsr/ and cran/ tests
• b39c2f0 cran/pkg_nexus_test.go: switch Microsoft CRAN URLs to MPN URLs
• ec872b3 gpsr tests: switch Microsoft CRAN URL to MPN URL
• fabd647 gpsr tests: simplify desc.Desc construction
• 27c581c Merge pull request #408 from metrumresearchgroup/renv-lib-markers
• 079ab93 config: mark renv library path for more reliable detection
• 17d6bf3 integration_tests/bad-customization: replace dead link
• 540b4a8 integration_tests/bad-customization: avoid index error in test code
• 41fd8e1 Merge pull request #406 from billdenney/patch-1
• 6a070b6 Update Linux installation to current version

Installation Instructions

Mac

first time:

brew tap metrumresearchgroup/tap
brew install pkgr

upgrade:

brew upgrade pkgr

Linux

sudo wget https://github.com/metrumresearchgroup/pkgr/releases/download/v3.1.1/pkgr_3.1.1_linux_amd64.tar.gz -O /tmp/pkgr.tar.gz
sudo tar xzf /tmp/pkgr.tar.gz pkgr
sudo mv pkgr /usr/local/bin/pkgr
sudo chmod +x /usr/local/bin/pkgr

v3.1.0

Release notes

For Lockfile: Type: renv, pkgr now invokes renv to discover the library location rather than assuming it is under the current directory's renv/library/. This change is important for compatibility with renv 0.15 and later, where the default behavior is now to put a package project library outside of the main project directory. (#396)

Installation Instructions

Mac

first time:

brew tap metrumresearchgroup/tap
brew install pkgr

upgrade:

brew upgrade pkgr

Linux

sudo wget https://github.com/metrumresearchgroup/pkgr/releases/download/v3.1.0/pkgr_3.1.0_linux_amd64.tar.gz -O /tmp/pkgr.tar.gz
sudo tar xzf /tmp/pkgr.tar.gz pkgr
sudo mv pkgr /usr/local/bin/pkgr
sudo chmod +x /usr/local/bin/pkgr

v3.1.0-rc1

Changelog

• e24ccac Merge pull request #396 from metrumresearchgroup/renv-library-loc
• f276f2e TestLibrary: extract renv subtests to dedicated test
• 5b4299d config_test.go: don't force renv case onto existing tests
• 774a71a SetupEndToEndWithInstallFull: rewrite error check for clarity
• 5cd5e31 SetupEndToEndWithInstallFull: rename expectFail parameter to expectError
• ca3af92 Merge pull request #395 from metrumresearchgroup/upgrade-retracted
• e787bf4 integration_tests/library: add more renv tests
• f5c120d config: invoke renv to discover library path
• 0a4a8ee ci: test configlib and integration_tests/library with system renv
• 4af8659 config_test.go: replace some cran.microsoft URLs with MPN ones
• bb1cef0 ci: test configlib
• c58d65d config_test.go: don't assume top-level directory is under pkgr/
• 2095218 .drone.yml: add trailing newline
• ac2be28 e2e_tests: add extended SetupEndToEndWithInstall variant
• 4d0e16e TestGetLibraryPath: loosen renv library path expectation
• 8e041a6 TestGetLibraryPath: match system R version
• bac6bf5 TestGetLibraryPath: drop unused message field from struct of cases
• 9dcb8ff rcmd: extract most of RunR to new RunRscriptWithArgs function
• 39a22de rcmd: fix malformed Rscript program on Windows
• fcfe6c9 rcmd: delete commented out code from RunR
• a3d9cca Merge pull request #399 from billdenney/extra-space
• 9de34bc remove extra space in log message
• b5780c6 dep: update retracted brotli version to latest version

Installation Instructions

Mac

first time:

brew tap metrumresearchgroup/tap
brew install pkgr

upgrade:

brew upgrade pkgr

Linux

sudo wget https://github.com/metrumresearchgroup/pkgr/releases/download/v3.1.0-rc1/pkgr_3.1.0-rc1_linux_amd64.tar.gz -O /tmp/pkgr.tar.gz
sudo tar xzf /tmp/pkgr.tar.gz pkgr
sudo mv pkgr /usr/local/bin/pkgr
sudo chmod +x /usr/local/bin/pkgr

v3.0.0

Release Notes

This release is primarily about adding a more robust test suite, with minimal user-facing changes. One notable exception is the first point below, relating to the new --no-update flag.

• Reversed default behavior to update to newest available versions of packages when pkgr install is run, unless --no-update flag is present (305a835). Previously pkgr did not update installed packages unless --update was passed.
• Add explicit version flag (6dd9c3e).
• Added IgnorePackages to ignore specific packages from being installed even if they're in the dependency tree (104f1c9).
• Extend integration test coverage and refactored test suite to position better for future changes.
• System CPU quotas are now respected when setting the number of CPUs that are used if the --threads option isn't explicitly passed and the GOMAXPROCS environment variable isn't set. (#385)

Changelog

• 3f19360 Ci/add goreleaser to drone (#394)
• 164254d CI: document get for linux without using .ArtifactName, as this isn't available to stages. (#393)
• b9fb24a Test/turn off 329 test (#391)
• 6214f48 Update go.mod to patch around a dependabot vulnerability.
• 04c4c60 Update command package (#388)
• 31704f4 Add go.uber.org/automaxprocs to cmd/pkgr/pkgr.go (#385)
• c19617f change: improving the labeling of a few of the tagged unit-tests.
• 8f55610 change: making the issue #329 test a bit easier to maintain and fixing its position in the test hierarchy.
• 806b2a0 change: adding os-specific test files to the mixed-source tests to allow me to run this as part of validation.
• c6b0993 add: adding a test for issue #329. This will fail right now, but we want to make sure we're keeping track of this.
• 550eb1a fix: actually pulling R 4.0.5 image before trying to use it . . .
• 57fe580 change: changing mixed-source integration tests to use R4.0.5 as per Devin's comment.
• f46181d change: unskipping test and modifying expected results after confirming behavior described in #380 is correct.
• 6e8df9d change: as I feared, the R 4.0 image did not readily exist. Resetting for now.
• 4f52bc5 change: changing the image for mixed source to be R 4.0 to see if that makes binaries available.
• 4333788 add: adding mixed-source tests to drone.
• 841679c change: changing testhelper.PkgRepoSetLogs.ToString to, by default, exclude type information. The reason for this is to allow golden files to be platform agnostic in cases * where we are not specifically testing install_type.
• f143454 change: skipping a test that's failing as a result of issue #380.
• 2bec960 add: adding mixed-source test, although it is currently failing on Mac because of issue #329, as well as the fact that R 4.0 binaries are not available on the latest MPN * snapshot known to have Linux binaries.
• 21b7179 fix: correcting a false negative in an E2E test. The remaining negative in BSLNPLN-E2E-003 is a real problem though.
• 20efcfd change: improving pre-installed baseline plan test to cover more scenarios. Found a bug.
• 0f982fd add: adding E2E tests for situations with packages not installed by pkgr.
• 92bca52 change: adding test tags to some tests that were missing them.
• ca0054d change: adding test IDs to outdated pkg e2e tests.
• 0c2799c change: updating test tags in baseline install (updating as I assign them so this is safe)
• 737d25f change: changing the localrepo used in tarball-install tests to prevent collisions in the pkgr global pkgdb cache.
• 7dc8184 change: some more refactoring to help narrow down the cause of some testing weirdness. Disabling suite-test, as it isn't really doing anything but marking failures.
• 44ed063 change: adding some IDs to a few unit tests that are relevant for validation.
• 8f6fccb change: repairing configlib unit tests.
• 249f54a fix: fixing locale settings for multi-repo test.
• 6bf551b change: removing a unit test that is not worth the maintenance given that we are moving Rcmd to a new package.
• ebad5fe wip: tidying up some tests to make it easier to run them consistently alongside the unit tests.
• 66b17ef fix: rollback test since normalized naming to capitalcase in yaml
• 0196589 rm additional old outdated packages test
• 4a17b5a rm old outdated pkg test
• a3b4c5e refactor: update tests and behavior to reflect new default behavior
• 305a835 refactor: use noupdate to normalize to the inverse pattern elsewhere and change default
• 928523a add: adding tests for cache-partial and cache-extraneous.
• acf6198 add: adding tests for idempotence.
• e277922 change: updating .drone.yml file to include library tests.
• 216c5bc change: changing the tarball-install tests to reflect the undesired but expected behavior described in #376
• 1fa3b81 add: test for the -v flag.
• 2ec8070 add: packrat and renv tests.
• 3d66de4 add: strict mode test, as well as some setup for renv and packrat tests.
• e342404 add: adding a test for tarball overwrite.
• 40ff502 add: tarball installation test.
• 10a9504 add: adding a test for the 'Suggests' option in baseline.
• 8405976 add: rpath env var E2E test.
• d08c8b4 change: adding a line to regular (non-test) code to standardize a log message.
• 6b011a1 add: tests for the 'NoRecommended' flag.
• aa08b72 add: adding a test for bad-customization, refactoring some things.
• 9e3fcf7 change: adding validation test tags to some of our relevant unit tests.
• 94eb200 add: updating golden file for multi-repo plan test.
• bddd4ae add: adding explicit test for repo order and refactoring multi-repo tests to not use regex.
• 4974d91 change: adding a 'delete test-library' to the beginning of baseline install, fleshing out the clean cache tests a bit more.
• 1613621 change: improving the clean tests.
• 315c418 add: sort methods so that we can do a golden-file option for tests hitting the logs.
• 61210c2 wip: swapping out regex match with JSON-parsing strategy.
• 145c6cf wip: bulking up the baseline tests to cover some of what was previously done in simple.
• 36f8027 ci: sync additional tests
• 86a8180 ci: adjust go env so can use mod cache to not re-dl deps for tests
• f1c13a1 add: multi-repo tests.
• 200b468 fix: fixing .drone.yml
• 554fcbf add: Makefile and drone config.
• 6baf0b0 change: removing defunct folders and files.
• ae5a917 add: load-fail tests.
• 1ea9511 change: trimming down dependencies invoked in load test and adding a test for the load report.
• 7715ee5 wip: working through some of the needs of the load test. Need to trim down deps.
• 33ab691 change: some minor cleanup for consistency.
• 15ce7fd wip: fixing a typo in the drone.yml file.
• b180e5a wip: adding drone, adding makefile, adding test for update flag.
• 3e31ea5 wip: automating Outdated tests using new pattern.
• 75383d4 review: respond to JC code review comments around setup
• 5585360 ci: add rollback tests
• 182cf53 doc: information about how rollback test works
• 346a8c1 refactor and test rollback
• eaca927 ci: add baseline
• 2ce85a7 ci: first shot at drone ci
• 40bff60 fixup: version to be specific to target
• 6dd9c3e feat: add version flags --version and -v
• 6b0c17b update to latest command and restructure based on output being byteslice
• 3008a65 test: add additional run tests and invocation by make
• 643010c improve test structuring with makefile plus subtests
• 10c86d2 dep: update deps
• ca63e9c reconcile
• 5445e20 update test to be a test.
• 26024a9 This includes a -logjson flag for most logging cases, along with some stuff in integration_test/integration_helper for making and running a test from an enumerated list.
• 6e21a15 test: add example snapshot test
• b6b3e32 feat: sort dependency arrays to make more deterministic
• ba67e4f refactor: drop forced colors so file and piped outputs will be easier to manage
• a32e868 refactor: use combined output, clean up log messages and consistent casing
• b2954f8 bump go releaser
• ba34e26 chore: remove todo since actually has tests
• 8ad331c fix: customizations structures
• cce50ea chore: bump to 3.x series
• be59972 fix: cache /etc/os-release
• 1437d4f fix/break: linux binary compat major changes
• 765933d chore: whitespace changes that might have been needed for parsing the tests, but might have been a red-herring. Either way... whitespace changes.
• 91e112b change: minor tweaks to the tilde-expansion test.
• e9262cf change: updating threads test to use latest MPN snapshot and updating expected packages to match.
• 3c14e9e change: minor tweaks to the tarball-install test.
• 8e24d26 change: tweaking strict-mode tests to also include a config file with Lockfile: type: renv.
• 32f2c91 change: completely overhauling the simple-suggests test. It's still not great, but it wasn't even finished before so this was necessary.
• a1eb1b8 change: updating 'recommended' test to pull from source for all repos involved after discovering #333
• 77567b8 change: minor tweaks to the simple test for clarity.
• 256be0a change: updating the simple integration test to use a later MPN snapshot.
• 951e34d chore: fixing a typo in rollback-disabled.
• 925e0a6 change: updating repo-order test to only require 'plan' to be run -- mrgsolve has system dependencies that make installing it problematic, but verifying plan should be * sufficient.
• 853e4b6 change: minor updates to repo-local-and-remote test.
• d9f73c1 change: updating packrat-library test to reflect current behavior.
• 67720d2 change: updating the outdated-pkgs-no-update test and making it less redundant.
• daf1b9f change: updating outdated-pkgs pkgr.yml to point to MPN.
• 4531372 change: updating the mixed-source guide.md to actually make sense.
• 1670305 change: updating the 'misc' integration test for clarity and updated package environments.
• f76555c chore: tweaking linux-binaries test.
• 9189c34 change: modifying linux-binaries...

Testing CI of goreleaser - pre-release

Test of CI build. Do not consume.

v3.0.0-rc1

Changelog

ed7fe79 chore: more attempts to fix goreleaser
3eaf34f chore: try to fix goreleaser template goreleaser/goreleaser#1456
66b17ef fix: rollback test since normalized naming to capitalcase in yaml
0196589 rm additional old outdated packages test
4a17b5a rm old outdated pkg test
a3b4c5e refactor: update tests and behavior to reflect new default behavior
305a835 refactor: use noupdate to normalize to the inverse pattern elsewhere and change default
928523a add: adding tests for cache-partial and cache-extraneous.
acf6198 add: adding tests for idempotence.
e277922 change: updating .drone.yml file to include library tests.
216c5bc change: changing the tarball-install tests to reflect the undesired but expected behavior described in #376
1fa3b81 add: test for the -v flag.
2ec8070 add: packrat and renv tests.
3d66de4 add: strict mode test, as well as some setup for renv and packrat tests.
e342404 add: adding a test for tarball overwrite.
40ff502 add: tarball installation test.
10a9504 add: adding a test for the 'Suggests' option in baseline.
8405976 add: rpath env var E2E test.
d08c8b4 change: adding a line to regular (non-test) code to standardize a log message.
6b011a1 add: tests for the 'NoRecommended' flag.
aa08b72 add: adding a test for bad-customization, refactoring some things.
9e3fcf7 change: adding validation test tags to some of our relevant unit tests.
94eb200 add: updating golden file for multi-repo plan test.
bddd4ae add: adding explicit test for repo order and refactoring multi-repo tests to not use regex.
74383b1 Merge branch 'develop' of github.com:metrumresearchgroup/pkgr into test/end-to-end-tests
4974d91 change: adding a 'delete test-library' to the beginning of baseline install, fleshing out the clean cache tests a bit more.
1613621 change: improving the clean tests.
315c418 add: sort methods so that we can do a golden-file option for tests hitting the logs.
61210c2 wip: swapping out regex match with JSON-parsing strategy.
145c6cf wip: bulking up the baseline tests to cover some of what was previously done in simple.
36f8027 ci: sync additional tests
9366ffc Merge pull request #374 from metrumresearchgroup/ci/tweaks
86a8180 ci: adjust go env so can use mod cache to not re-dl deps for tests
35cb583 Merge pull request #372 from metrumresearchgroup/test/multi-repo
f1c13a1 add: multi-repo tests.
ee82c8a ./localcache/CRAN-9a8e3d5f8621/src/sys_3.4.tar.gz
200b468 fix: fixing .drone.yml
554fcbf add: Makefile and drone config.
6baf0b0 change: removing defunct folders and files.
ae5a917 add: load-fail tests.
91233c1 Merge pull request #366 from metrumresearchgroup/test/rollback
2e467f5 Merge pull request #359 from metrumresearchgroup/exp/testing
1ea9511 change: trimming down dependencies invoked in load test and adding a test for the load report.
7715ee5 wip: working through some of the needs of the load test. Need to trim down deps.
33ab691 change: some minor cleanup for consistency.
15ce7fd wip: fixing a typo in the drone.yml file.
b180e5a wip: adding drone, adding makefile, adding test for update flag.
3e31ea5 wip: automating Outdated tests using new pattern.
75383d4 review: respond to JC code review comments around setup
5585360 ci: add rollback tests
182cf53 doc: information about how rollback test works
346a8c1 refactor and test rollback
5c4c089 Merge pull request #364 from metrumresearchgroup/feat/version
eaca927 ci: add baseline
2ce85a7 ci: first shot at drone ci
40bff60 fixup: version to be specific to target
6dd9c3e feat: add version flags --version and -v
6b0c17b update to latest command and restructure based on output being byteslice
3008a65 test: add additional run tests and invocation by make
643010c improve test structuring with makefile plus subtests
10c86d2 dep: update deps
ca63e9c reconcile
d354447 Merge pull request #360 from elisarver/test_repo-local
7c97918 Merge pull request #357 from metrumresearchgroup/refactor/combined-output
c930cd6 Merge pull request #352 from metrumresearchgroup/fix/customization-structure
5445e20 update test to be a test.
26024a9 This includes a -logjson flag for most logging cases, along with some stuff in integration_test/integration_helper for making and running a test from an enumerated list.
6e21a15 test: add example snapshot test
b6b3e32 feat: sort dependency arrays to make more deterministic
ba67e4f refactor: drop forced colors so file and piped outputs will be easier to manage
a32e868 refactor: use combined output, clean up log messages and consistent casing

Installation Instructions

Mac

first time:

brew tap metrumresearchgroup/tap
brew install pkgr

upgrade:

brew upgrade pkgr

Linux

sudo wget https://github.com/metrumresearchgroup/pkgr/releases/download/v3.0.0-rc1/pkgr_3.0.0-rc1_linux_amd64.tar.gz -O /tmp/pkgr.tar.gz
sudo tar xzf /tmp/pkgr.tar.gz pkgr
sudo mv pkgr /usr/local/bin/pkgr
sudo chmod +x /usr/local/bin/pkgr

v3.0.0-alpha.3

Changelog

b2954f8 bump go releaser
ba34e26 chore: remove todo since actually has tests
8ad331c fix: customizations structures
cce50ea chore: bump to 3.x series
3deec0a Merge pull request #343 from metrumresearchgroup/feat/skip
e85e397 Merge pull request #340 from metrumresearchgroup/fix/linux-binary-compat
104f1c9 exp: allow for ignoring certain packages in the solve

v3.0.0-alpha.2

sudo wget https://github.com/metrumresearchgroup/pkgr/releases/download/v3.0.0-alpha.2/pkgr_3.0.0-alpha.2_linux_amd64.tar.gz -O /tmp/pkgr.tar.gz
sudo tar xzf /tmp/pkgr.tar.gz pkgr
sudo mv pkgr /usr/local/bin/pkgr
sudo chmod +x /usr/local/bin/pkgr

Changelog

be59972 fix: cache /etc/os-release
ab59c16 Merge branch 'develop' of github.com:metrumresearchgroup/pkgr into fix/linux-binary-compat
76022cc Merge pull request #339 from metrumresearchgroup/featuer/2.0.2-validation-todev
c2cd38d chore: resolving merge conflicts.
6f8974c wip: trying to work around the R version dependencies for the failing Load tests.