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REVDEP: 506 reverse dependencies (481 from CRAN + 25 from Bioconductor) with R_FUTURE_RESOLVED_RUN=defunct + all the others [ci skip]
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‎revdep/README.md‎

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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |America/Los_Angeles |
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|date |2025-12-07 |
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|date |2025-12-08 |
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|pandoc |3.8.2.1 @ /software/c4/cbi/software/pandoc-3.8.2.1/bin/pandoc |
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|quarto |1.8.26 @ /software/c4/cbi/software/quarto-1.8.26/bin/quarto |
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# Dependencies
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|package |old |new |Δ |
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|:----------|:------|:-----------|:--|
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|future |1.68.0 |1.68.0-9031 |* |
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|future |1.68.0 |1.68.0-9032 |* |
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|codetools |0.2-20 |0.2-20 | |
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|digest |0.6.39 |0.6.39 | |
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|globals |0.18.0 |0.18.0 | |
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|cft |1.0.0 | | | |
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|chatAI4R |0.3.6 | | | |
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|chatLLM |0.1.3 | | | |
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|[chevreulShiny](problems.md#chevreulshiny)|1.0.0 | | |1 |
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|[chevreulShiny](problems.md#chevreulshiny)|1.2.0 | | |1 |
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|chopin |0.9.9 | | | |
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|[ChromSCape](problems.md#chromscape)|1.20.0 | |1 |2 |
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|CimpleG |1.0.1 | | | |
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|[codalm](problems.md#codalm) |0.1.2 | | |1 |
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|codebook |0.9.6 | | | |
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|coFAST |0.1.0 | | | |
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|[collinear](problems.md#collinear)|2.0.0 | | |1 |
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|collinear |3.0.0 | | | |
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|conformalInference.fd |1.1.1 | | | |
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|conformalInference.multi |1.1.2 | | | |
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|Coxmos |1.1.5 | | | |
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|flexFitR |1.2.1 | | | |
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|[flowGraph](problems.md#flowgraph)|1.18.0 | | |2 |
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|flowml |0.1.3 | | | |
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|fmeffects |0.1.4 | | | |
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|[fmeffects](problems.md#fmeffects)|0.1.4 |1 | | |
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|[forecastML](problems.md#forecastml)|0.9.0 |1 | |1 |
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|[FracFixR](problems.md#fracfixr)|1.0.0 |1 | | |
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|fst4pg |1.0.0 | | | |

‎revdep/problems.md‎

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<details>
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* Version: 1.0.0
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* Version: 1.2.0
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* GitHub: https://github.com/cobriniklab/chevreulShiny
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* Source code: https://github.com/cran/chevreulShiny
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* Date/Publication: 2025-04-15
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* Date/Publication: 2025-12-04
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* Number of recursive dependencies: 267
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Run `revdepcheck::revdep_details(, "chevreulShiny")` for more info
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checkRd: (-1) educFM.Rd:28: Lost braces in \itemize; meant \describe ?
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```
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# collinear
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<details>
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* Version: 2.0.0
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* GitHub: https://github.com/blasbenito/collinear
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* Source code: https://github.com/cran/collinear
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* Date/Publication: 2024-11-08 13:50:02 UTC
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* Number of recursive dependencies: 47
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Run `revdepcheck::revdep_details(, "collinear")` for more info
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</details>
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## In both
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* checking DESCRIPTION meta-information ... NOTE
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```
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Missing dependency on R >= 4.1.0 because package code uses the pipe
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|> or function shorthand \(...) syntax added in R 4.1.0.
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File(s) using such syntax:
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‘collinear.R’ ‘cor_cramer_v.R’ ‘cor_df.R’ ‘cor_select.R’ ‘f_auc.Rd’
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‘f_r2.Rd’ ‘f_r2_counts.Rd’ ‘f_v.Rd’ ‘f_v_rf_categorical.Rd’
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‘identify.R’ ‘model_formula.R’ ‘preference_order.R’
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‘preference_order_methods.R’ ‘target_encoding_methods.R’ ‘validate.R’
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‘vif_df.R’ ‘vif_select.R’
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```
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# cSEM
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<details>
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ERROR
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Running the tests in ‘tests/testthat.R’ failed.
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Last 50 lines of output:
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> test-adjust_frm.R: [1;30m2025-12-07 14:09:07.39[0m Preprocessing data
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> test-adjust_frm.R: [1;30m2025-12-07 14:09:07.39[0m Formula: RT_ADJ ~ RT + I(RT^2) + I(RT^3) + log(RT) + exp(RT) + sqrt(RT)
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> test-adjust_frm.R: [1;30m2025-12-07 14:09:07.40[0m Estimating performance of adjusted model in CV
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> test-adjust_frm.R: [1;30m2025-12-07 14:09:07.44[0m Fitting adjustment model on full new data set
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> test-adjust_frm.R: [1;30m2025-12-07 14:09:07.44[0m Returning adjusted frm object
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> test-plot_frm.R: [1;30m2025-12-07 14:09:06.64[0m dim(new_data): 25 x 3
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> test-selective_measuring.R: [1;30m2025-12-08 13:07:48.90[0m Scaling features by coefficients of Ridge Regression model
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> test-selective_measuring.R: [1;30m2025-12-08 13:07:48.91[0m Applying PAM clustering
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> test-adjust_frm.R: [1;30m2025-12-08 13:07:48.93[0m Starting model Adjustment
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> test-adjust_frm.R: [1;30m2025-12-08 13:07:48.94[0m dim(original_data): 442 x 126
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> test-adjust_frm.R: [1;30m2025-12-08 13:07:48.94[0m dim(new_data): 25 x 3
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> test-adjust_frm.R: [1;30m2025-12-08 13:07:48.94[0m predictors: 1, 2
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...
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Backtrace:
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▆
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| ^
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```
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# fmeffects
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<details>
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* Version: 0.1.4
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* GitHub: https://github.com/holgstr/fmeffects
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* Source code: https://github.com/cran/fmeffects
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* Date/Publication: 2024-11-05 18:50:02 UTC
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* Number of recursive dependencies: 182
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Run `revdepcheck::revdep_details(, "fmeffects")` for more info
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</details>
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## In both
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* checking re-building of vignette outputs ... ERROR
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```
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Error(s) in re-building vignettes:
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...
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--- re-building ‘fme_theory.Rmd’ using rmarkdown
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[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
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--- finished re-building ‘fme_theory.Rmd’
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--- re-building ‘fmeffects.Rmd’ using rmarkdown
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Quitting from fmeffects.Rmd:121-127 [unnamed-chunk-11]
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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...
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ℹ In index: 1.
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Caused by error in `.__Task__col_roles()`:
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! Assertion on 'names(rhs)' failed: Names must be a permutation of set {'feature','target','name','order','stratum','group','offset','weights_learner','weights_measure'}, but has extra elements {'always_included'}.
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--- failed re-building ‘fmeffects.Rmd’
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SUMMARY: processing the following file failed:
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‘fmeffects.Rmd’
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Error: Vignette re-building failed.
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Execution halted
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```
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# forecastML
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<details>
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* checking re-building of vignette outputs ... ERROR
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```
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Error(s) in re-building vignettes:
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...
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--- re-building ‘overview.Rmd’ using rmarkdown
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Quitting from overview.Rmd:199-201 [unnamed-chunk-25]
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<error/rlang_error>
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Error:
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! Cannot open "/scratch/henrik/943230/Rtmp2SPJZq/file865372b6afe3f.json"; The source could be corrupt or not supported. See `st_drivers()` for a list of supported formats.
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---
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Backtrace:
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...
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Error: processing vignette 'overview.Rmd' failed with diagnostics:
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Cannot open "/scratch/henrik/943230/Rtmp2SPJZq/file865372b6afe3f.json"; The source could be corrupt or not supported. See `st_drivers()` for a list of supported formats.
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--- failed re-building ‘overview.Rmd’
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SUMMARY: processing the following file failed:
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‘overview.Rmd’
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Quitting from overview.Rmd:218-221 [unnamed-chunk-28]
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Error: Vignette re-building failed.
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Execution halted
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```
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* checking dependencies in R code ... NOTE
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```
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c4-n43:pid4119007: PSM3 can't open nic unit: 0 (err=23)
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c4-n43:pid4119007.R: Unable to create UDP socket for ens13f0np0: Address family not supported by protocol
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c4-n43:pid4119007.R: Unable to initialize sockets NIC /sys/class/net/ens13f0np0 (unit 0:0)
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c4-n43:pid4119007: PSM3 can't open nic unit: 0 (err=23)
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c4-n43:pid4119007.R: Unable to create UDP socket for ens13f0np0: Address family not supported by protocol
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c4-n43:pid4119007.R: Unable to initialize sockets NIC /sys/class/net/ens13f0np0 (unit 0:0)
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c4-n43:pid4119007: PSM3 can't open nic unit: 1 (err=23)
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c4-n43:pid4119007.R: Unable to create UDP socket for ens13f1np1: Address family not supported by protocol
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c4-n43:pid4119007.R: Unable to initialize sockets NIC /sys/class/net/ens13f1np1 (unit 1:0)
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c4-n43:pid4119007: PSM3 can't open nic unit: 0 (err=23)
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c4-n43:pid784059: PSM3 can't open nic unit: 0 (err=23)
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c4-n43:pid784059.R: Unable to create UDP socket for ens13f0np0: Address family not supported by protocol
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c4-n43:pid784059.R: Unable to initialize sockets NIC /sys/class/net/ens13f0np0 (unit 0:0)
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c4-n43:pid784059: PSM3 can't open nic unit: 0 (err=23)
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c4-n43:pid784059.R: Unable to create UDP socket for ens13f0np0: Address family not supported by protocol
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c4-n43:pid784059.R: Unable to initialize sockets NIC /sys/class/net/ens13f0np0 (unit 0:0)
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c4-n43:pid784059: PSM3 can't open nic unit: 1 (err=23)
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c4-n43:pid784059.R: Unable to create UDP socket for ens13f1np1: Address family not supported by protocol
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c4-n43:pid784059.R: Unable to initialize sockets NIC /sys/class/net/ens13f1np1 (unit 1:0)
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c4-n43:pid784059: PSM3 can't open nic unit: 0 (err=23)
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...
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c4-n43:pid4119007.R: Unable to create UDP socket for ens13f1np1: Address family not supported by protocol
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c4-n43:pid4119007.R: Unable to initialize sockets NIC /sys/class/net/ens13f1np1 (unit 1:0)
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c4-n43:pid784059.R: Unable to create UDP socket for ens13f1np1: Address family not supported by protocol
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c4-n43:pid784059.R: Unable to initialize sockets NIC /sys/class/net/ens13f1np1 (unit 1:0)
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--------------------------------------------------------------------------
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Open MPI failed an OFI Libfabric library call (fi_endpoint). This is highly
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unusual; your job may behave unpredictably (and/or abort) after this.
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[shinyOAuth] - HTTP request failed
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x Failed to fetch OIDC discovery document
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x Status 503: Service Unavailable.
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i URL: http://127.0.0.1:36019/.well-known/openid-configuration
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i Trace ID: j-lbAyjRv8ko
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i URL: http://127.0.0.1:40113/.well-known/openid-configuration
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i Trace ID: Z8Pi2b5AGXNA
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[ FAIL 23 | WARN 0 | SKIP 12 | PASS 671 ]
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Error:
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test_learner_stratify.R....... 0 tests
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test_learner_stratify.R....... 3 tests OK
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test_learner_stratify.R....... 3 tests OK
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test_learner_stratify.R....... 5 tests [0;32mOK[0m [0;36m29ms[0m
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test_learner_stratify.R....... 5 tests [0;32mOK[0m [0;36m32ms[0m
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...
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In addition: Warning messages:
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1: In throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), :
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* GitHub: NA
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* Source code: https://github.com/cran/tramvs
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* Date/Publication: 2025-11-18 18:00:02 UTC
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* Number of recursive dependencies: 104
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* Number of recursive dependencies: 106
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Run `revdepcheck::revdep_details(, "tramvs")` for more info
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‎revdep/revdepcheck.Renviron‎

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GOTO_NUM_THREADS=8
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## Turn on more checks
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NOT_CRAN=true
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#NOT_CRAN=true
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R_FUTURE_PLAN_EARLYSIGNAL=defunct
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R_FUTURE_FUTURE_EARLYSIGNAL=defunct
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R_FUTURE_FUTURE_LOCAL=defunct
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R_FUTURE_FUTURE_GC=defunct
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R_FUTURE_RESOLVED_RUN=defunct

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