- using R Under development (unstable) (2025-12-02 r89085)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘automatedRecLin/DESCRIPTION’ ... OK
- this is package ‘automatedRecLin’ version ‘1.0.0’
- 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 ‘automatedRecLin’ can be installed ... [21s/87s] OK
See the install log for details.
- 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 ... [6s/31s] OK
- checking whether the package can be loaded with stated dependencies ... [5s/23s] OK
- checking whether the package can be unloaded cleanly ... [5s/24s] OK
- checking whether the namespace can be loaded with stated dependencies ... [5s/22s] OK
- checking whether the namespace can be unloaded cleanly ... [6s/27s] OK
- checking loading without being on the library search path ... [5s/26s] 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 ... [32s/115s] 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 ... [6s/17s] ERROR
Running examples in ‘automatedRecLin-Ex.R’ failed
The error most likely occurred in:
> ### Name: custom_rec_lin_model
> ### Title: Create a Custom Record Linkage Model
> ### Aliases: custom_rec_lin_model
>
> ### ** Examples
>
> if (requireNamespace("xgboost", quietly = TRUE)) {
+ df_1 <- data.frame(
+ "name" = c("James", "Emma", "William", "Olivia", "Thomas",
+ "Sophie", "Harry", "Amelia", "George", "Isabella"),
+ "surname" = c("Smith", "Johnson", "Brown", "Taylor", "Wilson",
+ "Davis", "Clark", "Harris", "Lewis", "Walker")
+ )
+ df_2 <- data.frame(
+ "name" = c("James", "Ema", "Wimliam", "Olivia", "Charlotte",
+ "Henry", "Lucy", "Edward", "Alice", "Jack"),
+ "surname" = c("Smith", "Johnson", "Bron", "Tailor", "Moore",
+ "Evans", "Hall", "Wright", "Green", "King")
+ )
+ comparators <- list("name" = jarowinkler_complement(),
+ "surname" = jarowinkler_complement())
+ matches <- data.frame("a" = 1:4, "b" = 1:4)
+ vectors <- comparison_vectors(A = df_1, B = df_2, variables = c("name", "surname"),
+ comparators = comparators, matches = matches)
+ train_data <- xgboost::xgb.DMatrix(
+ data = as.matrix(vectors$Omega[, c("gamma_name", "gamma_surname")]),
+ label = vectors$Omega$match
+ )
+ params <- list(objective = "binary:logistic",
+ eval_metric = "logloss")
+ model_xgb <- xgboost::xgboost(data = train_data, params = params,
+ nrounds = 100, verbose = 0)
+ custom_xgb_model <- custom_rec_lin_model(model_xgb, vectors)
+ custom_xgb_model
+ }
Warning in throw_err_or_depr_msg("Parameter(s) have been removed from this function: ", :
Parameter(s) have been removed from this function: params. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), :
Passed unrecognized parameters: verbose. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :
Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Error in xgboost::xgboost(data = train_data, params = params, nrounds = 100, :
argument "y" is missing, with no default
Calls: <Anonymous> -> process.y.margin.and.objective -> NROW
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [1s/42s] ERROR
Running ‘tinytest.R’ [1s/41s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("automatedRecLin", ncpu = 1)
+ }
starting worker pid=3286618 on localhost:11463 at 12:02:26.657
test_comparators.R............ 2 tests [0;32mOK [0m [0;34m0.6s [0m
test_comparison_vectors.R..... 2 tests [0;32mOK [0m [0;34m0.3s [0m
kliep function error: missing value where TRUE/FALSE needed
========================================================
kliep function error: missing value where TRUE/FALSE needed
========================================================
test_mec.R.................... 11 tests [0;32mOK [0m [0;34m8.8s [0m
Error in checkForRemoteErrors(val) :
one node produced an error: argument "y" is missing, with no default
Calls: <Anonymous> ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Warning messages:
1: In check.sigma(nsigma, sigma_quantile, sigma, dist_nu) :
There are duplicate values in 'sigma', only the unique values are used.
2: In check.sigma(nsigma, sigma_quantile, sigma, dist_nu) :
There are duplicate values in 'sigma', only the unique values are used.
3: In check.sigma(nsigma, sigma_quantile, sigma, dist_nu) :
There are duplicate values in 'sigma', only the unique values are used.
4: In check.sigma(nsigma, sigma_quantile, sigma, dist_nu) :
There are duplicate values in 'sigma', only the unique values are used.
5: In check.sigma(nsigma, sigma_quantile, sigma, dist_nu) :
There are duplicate values in 'sigma', only the unique values are used.
6: In throw_err_or_depr_msg("Parameter(s) have been removed from this function: ", :
Parameter(s) have been removed from this function: params. This warning will become an error in a future version.
7: In throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), :
Passed unrecognized parameters: verbose. This warning will become an error in a future version.
8: In throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :
Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Execution halted
- checking PDF version of manual ... [8s/26s] OK
- checking HTML version of manual ... [3s/12s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 2 ERRORs