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Dec 17 2020

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 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)
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 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)

Dec 16 2020

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

wiesenfa added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

seems to not fail on windows machines. but does on my Mac (and thus might also on linux). minor issue, defer to post 1.0.0

Dec 14 2020, 6:47 PM · challengeR (v1.0)
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)
wiesenfa moved T28112: colors in box plots multitask not consistent from In Progress to Done on the challengeR (v1.0) board.
Dec 14 2020, 2:09 PM · challengeR (v1.0)
wiesenfa moved T28112: colors in box plots multitask not consistent from Backlog to In Progress on the challengeR (v1.0) board.
Dec 14 2020, 2:07 PM · challengeR (v1.0)
wiesenfa created T28112: colors in box plots multitask not consistent.
Dec 14 2020, 1:33 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

wiesenfa moved T27292: Fix toolkit authors from In Progress to Done on the challengeR (v1.0) board.
Dec 10 2020, 1:25 PM · challengeR (v1.0)
wiesenfa moved T27292: Fix toolkit authors from Backlog to In Progress on the challengeR (v1.0) board.
Dec 10 2020, 1:25 PM · challengeR (v1.0)
wiesenfa created T28097: test errors in aggregateThenRank and rankThenAggregate.
Dec 10 2020, 11:11 AM · challengeR (v1.0)
wiesenfa moved T28085: Report generation is broken from In Progress to Done on the challengeR (v1.0) board.
Dec 10 2020, 11:09 AM · challengeR (v1.0)
wiesenfa moved T28085: Report generation is broken from Backlog to In Progress on the challengeR (v1.0) board.
Dec 10 2020, 11:09 AM · challengeR (v1.0)
wiesenfa claimed T28085: Report generation is broken.
Dec 10 2020, 11:09 AM · challengeR (v1.0)

Dec 8 2020

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

Dec 7 2020

wiesenfa added a comment to T27925: Use cases of annotator option.

would defer to after release

Dec 7 2020, 3:58 PM · challengeR
wiesenfa added a comment to T27494: Check which files are still relevant.

please close if ok

Dec 7 2020, 3:58 PM · challengeR
wiesenfa added a comment to T27925: Use cases of annotator option.

added to documentation of as.challenge():
(arg annotator:) If multiple annotators annotated the test cases, a string specifying the name of the column that contains the annotator identifiers. Only applies to rang-then-aggregate. Use with caution: Currently not tested.

Dec 7 2020, 3:18 PM · challengeR
wiesenfa moved T27925: Use cases of annotator option from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 3:16 PM · challengeR
wiesenfa added a comment to T27971: Provide code for podium plot in vignette "Visualizations".

added

podium(ranking)

to vignette.
podium() does have a different syntax for layouting (it is not ggplot2 but base graphics) but vignette does not describe layouting for ggplot2 plots either

Dec 7 2020, 2:20 PM · challengeR (v1.0)
wiesenfa moved T27971: Provide code for podium plot in vignette "Visualizations" from Backlog to Done on the challengeR (v1.0) board.
Dec 7 2020, 2:18 PM · challengeR (v1.0)
wiesenfa placed T27998: Interpretation of consensus ranking values needs further explanation up for grabs.
Dec 7 2020, 2:03 PM · challengeR (v1.0)
wiesenfa moved T27998: Interpretation of consensus ranking values needs further explanation from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 2:03 PM · challengeR (v1.0)
wiesenfa added a comment to T27998: Interpretation of consensus ranking values needs further explanation.

report() does not know what type of consensus ranking method had been used.
I added sentence
"Consensus ranking according to mean ranks across tasks if method="euclidean" where in case of ties (equal ranks for multiple algorithms) the average rank is used, i.e. ties.method="average"."
to help for consensus() and would suggest to also add this to the vignette/readme, but not to report. Could someone of you please take care of this?

Dec 7 2020, 2:03 PM · challengeR (v1.0)
wiesenfa added a comment to T27775: only export functions to be used by user.

@eisenman do you want to do this with roxygen?

Dec 7 2020, 1:10 PM · challengeR
wiesenfa assigned T27494: Check which files are still relevant to eisenman.
Dec 7 2020, 1:09 PM · challengeR
wiesenfa assigned T28016: embed web app in package to eisenman.
Dec 7 2020, 1:09 PM · challengeR (v1.0)
wiesenfa claimed T27998: Interpretation of consensus ranking values needs further explanation.
Dec 7 2020, 1:08 PM · challengeR (v1.0)
wiesenfa moved T28016: embed web app in package from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 1:08 PM · challengeR (v1.0)
wiesenfa moved T27943: Plot function stability() raises error when used with default values from In Progress to Done on the challengeR (v1.0) board.
Dec 7 2020, 1:07 PM · challengeR (v1.0)
wiesenfa added a comment to T27494: Check which files are still relevant.

kept select.if(), winner(), extract.workfolow and compareRanks()
and removed everything not supported anymore.
as.warehouse (benchmarkUtils) is not exported, recommend to leave because this may come handy for specific situations

Dec 7 2020, 1:07 PM · challengeR
wiesenfa moved T27494: Check which files are still relevant from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 12:56 PM · challengeR
wiesenfa moved T27943: Plot function stability() raises error when used with default values from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 11:21 AM · challengeR (v1.0)
wiesenfa added a comment to T27494: Check which files are still relevant.

removed second()

Dec 7 2020, 11:19 AM · challengeR

Dec 4 2020

wiesenfa placed T27971: Provide code for podium plot in vignette "Visualizations" up for grabs.
Dec 4 2020, 8:46 PM · challengeR (v1.0)
wiesenfa added a comment to T27971: Provide code for podium plot in vignette "Visualizations".

What is the problem?
in the extend of the vignette it would be simply

Dec 4 2020, 8:46 PM · challengeR (v1.0)
wiesenfa moved T27915: Podium plot shrinks for long algorithm names from In Progress to Done on the challengeR (v1.0) board.
Dec 4 2020, 8:40 PM · challengeR (v1.0)
wiesenfa added a comment to T27915: Podium plot shrinks for long algorithm names.

legend now always at bottom and dynamically adjusts to number of algorithms and algorithm name length.
Took me almost the day...

Dec 4 2020, 8:40 PM · challengeR (v1.0)
wiesenfa moved T27748: Decide on limit for algorithms in plot legends from In Progress to Done on the challengeR (v1.0) board.
Dec 4 2020, 8:39 PM · challengeR (v1.0)
wiesenfa added a comment to T27748: Decide on limit for algorithms in plot legends.

max number of tasks / algorithms now 20 in stacked frequency and line plots, respectively for legend appear on right, otherwise put on bottom of plot. could also be put to lower number

Dec 4 2020, 12:00 PM · challengeR (v1.0)
wiesenfa added a comment to T27748: Decide on limit for algorithms in plot legends.

only podium plots and line plots actually require algorithms in legend, otherwise algorithm is identifiable from x-axis or facet label. Now, these redundant legends are removed.
besides that stacked frequency plots have colored tasks and respective legend

Dec 4 2020, 11:52 AM · challengeR (v1.0)
wiesenfa moved T27915: Podium plot shrinks for long algorithm names from Backlog to In Progress on the challengeR (v1.0) board.
Dec 4 2020, 9:55 AM · challengeR (v1.0)
wiesenfa moved T27748: Decide on limit for algorithms in plot legends from Backlog to In Progress on the challengeR (v1.0) board.
Dec 4 2020, 9:55 AM · challengeR (v1.0)
wiesenfa moved T27707: na.treat obligatory for report from In Progress to Done on the challengeR (v1.0) board.
Dec 4 2020, 9:36 AM · challengeR (v1.0)
wiesenfa moved T27707: na.treat obligatory for report from Backlog to In Progress on the challengeR (v1.0) board.
Dec 4 2020, 9:36 AM · challengeR (v1.0)

Dec 3 2020

wiesenfa claimed T27748: Decide on limit for algorithms in plot legends.
Dec 3 2020, 10:22 PM · challengeR (v1.0)
wiesenfa moved T27963: Task names printed as R output in Sec. 3.1 of multi-task report from In Progress to Done on the challengeR (v1.0) board.
Dec 3 2020, 10:21 PM · challengeR (v1.0)
wiesenfa moved T27963: Task names printed as R output in Sec. 3.1 of multi-task report from Backlog to In Progress on the challengeR (v1.0) board.
Dec 3 2020, 10:14 PM · challengeR (v1.0)
wiesenfa moved T28033: +scale_* seems to not work in combination with ggList objects from In Progress to Done on the challengeR (v1.0) board.
Dec 3 2020, 10:11 PM · challengeR (v1.0)
wiesenfa added a comment to T28033: +scale_* seems to not work in combination with ggList objects.

works again for single task visualizations. in case multiple plots (a list of plots) is created %++% instead of + must be used for scale_*_() etc
mention in vignette

Dec 3 2020, 10:09 PM · challengeR (v1.0)
wiesenfa moved T28033: +scale_* seems to not work in combination with ggList objects from Backlog to In Progress on the challengeR (v1.0) board.
Dec 3 2020, 9:52 PM · challengeR (v1.0)
wiesenfa added a comment to T28016: embed web app in package.

ok. just an idea, thought this might help issues with the server because people can run stuff by themselves and still seize the user interface.
can be closed or considered later

Dec 3 2020, 8:48 PM · challengeR (v1.0)
wiesenfa moved T28055: respect color scheme also for box plots from In Progress to Done on the challengeR (v1.0) board.
Dec 3 2020, 1:57 PM · challengeR (v1.0)
wiesenfa moved T28055: respect color scheme also for box plots from Backlog to In Progress on the challengeR (v1.0) board.
Dec 3 2020, 1:57 PM · challengeR (v1.0)
wiesenfa created T28055: respect color scheme also for box plots.
Dec 3 2020, 12:03 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 27 2020

wiesenfa claimed T28033: +scale_* seems to not work in combination with ggList objects.
Nov 27 2020, 3:23 PM · challengeR (v1.0)
wiesenfa created T28033: +scale_* seems to not work in combination with ggList objects.
Nov 27 2020, 1:55 PM · 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 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)
wiesenfa created T28016: embed web app in package.
Nov 26 2020, 8:48 AM · 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)
eisenman moved T27996: Restructure troubleshooting section from In Progress to Done on the challengeR (v1.0) board.
Nov 23 2020, 3:00 PM · challengeR (v1.0)
eisenman moved T27996: Restructure troubleshooting section from Backlog to In Progress on the challengeR (v1.0) board.
Nov 23 2020, 2:53 PM · challengeR (v1.0)
eisenman created T27996: Restructure troubleshooting section.
Nov 23 2020, 2:53 PM · challengeR (v1.0)
wiesenfa claimed T27971: Provide code for podium plot in vignette "Visualizations".
Nov 23 2020, 12:08 PM · challengeR (v1.0)
wiesenfa claimed T27963: Task names printed as R output in Sec. 3.1 of multi-task report.
Nov 23 2020, 12:07 PM · challengeR (v1.0)
eisenman moved T27930: Revise examples given in the vignettes from In Progress to Done on the challengeR (v1.0) board.
Nov 23 2020, 10:53 AM · challengeR (v1.0)

Nov 18 2020

eisenman created T27971: Provide code for podium plot in vignette "Visualizations".
Nov 18 2020, 12:36 PM · challengeR (v1.0)

Nov 16 2020

eisenman moved T27930: Revise examples given in the vignettes from Backlog to In Progress on the challengeR (v1.0) board.
Nov 16 2020, 6:30 PM · challengeR (v1.0)
eisenman moved T27929: Provide documentation for plot functions from In Progress to Done on the challengeR (v1.0) board.

The plot functions that are used in the report have Roxygen documentation now. There's also a vignette called "Visualizations" that shows and explains the plots along with the corresponding plot function.

Nov 16 2020, 5:52 PM · challengeR (v1.0)
eisenman created T27963: Task names printed as R output in Sec. 3.1 of multi-task report.
Nov 16 2020, 10:52 AM · challengeR (v1.0)

Nov 12 2020

eisenman added a comment to T27943: Plot function stability() raises error when used with default values.

Thank you for clarification!

Nov 12 2020, 2:09 PM · challengeR (v1.0)
wiesenfa claimed T27943: Plot function stability() raises error when used with default values.
Nov 12 2020, 1:20 PM · challengeR (v1.0)
wiesenfa added a comment to T27943: Plot function stability() raises error when used with default values.

It has to be
ordering= names(meanRanks)
i.e. a vector of algorithm names in the ranking order
see reportMultiple.Rmd: ordering_consensus=names(params$consensus)

Nov 12 2020, 1:20 PM · challengeR (v1.0)

Nov 10 2020

eisenman moved T27929: Provide documentation for plot functions from Backlog to In Progress on the challengeR (v1.0) board.
Nov 10 2020, 6:54 PM · challengeR (v1.0)
eisenman updated the task description for T27943: Plot function stability() raises error when used with default values.
Nov 10 2020, 6:24 PM · challengeR (v1.0)