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Dec 20 2020

eisenman closed T27337: Report contains wrong ranking method when rank-then-aggregate is used as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)
eisenman closed T27452: Provide plot function for dendrogram as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)
eisenman closed T27714: Report contains weird R output as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)
eisenman closed T27453: Create complete network plot in its function as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)
eisenman closed T27776: Failing unit tests for subset of tasks as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)
eisenman closed T27685: changes in subset() as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)
eisenman closed T27777: Failing unit tests for challenge as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)
eisenman closed T27774: wrong text in report on algorithm subsets as Resolved.
Dec 20 2020, 9:28 PM · challengeR (v1.0)
eisenman closed T27447: significanceMap function raises warning about deprecated function call as Resolved.
Dec 20 2020, 9:27 PM · challengeR (v1.0)
eisenman closed T27770: Inconsistency in report description as Resolved.
Dec 20 2020, 9:27 PM · challengeR (v1.0)
eisenman closed T27282: Implement tests for ranking method "test-then-rank" based on Wilcoxon signed rank test as Resolved.
Dec 20 2020, 9:27 PM · challengeR (v1.0)
eisenman closed T27686: tutorial can be added as vignette to embed it in the package as Resolved.
Dec 20 2020, 9:27 PM · challengeR (v1.0)
eisenman closed T27450: Consistent use of attribute indicating whether small metric values lead to a better rank as Resolved.
Dec 20 2020, 9:26 PM · challengeR (v1.0)
eisenman closed T27804: Message text from violin plot is cut off in the PDF report as Resolved.
Dec 20 2020, 9:26 PM · challengeR (v1.0)
eisenman closed T27793: Plot titles are missing in some line plots as Resolved.
Dec 20 2020, 9:26 PM · challengeR (v1.0)
eisenman closed T27778: turn off networks as Resolved.
Dec 20 2020, 9:26 PM · challengeR (v1.0)
eisenman closed T27456: Extraction of task subset from (bootstrap) ranking does not raise an error for invalid task name as Resolved.
Dec 20 2020, 9:26 PM · challengeR (v1.0)
eisenman closed T27794: Stacked frequency plots should switch to single page layout as Resolved.
Dec 20 2020, 9:26 PM · challengeR (v1.0)
eisenman closed T27802: Revise signature of function testThenRank as Resolved.
Dec 20 2020, 9:26 PM · challengeR (v1.0)
eisenman closed T27922: Remove network plot from report overview as Resolved.
Dec 20 2020, 9:25 PM · challengeR (v1.0)
eisenman closed T27278: Writing documentation for main functions as Resolved.
Dec 20 2020, 9:25 PM · challengeR (v1.0)
eisenman closed T27929: Provide documentation for plot functions as Resolved.
Dec 20 2020, 9:25 PM · challengeR (v1.0)
eisenman closed T27930: Revise examples given in the vignettes as Resolved.
Dec 20 2020, 9:25 PM · challengeR (v1.0)
eisenman closed T27996: Restructure troubleshooting section as Resolved.
Dec 20 2020, 9:25 PM · challengeR (v1.0)
eisenman closed T27420: report text as Resolved.
Dec 20 2020, 9:25 PM · challengeR (v1.0)
eisenman closed T28055: respect color scheme also for box plots as Resolved.
Dec 20 2020, 9:25 PM · challengeR (v1.0)
eisenman closed T28033: +scale_* seems to not work in combination with ggList objects as Resolved.
Dec 20 2020, 9:25 PM · challengeR (v1.0)
eisenman closed T27963: Task names printed as R output in Sec. 3.1 of multi-task report as Resolved.
Dec 20 2020, 9:25 PM · challengeR (v1.0)
eisenman closed T27360: compatibility with R4.0.0 as Resolved.

Also successfully checked for Ubuntu 18.04 and R version 4.0.3.

Dec 20 2020, 9:24 PM · challengeR (v1.0)
eisenman closed T27707: na.treat obligatory for report as Resolved.
Dec 20 2020, 9:23 PM · challengeR (v1.0)
eisenman closed T27241: Readme improvements as Resolved.
Dec 20 2020, 9:23 PM · challengeR (v1.0)
eisenman closed T27915: Podium plot shrinks for long algorithm names as Resolved.
Dec 20 2020, 9:22 PM · challengeR (v1.0)
eisenman closed T27748: Decide on limit for algorithms in plot legends as Resolved.
Dec 20 2020, 9:22 PM · challengeR (v1.0)
eisenman closed T27943: Plot function stability() raises error when used with default values as Resolved.
Dec 20 2020, 9:22 PM · challengeR (v1.0)
eisenman closed T28085: Report generation is broken as Resolved.
Dec 20 2020, 9:22 PM · challengeR (v1.0)
eisenman closed T27971: Provide code for podium plot in vignette "Visualizations" as Resolved.
Dec 20 2020, 9:22 PM · challengeR (v1.0)
eisenman closed T27292: Fix toolkit authors as Resolved.
Dec 20 2020, 9:22 PM · challengeR (v1.0)
eisenman closed T28112: colors in box plots multitask not consistent as Resolved.
Dec 20 2020, 9:22 PM · challengeR (v1.0)
eisenman closed T27291: update license file as Resolved.
Dec 20 2020, 9:22 PM · challengeR (v1.0)
eisenman closed T27998: Interpretation of consensus ranking values needs further explanation as Resolved.
Dec 20 2020, 9:21 PM · challengeR (v1.0)
eisenman closed T28119: Unit tests are failing on Ubuntu due to mismatching messages as Resolved.
Dec 20 2020, 9:21 PM · challengeR (v1.0)
eisenman closed T28097: test errors in aggregateThenRank and rankThenAggregate as Resolved.
Dec 20 2020, 9:21 PM · challengeR (v1.0)
eisenman closed T28123: Add notes for Linux users to readme as Resolved.
Dec 20 2020, 9:21 PM · challengeR (v1.0)
eisenman closed T28120: Write release notes for challengeR v1.0 as Resolved.
Dec 20 2020, 9:21 PM · challengeR (v1.0)
eisenman committed rCHALLENGER565de37af81a: Merge tag 'T28125-v1.0.0' into develop (authored by eisenman).
Merge tag 'T28125-v1.0.0' into develop
Dec 20 2020, 9:18 PM
eisenman committed rCHALLENGER55b014bdb3b9: Merge branch 'release/T28125-v1.0.0' (authored by eisenman).
Merge branch 'release/T28125-v1.0.0'
Dec 20 2020, 9:12 PM
eisenman committed rCHALLENGER99079cc3c626: Bump version number (authored by eisenman).
Bump version number
Dec 20 2020, 9:00 PM
eisenman committed rCHALLENGER4bdcc0e9afb4: Add release notes (authored by eisenman).
Add release notes
Dec 20 2020, 8:58 PM
eisenman moved T28125: challangeR Release v1.0.0 from Backlog to In Progress on the challengeR (v1.0) board.
Dec 20 2020, 8:29 PM · challengeR (v1.0)
eisenman moved T28120: Write release notes for challengeR v1.0 from In Progress to Done on the challengeR (v1.0) board.
Dec 20 2020, 8:27 PM · challengeR (v1.0)
eisenman closed T28121: Remove parallel bootstrapping from quick-start scripts as Wontfix.
Dec 20 2020, 8:26 PM · challengeR (v1.0)
eisenman triaged T28125: challangeR Release v1.0.0 as High priority.
Dec 20 2020, 8:26 PM · challengeR (v1.0)
eisenman closed T28122: Fix layout of logos at the end of the readme file as Resolved.
Dec 20 2020, 8:20 PM · challengeR (v1.0)

Dec 18 2020

wiesenfa created T28124: add line plot (like methods plot) across tasks to report.
Dec 18 2020, 6:28 PM · challengeR
eisenman added a comment to T28120: Write release notes for challengeR v1.0.

Changes:

  • Revision of the underlying data structure
  • Roxygen documentation for main functionality
  • Vignettes for quickstart and overview of available plots demonstrating the use of their corresponding plot functions
  • Introduction of unit tests (package coverage >70%)
  • Troubleshooting section covering potential issues during setup
  • Finally: Extensive bug fixes and improvements (for a complete overview please check the Phabricator tasks)
Dec 18 2020, 12:22 PM · challengeR (v1.0)
eisenman moved T28120: Write release notes for challengeR v1.0 from Backlog to In Progress on the challengeR (v1.0) board.
Dec 18 2020, 12:01 PM · challengeR (v1.0)
eisenman moved T28122: Fix layout of logos at the end of the readme file from In Progress to Done on the challengeR (v1.0) board.
Dec 18 2020, 10:35 AM · challengeR (v1.0)
eisenman committed rCHALLENGERe70e0f204d79: Merge branch 'feature/T28122-LogoLayout' into develop (authored by eisenman).
Merge branch 'feature/T28122-LogoLayout' into develop
Dec 18 2020, 10:35 AM
eisenman committed rCHALLENGER7ba034d29fab: Adapt size of logos (authored by eisenman).
Adapt size of logos
Dec 18 2020, 10:28 AM
eisenman committed rCHALLENGERda0a62e8bd7e: Use HIP logo with transparent background (authored by eisenman).
Use HIP logo with transparent background
Dec 18 2020, 10:28 AM
eisenman moved T28122: Fix layout of logos at the end of the readme file from Backlog to In Progress on the challengeR (v1.0) board.
Dec 18 2020, 10:15 AM · challengeR (v1.0)
eisenman moved T28123: Add notes for Linux users to readme from In Progress to Done on the challengeR (v1.0) board.
Dec 18 2020, 10:15 AM · challengeR (v1.0)
eisenman committed rCHALLENGER30158bc6e88b: Merge branch 'feature/T28123-ReadmeImprovements' into develop (authored by eisenman).
Merge branch 'feature/T28123-ReadmeImprovements' into develop
Dec 18 2020, 10:14 AM
eisenman committed rCHALLENGERcabb1f1d24f7: Add reference to vignettes (authored by eisenman).
Add reference to vignettes
Dec 18 2020, 10:12 AM
eisenman committed rCHALLENGER37e3667b357c: Add hint for Linux users how to resolve some errors during installation (authored by eisenman).
Add hint for Linux users how to resolve some errors during installation
Dec 18 2020, 10:12 AM
eisenman moved T28123: Add notes for Linux users to readme from Backlog to In Progress on the challengeR (v1.0) board.
Dec 18 2020, 9:26 AM · challengeR (v1.0)
kislinsk closed T26237: Improve performance for interactions in 2d widgets as Resolved.
Dec 18 2020, 4:03 AM · MITK
kislinsk added a comment to T26237: Improve performance for interactions in 2d widgets.

Deleted branch bugfix/T26237-ImprovePerformance.

Dec 18 2020, 4:02 AM · MITK
kislinsk committed rMITKbf264ce891b8: Improve performance (authored by kislinsk).
Improve performance
Dec 18 2020, 4:02 AM
kislinsk committed rMITKd05bd6a2660b: Merge remote-tracking branch 'origin/develop' into bugfix/T26237… (authored by kislinsk).
Merge remote-tracking branch 'origin/develop' into bugfix/T26237…
Dec 18 2020, 4:02 AM
kislinsk committed rMITKdbbf947882f4: Improve ITK patch (authored by kislinsk).
Improve ITK patch
Dec 18 2020, 4:02 AM
kislinsk committed rMITKdc76958e5051: Merge branch 'bugfix/T26237-ImprovePerformance' into develop (authored by kislinsk).
Merge branch 'bugfix/T26237-ImprovePerformance' into develop
Dec 18 2020, 4:02 AM

Dec 17 2020

kislinsk renamed Phabricator Onboarding from Phabricator onboarding to Phabricator Onboarding.
Dec 17 2020, 7:59 PM · Onboarding
eisenman created T28123: Add notes for Linux users to readme.
Dec 17 2020, 6:46 PM · challengeR (v1.0)
eisenman moved T28097: test errors in aggregateThenRank and rankThenAggregate from In Progress to Done on the challengeR (v1.0) board.
Dec 17 2020, 6:38 PM · challengeR (v1.0)
eisenman committed rCHALLENGER1239f2bdc6aa: Merge branch 'feature/T28097-IrrelevantRowOrder' into develop (authored by eisenman).
Merge branch 'feature/T28097-IrrelevantRowOrder' into develop
Dec 17 2020, 6:37 PM
eisenman committed rCHALLENGER19b804226ac7: Remove irrelevant tests that assume a specific row order (authored by eisenman).
Remove irrelevant tests that assume a specific row order
Dec 17 2020, 6:36 PM
eisenman claimed T28097: test errors in aggregateThenRank and rankThenAggregate.
Dec 17 2020, 6:05 PM · challengeR (v1.0)
eisenman moved T28097: test errors in aggregateThenRank and rankThenAggregate from Backlog to In Progress on the challengeR (v1.0) board.
Dec 17 2020, 6:03 PM · challengeR (v1.0)
eisenman moved T28119: Unit tests are failing on Ubuntu due to mismatching messages from In Progress to Done on the challengeR (v1.0) board.
Dec 17 2020, 6:03 PM · challengeR (v1.0)
eisenman committed rCHALLENGER016b847dbb7a: Merge branch 'feature/T28119-MismatchingStringsWithQuotationMarks' into develop (authored by eisenman).
Merge branch 'feature/T28119-MismatchingStringsWithQuotationMarks' into develop
Dec 17 2020, 6:02 PM
eisenman committed rCHALLENGER4374432aa096: Check only for beginning of error message to avoid escaped quotation marks (authored by eisenman).
Check only for beginning of error message to avoid escaped quotation marks
Dec 17 2020, 6:01 PM
wiesenfa added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

platform is output with Sys.info(); linux and Mac systems are equal and windows may differ

Dec 17 2020, 5:55 PM · challengeR (v1.0)
wiesenfa added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

good idea!
otherwise you could use a platform dependent expect_equal but I think your idea is sufficient

Dec 17 2020, 5:53 PM · challengeR (v1.0)
eisenman created T28122: Fix layout of logos at the end of the readme file.
Dec 17 2020, 5:47 PM · challengeR (v1.0)
eisenman moved T27998: Interpretation of consensus ranking values needs further explanation from In Progress to Done on the challengeR (v1.0) board.
Dec 17 2020, 5:44 PM · challengeR (v1.0)
eisenman committed rCHALLENGER3f9e443d1f47: Merge branch 'feature/T27998-ConsensusRankingExplanation' into develop (authored by eisenman).
Merge branch 'feature/T27998-ConsensusRankingExplanation' into develop
Dec 17 2020, 5:43 PM
eisenman committed rCHALLENGER598a4d4ccc2d: Add explanation of consensus ranks (authored by eisenman).
Add explanation of consensus ranks
Dec 17 2020, 5:42 PM
eisenman added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

After investing several hour trying different encodings, e.g. using raw strings, I still don't find a way to make this work. I also don't see a way of changing the source message, because it's originating from another package.

Dec 17 2020, 5:20 PM · challengeR (v1.0)
eisenman added a comment to T28121: Remove parallel bootstrapping from quick-start scripts.

We should definitely keep it in the README.

Dec 17 2020, 5:16 PM · challengeR (v1.0)
wiesenfa added a comment to T28121: Remove parallel bootstrapping from quick-start scripts.

would mention it there at least though because bootstrapping may be time consuming

Dec 17 2020, 5:14 PM · challengeR (v1.0)
wiesenfa added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

don't think its necessary. there is anyway ordering applied to it in later stages.
otherwise ranking step (rank.aggregated.list()) could always do the ordering directly (then the test would check whether ordering is working). As mentioned before I avoided such change before the release because of (very unlikely) risk of breaking something in the first level hierarchy

Dec 17 2020, 5:13 PM · challengeR (v1.0)
eisenman created T28121: Remove parallel bootstrapping from quick-start scripts.
Dec 17 2020, 5:02 PM · challengeR (v1.0)
eisenman added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

Is the order of the rows relevant in any processing step? If not, the tests can be removed. Currently, I don't see a way making it work for both systems I have available for testing (Win10, R 3.6.3 and Ubuntu 18.04, R 4.0.3).

Dec 17 2020, 4:59 PM · challengeR (v1.0)
wiesenfa added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

I do see those as well on Mac

Dec 17 2020, 4:46 PM · challengeR (v1.0)
wiesenfa added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

R 4.0.2.
testthat previously 2.3.2, now 3.0.1.
the issue is however not connected to test_that I see that in the first 2 tests in aggregate-then-rank the ordering in the data set is not used but sorted

Dec 17 2020, 4:45 PM · challengeR (v1.0)
eisenman added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

The platform might not be the (only) reason.
@wiesenfa: Which version of R and testthat are you using?

Dec 17 2020, 1:50 PM · challengeR (v1.0)
eisenman updated the task description for T28119: Unit tests are failing on Ubuntu due to mismatching messages.
Dec 17 2020, 1:45 PM · challengeR (v1.0)
eisenman updated the task description for T28119: Unit tests are failing on Ubuntu due to mismatching messages.
Dec 17 2020, 1:22 PM · challengeR (v1.0)
eisenman triaged T28120: Write release notes for challengeR v1.0 as High priority.
Dec 17 2020, 1:03 PM · challengeR (v1.0)