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Fix xgboost related issues and update devel branch #527

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cying111 merged 27 commits intodevelfrom
devel_pre
Jan 15, 2026
Merged

Fix xgboost related issues and update devel branch #527
cying111 merged 27 commits intodevelfrom
devel_pre

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@cying111 cying111 commented Jan 15, 2026

This PR fixes the following issues or warnings:

  • Bioconductor installation issue 523
  • Resolve xgboost object incompatibility error in issue 447 and 407
  • Resolve process.y.margin.and.object error in isse 505
  • Resolve xgboost warnings related to argument updates in the recent xgboost version
  • Resolve the dplyr warning related to summarise usage in issue 380, 408, and 502

federicomarini and others added 22 commits December 21, 2023 13:14
@federicomarini
fixing the chunk when showing the import from the TxDb object
6f1e21d
@cying111
fix xgboost label as logical in scoreReadClass step
77a1aa6
@cying111
fix xgboost label logical issue in junction site prediction step
8f43a20
@cying111
update xgb.save binary files and internal models
44fd16d
@cying111
re-create terms attributes for lmNDR from formula
faf60f4
@cying111
re-create spliceJunction models from original saved standardJunctionM…
99745f4 
…odels_temp data
@cying111
update unsupported .model binary format to .ubj for xgboost saved model
b59c501
@cying111
update internal data and code to update defaultModels and standardJun…
b26518c 
…ctionModels_temp
@cying111
update label to logical for testing fixXGboostmodels
c403413
@cying111
clean up code
960a881
@cying111
fix xgboost data and label rename to x and y warning
c3d6b47
@SuiYue-2308
change summarise to mutate to avoid dplyr warnings
6a402ad
@cying111
resolve the warning caused by using old argument name data and label,…
531250b 
… and also using verbose argument
@cying111
update release notes for recent changes
052c9ff
@cying111
Merge pull request #520 from GoekeLab/xgboost_x_y_rename
323a151 
fix xgboost data and label rename to x and y warning
@cying111
Merge pull request #516 from GoekeLab/xgboost_bug_fix
b61c9a3 
Xgboost bug fix
@cying111
Merge pull request #406 from federicomarini/devel
f5dfcc9 
fixing the chunk when showing the import from the TxDb object
@cying111
set nthread config for xgboost so that 1 thread is used for 1 xgboost
6a93943
@cying111
remove the warning message
58b4d3a
@cying111
update release notes
1a484d3
@SuiYue-2308
fix the bug in unspliced tibble construction. This will fix the dplyr…
b7190ec 
… as well.
@cying111
Merge pull request #518 from GoekeLab/devel_pre_dplyr
e8a0f4a 
Switching from summarise() to reframe() to avoid dplyr warnings
@cying111 cying111 changed the title Fix xgboost related issues and update main branch Fix xgboost related issues and update devel branch Jan 15, 2026
@jonathangoeke jonathangoeke self-requested a review January 15, 2026 09:25
jonathangoeke
jonathangoeke approved these changes Jan 15, 2026
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thanks to all who contributed to the code changes!

@cying111 cying111 requested a review from SuiYue-2308 January 15, 2026 09:27
@cying111 cying111 merged commit e9d87de into devel Jan 15, 2026
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@jonathangoeke jonathangoeke jonathangoeke approved these changes

@SuiYue-2308 SuiYue-2308 SuiYue-2308 approved these changes

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@cying111 @jonathangoeke @SuiYue-2308 @federicomarini

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