• using R Under development (unstable) (2025-12-02 r89085)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.6     flang version 21.1.6
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘IBLM/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘IBLM’ version ‘1.0.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘IBLM’ can be installed ... [13s/35s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [20s/59s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [7s/19s] ERROR Running examples in ‘IBLM-Ex.R’ failed The error most likely occurred in: > ### Name: beta_corrected_density > ### Title: Density Plot of Beta Corrections for a Variable > ### Aliases: beta_corrected_density > > ### ** Examples > > # This function is created inside explain_iblm() and is output as an item > > df_list <- freMTPLmini |> split_into_train_validate_test(seed = 9000) > > iblm_model <- train_iblm_xgb( + df_list, + response_var = "ClaimRate", + family = "poisson" + ) Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :   Parameter 'watchlist' has been renamed to 'evals'. This warning will become an error in a future version. > > explain_objects <- explain_iblm(iblm_model, df_list$test) Error in xgboost::xgb.DMatrix(data.matrix(data)) :   [10:42:21] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment. Stack trace:   [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7fc1ebe13b82]   [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7fc1ebf6c3cb]   [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7fc1ec1d8e12]   [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7fc1ebe096a2]   [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x5610a62266f3]   [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x5610a6275470]   [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5610a625e2ac]   [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5610a625da35]   [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5610a627ae29] Calls: explain_iblm ... data.frame -> <Anonymous> -> predict.xgb.Booster -> <Anonymous> Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [20s/26s] ERROR   Running ‘testthat.R’ [19s/26s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # This file is part of the standard setup for testthat.   > # It is recommended that you do not modify it.   > #   > # Where should you do additional test configuration?   > # Learn more about the roles of various files in:   > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview   > # * https://testthat.r-lib.org/articles/special-files.html   >   > library(testthat)   > library(IBLM)   >   > test_check("IBLM")   Saving _problems/test-explain_iblm-222.R   Saving _problems/test-explain_iblm-247.R   Saving _problems/test-explain_iblm-272.R   Saving _problems/test-explain_iblm-300.R   Saving _problems/test-explain_iblm-328.R   Saving _problems/test-explain_iblm-361.R   Saving _problems/test-explain_iblm-421.R   Saving _problems/test-explain_iblm-454.R   Saving _problems/test-explain_iblm-484.R   Saving _problems/test-predict-32.R   [ FAIL 10 | WARN 12 | SKIP 4 | PASS 2 ]      ══ Skipped tests (4) ═══════════════════════════════════════════════════════════   • On CRAN (4): 'test-explain_iblm.R:4:3', 'test-get_pinball_scores.R:5:3',     'test-get_pinball_scores.R:85:3', 'test-train_iblm.R:6:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-explain_iblm.R:214:3'): test explain completes when one categorical and one continuous ──   Expected `{ ... }` not to throw any errors.   Actually got a <simpleError> with message:     [10:42:38] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.     Stack trace:       [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]       [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]       [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]       [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]       [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]       [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]       [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]       [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]       [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]             ── Failure ('test-explain_iblm.R:239:3'): test explain completes when categorical only ──   Expected `{ ... }` not to throw any errors.   Actually got a <simpleError> with message:     [10:42:39] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.     Stack trace:       [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]       [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]       [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]       [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]       [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]       [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]       [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]       [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]       [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]             ── Failure ('test-explain_iblm.R:264:3'): test explain completes when continuous only ──   Expected `{ ... }` not to throw any errors.   Actually got a <simpleError> with message:     [10:42:39] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.     Stack trace:       [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]       [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]       [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]       [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]       [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]       [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]       [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]       [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]       [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]             ── Failure ('test-explain_iblm.R:292:3'): test explain completes when logical field ──   Expected `{ ... }` not to throw any errors.   Actually got a <simpleError> with message:     [10:42:40] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.     Stack trace:       [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]       [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]       [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]       [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]       [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]       [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]       [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]       [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]       [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]             ── Failure ('test-explain_iblm.R:320:3'): test explain completes when no reference/zero levels ──   Expected `{ ... }` not to throw any errors.   Actually got a <simpleError> with message:     [10:42:41] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.     Stack trace:       [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]       [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]       [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]       [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]       [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]       [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]       [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]       [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]       [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]             ── Error ('test-explain_iblm.R:361:3'): test migrate-to-bias vs non-migrate-to-bias options ──   Error in `xgboost::xgb.DMatrix(data.matrix(data))`: [10:42:42] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.   Stack trace:     [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]     [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]     [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]     [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]     [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]     [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]     [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]     [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]     [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]         Backtrace:       ▆    1. └─IBLM::explain_iblm(iblm_model = IBLM, data = splits$test, migrate_reference_to_bias = TRUE) at test-explain_iblm.R:361:3    2. ├─IBLM::extract_booster_shap(iblm_model$booster_model, data)    3. └─IBLM:::extract_booster_shap.xgb.Booster(...)    4. ├─base::data.frame(...)    5. ├─stats::predict(...)    6. ├─xgboost:::predict.xgb.Booster(...)    7. └─xgboost::xgb.DMatrix(data.matrix(data))   ── Failure ('test-explain_iblm.R:413:3'): test gaussian can run ────────────────   Expected `{ ... }` not to throw any errors.   Actually got a <simpleError> with message:     [10:42:42] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.     Stack trace:       [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]       [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]       [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]       [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]       [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]       [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]       [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]       [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]       [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]             ── Failure ('test-explain_iblm.R:445:3'): test gamma can run ───────────────────   Expected `{ ... }` not to throw any errors.   Actually got a <simpleError> with message:     [10:42:43] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.     Stack trace:       [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]       [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]       [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]       [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]       [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]       [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]       [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]       [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]       [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]             ── Failure ('test-explain_iblm.R:475:3'): test tweedie can run ─────────────────   Expected `{ ... }` not to throw any errors.   Actually got a <simpleError> with message:     [10:42:44] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.     Stack trace:       [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]       [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]       [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]       [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]       [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]       [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]       [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]       [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]       [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]             ── Error ('test-predict.R:32:3'): test corrected beta coeffecient predictions are same as predict iblm() ──   Error in `xgboost::xgb.DMatrix(data.matrix(data))`: [10:42:47] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.   Stack trace:     [bt] (0) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x13b82) [0x7f92b9213b82]     [bt] (1) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(+0x16c3cb) [0x7f92b936c3cb]     [bt] (2) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0xe2) [0x7f92b95d8e12]     [bt] (3) /data/gannet/ripley/R/test-clang/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x232) [0x7f92b92096a2]     [bt] (4) /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e6f3) [0x562a0de1e6f3]     [bt] (5) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x562a0de6d470]     [bt] (6) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x562a0de562ac]     [bt] (7) /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x562a0de55a35]     [bt] (8) /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x562a0de72e29]         Backtrace:       ▆    1. └─IBLM::explain_iblm(iblm_model = IBLM, data = splits$test, migrate_reference_to_bias = TRUE) at test-predict.R:32:3    2. ├─IBLM::extract_booster_shap(iblm_model$booster_model, data)    3. └─IBLM:::extract_booster_shap.xgb.Booster(...)    4. ├─base::data.frame(...)    5. ├─stats::predict(...)    6. ├─xgboost:::predict.xgb.Booster(...)    7. └─xgboost::xgb.DMatrix(data.matrix(data))      [ FAIL 10 | WARN 12 | SKIP 4 | PASS 2 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [8s/22s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs