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Dec 20 2020

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

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)

Dec 17 2020

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
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)
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)
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)
eisenman moved T28119: Unit tests are failing on Ubuntu due to mismatching messages from Backlog to In Progress on the challengeR (v1.0) board.
Dec 17 2020, 1:02 PM · challengeR (v1.0)
eisenman triaged T28119: Unit tests are failing on Ubuntu due to mismatching messages as High priority.
Dec 17 2020, 1:01 PM · challengeR (v1.0)
eisenman created T28117: Keep track of licenses of dependencies.
Dec 17 2020, 12:26 AM · challengeR
eisenman placed T27494: Check which files are still relevant up for grabs.
Dec 17 2020, 12:17 AM · challengeR
eisenman edited projects for T27494: Check which files are still relevant, added: challengeR; removed challengeR (v1.0).

Ok, we can keep them in this release.

Dec 17 2020, 12:16 AM · challengeR
eisenman edited projects for T27925: Use cases of annotator option, added: challengeR; removed challengeR (v1.0).
Dec 17 2020, 12:13 AM · challengeR
eisenman edited projects for T27775: only export functions to be used by user, added: challengeR; removed challengeR (v1.0).

Discussed with @wiesenfa that this issue is not critical for release v1.0.

Dec 17 2020, 12:13 AM · challengeR
eisenman moved T27291: update license file from In Progress to Done on the challengeR (v1.0) board.
Dec 17 2020, 12:09 AM · challengeR (v1.0)
eisenman committed rCHALLENGER381233357a63: Merge branch 'feature/T27291-AdaptLicense' into develop (authored by eisenman).
Merge branch 'feature/T27291-AdaptLicense' into develop
Dec 17 2020, 12:06 AM
eisenman committed rCHALLENGER53cc163e1907: Remove CSV file (authored by eisenman).
Remove CSV file
Dec 17 2020, 12:03 AM

Dec 16 2020

eisenman committed rCHALLENGERa8d863aa9084: Change license to GPLv2 or later to be compatible with licenses of dependencies (authored by eisenman).
Change license to GPLv2 or later to be compatible with licenses of dependencies
Dec 16 2020, 11:59 PM
eisenman added a comment to T27291: update license file.

Recap: The initially chosen license (GPLv3) is not compatible with GPLv2 only licenses of dependencies (e.g. ggplot2, relations)

Dec 16 2020, 11:44 PM · challengeR (v1.0)
eisenman moved T27291: update license file from Backlog to In Progress on the challengeR (v1.0) board.
Dec 16 2020, 9:25 AM · challengeR (v1.0)

Dec 14 2020

eisenman claimed T27998: Interpretation of consensus ranking values needs further explanation.
Dec 14 2020, 3:14 PM · challengeR (v1.0)
eisenman closed T28016: embed web app in package as Invalid.

The idea of the web app is to lower the entry level for users that are not familiar with and/or don't want to install R (as this is already a hurdle for some of them).

Dec 14 2020, 2:15 PM · challengeR (v1.0)

Dec 11 2020

eisenman added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.
Dec 11 2020, 9:51 AM · challengeR (v1.0)
eisenman updated subscribers of T28097: test errors in aggregateThenRank and rankThenAggregate.

It works for me on the latest develop branch (#921705).

Dec 11 2020, 9:45 AM · challengeR (v1.0)

Dec 10 2020

eisenman created T28100: [dash] Decide on a file management strategy.
Dec 10 2020, 11:45 PM · webChallengeR
eisenman created T28099: [dash] Indicate progress of file upload.
Dec 10 2020, 11:28 PM · webChallengeR

Dec 9 2020

eisenman created T28095: [dash] Develop landing page.
Dec 9 2020, 6:27 PM · webChallengeR
eisenman moved T28094: [dash] Develop web app based on Dash from Backlog to In Progress on the webChallengeR board.
Dec 9 2020, 6:23 PM · webChallengeR
eisenman triaged T28094: [dash] Develop web app based on Dash as High priority.
Dec 9 2020, 6:22 PM · webChallengeR

Dec 8 2020

eisenman triaged T28085: Report generation is broken as High priority.
Dec 8 2020, 1:16 PM · challengeR (v1.0)

Dec 2 2020

eisenman moved T27241: Readme improvements from In Progress to Done on the challengeR (v1.0) board.

I don't see that 1. is an issue. Further improvements were done in the scope of T27996 and T27420.

Dec 2 2020, 11:27 AM · challengeR (v1.0)
eisenman moved T27241: Readme improvements from Backlog to In Progress on the challengeR (v1.0) board.
Dec 2 2020, 11:14 AM · challengeR (v1.0)

Nov 26 2020

eisenman moved T27420: report text from In Progress to Done on the challengeR (v1.0) board.

Compensated for 2. Text was revised in T27677.

Nov 26 2020, 10:35 PM · challengeR (v1.0)
eisenman committed rCHALLENGEReffec2e25455: Merge branch 'feature/T27770-ImproveReportFormat' into develop (authored by eisenman).
Merge branch 'feature/T27770-ImproveReportFormat' into develop
Nov 26 2020, 10:33 PM
eisenman committed rCHALLENGER0f1d4a7a652a: Add page breaks such that descriptions appear along with the plot (authored by eisenman).
Add page breaks such that descriptions appear along with the plot
Nov 26 2020, 10:32 PM
eisenman moved T27420: report text from Backlog to In Progress on the challengeR (v1.0) board.
Nov 26 2020, 3:38 PM · challengeR (v1.0)
eisenman added a comment to T28016: embed web app in package.

It sounds nice, but I also think that we can run into cumbersome situations w.r.t. package management and version control with this approach: If the web app is located within the package, for each change to the package itself, it has to be investigated how the change affects the web app. The developer also has to adapt and test the web app then. This also means that for each package release, a corresponding web app has to be provided. In my opinion it makes more sense to focus either on the package or the web app during the development. Probably, we want to improve the web app that is based on a fixed package version x most frequently. This use case is then hampered by this approach as the package itself also evolves.

Nov 26 2020, 12:07 PM · challengeR (v1.0)

Nov 23 2020

eisenman created T27998: Interpretation of consensus ranking values needs further explanation.
Nov 23 2020, 3:19 PM · challengeR (v1.0)