* using log directory 'd:/RCompile/CRANincoming/R-devel/netSEM.Rcheck' * using R Under development (unstable) (2026-01-15 r89304 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'netSEM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'netSEM' version '0.7.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [16s] OK * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'netSEM' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' 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 ... WARNING '::' or ':::' imports not declared from: 'broom' 'butcher' 'dplyr' 'glue' 'janitor' 'purrr' 'rcompanion' 'stringr' 'tibble' 'tidyr' * checking S3 generic/method consistency ... WARNING plot: function(x, ...) plot.netSEMp1: function(df, cutoff, latent, plot.save, title, path, filename, style, ...) plot: function(x, ...) plot.netSEMp2: function(df, cutoff, latent, title, plot.save, filename, style, ...) See section 'Generic functions and methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [18s] NOTE netSEM_CP: no visible global function definition for 'mutate' netSEM_CP: no visible binding for global variable 'model_type' netSEM_CP: no visible binding for global variable 'pseudoR2.mcfadden' netSEM_CP: no visible binding for global variable 'pseudoR2.cox_snell' netSEM_CP: no visible binding for global variable 'pseudoR2.nagelkerke' netSEM_InvSqRt: no visible global function definition for 'everything' netSEM_InvSqRt: no visible binding for global variable 'pseudoR2.mcfadden' netSEM_InvSqRt: no visible binding for global variable 'pseudoR2.cox_snell' netSEM_InvSqRt: no visible binding for global variable 'pseudoR2.nagelkerke' netSEM_InvSqRt: no visible global function definition for 'across' netSEM_InvSqRt: no visible binding for global variable 'model_eq' netSEM_InvSqRt: no visible binding for global variable 'model_type' netSEM_SqRt: no visible global function definition for 'everything' netSEM_SqRt: no visible binding for global variable 'pseudoR2.mcfadden' netSEM_SqRt: no visible binding for global variable 'pseudoR2.cox_snell' netSEM_SqRt: no visible binding for global variable 'pseudoR2.nagelkerke' netSEM_SqRt: no visible global function definition for 'across' netSEM_SqRt: no visible binding for global variable 'model_eq' netSEM_SqRt: no visible binding for global variable 'model_type' netSEM_exponential: no visible global function definition for 'everything' netSEM_exponential: no visible binding for global variable 'pseudoR2.mcfadden' netSEM_exponential: no visible binding for global variable 'pseudoR2.cox_snell' netSEM_exponential: no visible binding for global variable 'pseudoR2.nagelkerke' netSEM_exponential: no visible global function definition for 'across' netSEM_exponential: no visible binding for global variable 'model_eq' netSEM_exponential: no visible binding for global variable 'model_type' netSEM_linear: no visible global function definition for 'everything' netSEM_linear: no visible binding for global variable 'pseudoR2.mcfadden' netSEM_linear: no visible binding for global variable 'pseudoR2.cox_snell' netSEM_linear: no visible binding for global variable 'pseudoR2.nagelkerke' netSEM_linear: no visible global function definition for 'across' netSEM_linear: no visible binding for global variable 'model_eq' netSEM_linear: no visible binding for global variable 'model_type' netSEM_log: no visible global function definition for 'everything' netSEM_log: no visible binding for global variable 'pseudoR2.mcfadden' netSEM_log: no visible binding for global variable 'pseudoR2.cox_snell' netSEM_log: no visible binding for global variable 'pseudoR2.nagelkerke' netSEM_log: no visible global function definition for 'across' netSEM_log: no visible binding for global variable 'model_eq' netSEM_log: no visible binding for global variable 'model_type' netSEM_nls: no visible binding for global variable 'pseudoR2.mcfadden' netSEM_nls: no visible binding for global variable 'pseudoR2.cox_snell' netSEM_nls: no visible binding for global variable 'pseudoR2.nagelkerke' netSEM_nls: no visible global function definition for 'everything' netSEM_nls: no visible binding for global variable 'term' netSEM_nls: no visible binding for global variable 'statistic' netSEM_nls: no visible binding for global variable 'p.value' netSEM_nls2 : : no visible global function definition for 'tibble' netSEM_quad: no visible global function definition for 'everything' netSEM_quad: no visible binding for global variable 'pseudoR2.mcfadden' netSEM_quad: no visible binding for global variable 'pseudoR2.cox_snell' netSEM_quad: no visible binding for global variable 'pseudoR2.nagelkerke' netSEM_quad: no visible global function definition for 'across' netSEM_quad: no visible binding for global variable 'model_eq' netSEM_quad: no visible binding for global variable 'model_type' netSEM_quadNoLinear: no visible global function definition for 'everything' netSEM_quadNoLinear: no visible binding for global variable 'pseudoR2.mcfadden' netSEM_quadNoLinear: no visible binding for global variable 'pseudoR2.cox_snell' netSEM_quadNoLinear: no visible binding for global variable 'pseudoR2.nagelkerke' netSEM_quadNoLinear: no visible global function definition for 'across' netSEM_quadNoLinear: no visible binding for global variable 'model_eq' netSEM_quadNoLinear: no visible binding for global variable 'model_type' netSEMp1: no visible global function definition for 'all_of' netSEMp1: no visible binding for '<<-' assignment to 'mfExt' netSEMp1: no visible binding for global variable 'resp' netSEMp1: no visible binding for global variable 'Resp' netSEMp1: no visible binding for global variable 'Var' netSEMp1: no visible binding for global variable 'adj.r.squared' netSEMp1: no visible binding for global variable 'model_type' netSEMp1: no visible binding for global variable 'mfExt' netSEMp2: no visible global function definition for 'all_of' netSEMp2: no visible global function definition for 'na.omit' paths : find_next_var: no visible binding for global variable 'p_value' paths : find_next_var: no visible binding for global variable 'R2adj' paths : find_next_var: no visible global function definition for 'head' paths: no visible binding for global variable 'Var' paths: no visible binding for global variable 'Resp' paths: no visible binding for global variable 'adj.r.squared' paths: no visible binding for global variable 'best_model' paths: no visible binding for global variable 'p.value' paths: no visible binding for global variable 'var1' paths: no visible binding for global variable 'var2' paths: no visible binding for global variable 'R2adj' paths: no visible binding for global variable 'model' paths: no visible binding for global variable 'p_value' paths: no visible global function definition for 'setNames' paths: no visible binding for global variable 'path' paths: no visible global function definition for 'desc' paths: no visible binding for global variable 'min_R2' plot.netSEMp1: no visible binding for global variable 'Resp' plot.netSEMp1: no visible binding for global variable 'Var' plot.netSEMp1: no visible binding for global variable 'best_model' plot.netSEMp1: no visible binding for global variable 'r.squared' plot.netSEMp1: no visible binding for global variable 'adj.r.squared' plot.netSEMp1: no visible global function definition for 'filter' plot.netSEMp1: no visible global function definition for 'arrange' plot.netSEMp1: no visible global function definition for 'regex' plot.netSEMp1: no visible global function definition for 'str_detect' plot.netSEMp2: no visible global function definition for 'filter' plot.netSEMp2: no visible binding for global variable 'Var' plot.netSEMp2: no visible binding for global variable 'Resp' plot.netSEMp2: no visible global function definition for 'arrange' plot.netSEMp2: no visible binding for global variable 'adj.r.squared' plot.netSEMp2: no visible binding for global variable 'conp1.c' var_selection: no visible global function definition for 'all_of' var_selection: no visible global function definition for 'filter' var_selection: no visible binding for global variable 'Var' var_selection: no visible binding for global variable 'Resp' var_selection: no visible global function definition for 'arrange' var_selection: no visible binding for global variable 'adj.r.squared' var_selection: no visible global function definition for 'row_number' Undefined global functions or variables: R2adj Resp Var across adj.r.squared all_of arrange best_model conp1.c desc everything filter head mfExt min_R2 model model_eq model_type mutate na.omit p.value p_value path pseudoR2.cox_snell pseudoR2.mcfadden pseudoR2.nagelkerke r.squared regex resp row_number setNames statistic str_detect term tibble var1 var2 Consider adding importFrom("stats", "filter", "na.omit", "setNames") importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) PVmodule.Rd:27: Lost braces; missing escapes or markup? 27 | In the resulting netSEM model, time was used as a proxy for damp heat exposure stress (S) variable and $P_{max}$ (maximum power generated by the modules) was used as the performance level response ($R$) variable, several mechanistic variables ($M$) were obtained through chemical evaluation methods, including FTIR and TGA on EVA encapsulant. | ^ checkRd: (-1) netSEMp1.Rd:37: Lost braces 37 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. | ^ checkRd: (-1) netSEMp1.Rd:37: Lost braces 37 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. | ^ checkRd: (-1) netSEMp1.Rd:37: Lost braces 37 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. | ^ * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'plot.netSEMp1.Rd': \examples lines wider than 100 characters: plot(ans, cutoff = c(0.3,0.6,0.8), title = "Acrylic", path = c('red', 'IAD1->IAD2p'), latent = c('IAD1' = 'FundAbsEdge'), style = FALSE ... [TRUNCATED] plot.netSEMp1(ans, acrylic, cutoff = c(0.3, 0.6, 0.8), plot.save = TRUE, filename = 'acrylic-netSEMp1') These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'plot.netSEMp2.Rd' 'title' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... ERROR Warning: parse error in file 'netSEM-Ex.R': 84: unexpected ')' 155: # plot the network diagram and save file 156: plot(ans, cutoff = c(0.3,0.6,0.8), plot.save = TRUE, filename = "acrylic-netSEMp2")) ^ ** will not attempt to run examples * 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... SKIPPED * checking for unstated dependencies in 'tests' ... OK * checking tests ... ERROR Running 'testthat.R' 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(netSEM) > > test_check("netSEM") Saving _problems/test-netSEMp1-2.R Saving _problems/test-netSEMp2-2.R Saving _problems/test-plot-3.R Saving _problems/test-plot-9.R [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-netSEMp1.R:2:3'): Check if netSEMp1 gives correct output ─────── Error in `map2(.x, .y, .f, ...)`: i In index: 1. Caused by error in `loadNamespace()`: ! there is no package called 'broom' Backtrace: ▆ 1. ├─testthat::expect_s3_class(...) at test-netSEMp1.R:2:3 2. │ └─testthat::quasi_label(enquo(object)) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─netSEM::netSEMp1(acrylic, exogenous = "IrradTot", endogenous = "YI") 5. │ ├─base::suppressWarnings(...) 6. │ │ └─base::withCallingHandlers(...) 7. │ └─purrr::map2_dfr(...) 8. │ └─purrr::map2(.x, .y, .f, ...) 9. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress) 10. │ ├─purrr:::with_indexed_errors(...) 11. │ │ └─base::withCallingHandlers(...) 12. │ ├─purrr:::call_with_cleanup(...) 13. │ └─netSEM (local) .f(.x[[i]], .y[[i]], ...) 14. │ └─netSEM:::collect_netSEM_models(Resp = .y, Var = .x, x = x) 15. │ └─netSEM:::netSEM_linear(Resp, Var, x) 16. │ └─broom::glance(model) %>% ... 17. ├─dplyr::mutate(...) 18. ├─base::loadNamespace(x) 19. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 20. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 21. │ │ └─base (local) doWithOneRestart(return(expr), restart) 22. │ └─base::stop(cond) 23. └─purrr (local) ``(``) 24. └─cli::cli_abort(...) 25. └─rlang::abort(...) ── Error ('test-netSEMp2.R:2:3'): Check if netSEMp2 gives correct output ─────── Error in `map2(.x, .y, .f, ...)`: i In index: 1. Caused by error in `loadNamespace()`: ! there is no package called 'broom' Backtrace: ▆ 1. ├─testthat::expect_s3_class(...) at test-netSEMp2.R:2:3 2. │ └─testthat::quasi_label(enquo(object)) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─netSEM::netSEMp2(acrylic, exogenous = "IrradTot", endogenous = "YI") 5. │ └─netSEM::netSEMp1(x, exogenous, endogenous) 6. │ ├─base::suppressWarnings(...) 7. │ │ └─base::withCallingHandlers(...) 8. │ └─purrr::map2_dfr(...) 9. │ └─purrr::map2(.x, .y, .f, ...) 10. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─netSEM (local) .f(.x[[i]], .y[[i]], ...) 15. │ └─netSEM:::collect_netSEM_models(Resp = .y, Var = .x, x = x) 16. │ └─netSEM:::netSEM_linear(Resp, Var, x) 17. │ └─broom::glance(model) %>% ... 18. ├─dplyr::mutate(...) 19. ├─base::loadNamespace(x) 20. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 21. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 22. │ │ └─base (local) doWithOneRestart(return(expr), restart) 23. │ └─base::stop(cond) 24. └─purrr (local) ``(``) 25. └─cli::cli_abort(...) 26. └─rlang::abort(...) ── Error ('test-plot.R:3:3'): Check if plot.netSEMp1 has correct output ──────── Error in `map2(.x, .y, .f, ...)`: i In index: 1. Caused by error in `loadNamespace()`: ! there is no package called 'broom' Backtrace: ▆ 1. ├─netSEM::netSEMp1(acrylic, exogenous = "IrradTot", endogenous = "YI") at test-plot.R:3:3 2. │ ├─base::suppressWarnings(...) 3. │ │ └─base::withCallingHandlers(...) 4. │ └─purrr::map2_dfr(...) 5. │ └─purrr::map2(.x, .y, .f, ...) 6. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress) 7. │ ├─purrr:::with_indexed_errors(...) 8. │ │ └─base::withCallingHandlers(...) 9. │ ├─purrr:::call_with_cleanup(...) 10. │ └─netSEM (local) .f(.x[[i]], .y[[i]], ...) 11. │ └─netSEM:::collect_netSEM_models(Resp = .y, Var = .x, x = x) 12. │ └─netSEM:::netSEM_linear(Resp, Var, x) 13. │ └─broom::glance(model) %>% ... 14. ├─dplyr::mutate(...) 15. ├─base::loadNamespace(x) 16. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 17. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 18. │ │ └─base (local) doWithOneRestart(return(expr), restart) 19. │ └─base::stop(cond) 20. └─purrr (local) ``(``) 21. └─cli::cli_abort(...) 22. └─rlang::abort(...) ── Error ('test-plot.R:9:3'): Check if plot.netSEMp2 has correct output ──────── Error in `map2(.x, .y, .f, ...)`: i In index: 1. Caused by error in `loadNamespace()`: ! there is no package called 'broom' Backtrace: ▆ 1. ├─netSEM::netSEMp2(acrylic, exogenous = "IrradTot", endogenous = "YI") at test-plot.R:9:3 2. │ └─netSEM::netSEMp1(x, exogenous, endogenous) 3. │ ├─base::suppressWarnings(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─purrr::map2_dfr(...) 6. │ └─purrr::map2(.x, .y, .f, ...) 7. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress) 8. │ ├─purrr:::with_indexed_errors(...) 9. │ │ └─base::withCallingHandlers(...) 10. │ ├─purrr:::call_with_cleanup(...) 11. │ └─netSEM (local) .f(.x[[i]], .y[[i]], ...) 12. │ └─netSEM:::collect_netSEM_models(Resp = .y, Var = .x, x = x) 13. │ └─netSEM:::netSEM_linear(Resp, Var, x) 14. │ └─broom::glance(model) %>% ... 15. ├─dplyr::mutate(...) 16. ├─base::loadNamespace(x) 17. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 18. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 19. │ │ └─base (local) doWithOneRestart(return(expr), restart) 20. │ └─base::stop(cond) 21. └─purrr (local) ``(``) 22. └─cli::cli_abort(...) 23. └─rlang::abort(...) [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [33s] OK * checking HTML version of manual ... OK * DONE Status: 2 ERRORs, 3 WARNINGs, 3 NOTEs