Package check result: OK Changes to worse in reverse depends: Package: FastRet Check: tests New result: ERROR Running ‘testthat.R’ [35s/21s] 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(FastRet) > > test_check("FastRet") Starting 2 test processes. Saving _problems/test-train_frm-gbtree-11.R Saving _problems/test-fit_gbtree-8.R Saving _problems/test-fit_gbtree-16.R > test-plot_frm.R: 2025-12-04 02:00:37.93 Starting training of a lasso model > test-plot_frm.R: 2025-12-04 02:00:37.93 Mocking is enabled. Returning 'mockdata/lasso_model.rds' > test-plot_frm.R: 2025-12-04 02:00:38.09 Starting training of a lasso model > test-plot_frm.R: 2025-12-04 02:00:38.09 Mocking is enabled. Returning 'mockdata/lasso_model.rds' > test-plot_frm.R: 2025-12-04 02:00:38.10 Starting model Adjustment > test-plot_frm.R: 2025-12-04 02:00:38.10 dim(original_data): 442 x 126 > test-plot_frm.R: 2025-12-04 02:00:38.10 dim(new_data): 25 x 3 > test-plot_frm.R: 2025-12-04 02:00:38.21 predictors: 1, 2, 3, 4, 5, 6 > test-plot_frm.R: 2025-12-04 02:00:38.21 nfolds: 5 > test-plot_frm.R: 2025-12-04 02:00:38.21 Preprocessing data > test-plot_frm.R: 2025-12-04 02:00:38.22 Formula: RT_ADJ ~ RT + I(RT^2) + I(RT^3) + log(RT) + exp(RT) + sqrt(RT) > test-plot_frm.R: 2025-12-04 02:00:38.22 Estimating performance of adjusted model in CV > test-plot_frm.R: 2025-12-04 02:00:38.28 Fitting adjustment model on full new data set > test-plot_frm.R: 2025-12-04 02:00:38.28 Returning adjusted frm object > test-adjust_frm.R: 2025-12-04 02:00:38.58 Starting model Adjustment > test-adjust_frm.R: 2025-12-04 02:00:38.58 dim(original_data): 442 x 126 > test-adjust_frm.R: 2025-12-04 02:00:38.58 dim(new_data): 25 x 3 > test-adjust_frm.R: 2025-12-04 02:00:38.58 predictors: 1, 2 > test-adjust_frm.R: 2025-12-04 02:00:38.58 nfolds: 5 > test-adjust_frm.R: 2025-12-04 02:00:38.58 Preprocessing data > test-adjust_frm.R: 2025-12-04 02:00:38.58 Formula: RT_ADJ ~ RT + I(RT^2) > test-adjust_frm.R: 2025-12-04 02:00:38.59 Estimating performance of adjusted model in CV > test-adjust_frm.R: 2025-12-04 02:00:38.64 Fitting adjustment model on full new data set > test-adjust_frm.R: 2025-12-04 02:00:38.64 Returning adjusted frm object > test-adjust_frm.R: 2025-12-04 02:00:38.64 Starting model Adjustment > test-adjust_frm.R: 2025-12-04 02:00:38.64 dim(original_data): 442 x 126 > test-adjust_frm.R: 2025-12-04 02:00:38.64 dim(new_data): 25 x 3 > test-adjust_frm.R: 2025-12-04 02:00:38.64 predictors: 1, 2, 3, 4, 5, 6 > test-adjust_frm.R: 2025-12-04 02:00:38.64 nfolds: 5 > test-adjust_frm.R: 2025-12-04 02:00:38.64 Preprocessing data > test-adjust_frm.R: 2025-12-04 02:00:38.65 Formula: RT_ADJ ~ RT + I(RT^2) + I(RT^3) + log(RT) + exp(RT) + sqrt(RT) > test-adjust_frm.R: 2025-12-04 02:00:38.65 Estimating performance of adjusted model in CV > test-adjust_frm.R: 2025-12-04 02:00:38.71 Fitting adjustment model on full new data set > test-adjust_frm.R: 2025-12-04 02:00:38.72 Returning adjusted frm object > test-selective_measuring.R: 2025-12-04 02:00:38.99 Starting Selective Measuring > test-selective_measuring.R: 2025-12-04 02:00:38.99 Preprocessing input data > test-selective_measuring.R: 2025-12-04 02:00:38.99 Mocking is enabled for 'preprocess_data'. Returning 'mockdata/RPCD_prepro.rds'. > test-selective_measuring.R: 2025-12-04 02:00:39.00 Standardizing features > test-selective_measuring.R: 2025-12-04 02:00:39.00 Training Ridge Regression model > test-selective_measuring.R: 2025-12-04 02:00:39.00 Fitting Ridge model > test-selective_measuring.R: 2025-12-04 02:00:39.44 End training > test-selective_measuring.R: 2025-12-04 02:00:39.44 Scaling features by coefficients of Ridge Regression model > test-selective_measuring.R: 2025-12-04 02:00:39.45 Applying PAM clustering > test-selective_measuring.R: 2025-12-04 02:00:39.77 Returning clustering results [ FAIL 3 | WARN 5 | SKIP 0 | PASS 19 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-train_frm-gbtree.R:5:5'): train_frm works if `method == "GBTree"` ── Error in `FUN(X[[i]], ...)`: subscript out of bounds Backtrace: ▆ 1. └─FastRet::train_frm(...) at test-train_frm-gbtree.R:5:5 2. └─base::lapply(tmp, "[[", 2) ── Error ('test-fit_gbtree.R:8:5'): fit.gbtrees works as expected ────────────── Error in `begin_iteration:end_iteration`: argument of length 0 Backtrace: ▆ 1. └─FastRet:::fit_gbtree(df, verbose = 0) at test-fit_gbtree.R:8:5 2. └─FastRet:::fit_gbtree_grid(...) 3. └─xgboost::xgb.train(...) ── Error ('test-fit_gbtree.R:16:5'): fit.gbtrees works for data from reverse phase column ── Error in `begin_iteration:end_iteration`: argument of length 0 Backtrace: ▆ 1. └─FastRet:::fit_gbtree(df, verbose = 0) at test-fit_gbtree.R:16:5 2. └─FastRet:::fit_gbtree_grid(...) 3. └─xgboost::xgb.train(...) [ FAIL 3 | WARN 5 | SKIP 0 | PASS 19 ] Error: ! Test failures. Execution halted Package: predictoR Check: examples New result: ERROR Running examples in ‘predictoR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: e_xgb_importance > ### Title: Var importance XGBoosting > ### Aliases: e_xgb_importance > > ### ** Examples > > model <- traineR::train.xgboost(Species ~ ., data = iris, nrounds = 20) Warning in check.deprecation(deprecated_train_params, match.call(), ...) : Passed invalid function arguments: eval_metric. These should be passed as a list to argument 'params'. Conversion from argument to 'params' entry will be done automatically, but this behavior will become an error in a future version. 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. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", : Parameter 'feval' has been renamed to 'custom_metric'. This warning will become an error in a future version. [1] train-mlogloss:0.736115 [2] train-mlogloss:0.524235 [3] train-mlogloss:0.387996 [4] train-mlogloss:0.294146 [5] train-mlogloss:0.226824 [6] train-mlogloss:0.177835 [7] train-mlogloss:0.141766 [8] train-mlogloss:0.115002 [9] train-mlogloss:0.094791 [10] train-mlogloss:0.078860 [11] train-mlogloss:0.066746 [12] train-mlogloss:0.057845 [13] train-mlogloss:0.050360 [14] train-mlogloss:0.044290 [15] train-mlogloss:0.039567 [16] train-mlogloss:0.035267 [17] train-mlogloss:0.032581 [18] train-mlogloss:0.030403 [19] train-mlogloss:0.028410 [20] train-mlogloss:0.026969 Error in model$prmdt <- `*vtmp*` : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Calls: -> create.model Execution halted Package: risk.assessr Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘How-to-use-risk.assessr.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘How-to-use-risk.assessr.Rmd’ --- re-building ‘Popularity_metric.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Popularity_metric.Rmd’ --- re-building ‘Pubmed_data.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Pubmed_data.Rmd’ --- re-building ‘Traceability_matrix.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Traceability_matrix.Rmd’ --- re-building ‘define_custom_risk_rules.Rmd’ using rmarkdown Quitting from define_custom_risk_rules.Rmd:35-37 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `curl::curl_fetch_memory()`: ! Timeout was reached [cran.r-project.org]: Connection timed out after 10001 milliseconds --- Backtrace: ▆ 1. ├─risk.assessr::assess_pkg_r_package("stringr") 2. │ └─risk.assessr::check_cran_package(package_name) 3. │ └─curl::curl_fetch_memory(package_url) 4. └─curl:::raise_libcurl_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'define_custom_risk_rules.Rmd' failed with diagnostics: Timeout was reached [cran.r-project.org]: Connection timed out after 10001 milliseconds --- failed re-building ‘define_custom_risk_rules.Rmd’ --- re-building ‘dependency_tree.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘dependency_tree.Rmd’ --- re-building ‘examples.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘examples.Rmd’ --- re-building ‘generate_html_report.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘generate_html_report.Rmd’ --- re-building ‘get-available-version.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘get-available-version.Rmd’ --- re-building ‘get-package-host.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘get-package-host.Rmd’ --- re-building ‘risk.assessr_metric.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘risk.assessr_metric.Rmd’ SUMMARY: processing the following file failed: ‘define_custom_risk_rules.Rmd’ Error: Vignette re-building failed. Execution halted Package: risk.assessr Check: tests New result: ERROR Running ‘testthat.R’ [31s/242s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # setting R_TESTS to empty string because of > # https://github.com/hadley/testthat/issues/144 > # and https://github.com/r-lib/testthat/issues/86 > # revert this when that issue in R is fixed. > Sys.setenv("R_TESTS" = "") > > library(testthat) > library(mockery) > library(risk.assessr) > library(withr) > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > library(jsonlite) > library(fs) > library(curl) Using libcurl 8.17.0 with GnuTLS/3.8.10 > library(xml2) > > test_check("risk.assessr") An error occurred in checking suggested functions: no 'restart' 'muffleError' found Checking for author in mockpkg Checking for License in mockpkg Checking host package Saving _problems/test-assess_pkg-681.R No testthat or testit configuration Checking for author in mockpkg Checking for License in mockpkg Checking host package Saving _problems/test-assess_pkg-726.R Checking SomePkg on CRAN... Saving _problems/test-assess_pkg_r_package-34.R Checking Biobase on CRAN... Saving _problems/test-assess_pkg_r_package-68.R Checking InternalPkg on CRAN... Saving _problems/test-assess_pkg_r_package-116.R Checking GhostPkg on CRAN... Saving _problems/test-assess_pkg_r_package-143.R Checking ggplot2 on CRAN... Saving _problems/test-assess_pkg_r_package-168.R Checking nonexistentpkg on CRAN... Saving _problems/test-assess_pkg_r_package-193.R Invalid 'which' value. Must be one or more of: Depends, Imports, LinkingTo, Suggests, Enhances or 'all'. No forbidden notes for mockpkg No forbidden notes for mockpkg unpacking file1ff12b1581685a.tar.gz locally unpacked file1ff12b1581685a.tar.gz locally installing test.package.0009 locally test.package.0009 installed locally Extracting exported function names for test.package.0009 Extracting exported function bodies for test.package.0009 unpacking file1ff12b1988bdeb.tar.gz locally unpacked file1ff12b1988bdeb.tar.gz locally installing test.package.0009 locally test.package.0009 is already installed Extracting exported function names for test.package.0009 Extracting exported function bodies for test.package.0009 unpacking file1ff12b233fcda1.tar.gz locally unpacked file1ff12b233fcda1.tar.gz locally installing test.package.0010 locally test.package.0010 installed locally Extracting exported function names for test.package.0010 Extracting exported function bodies for test.package.0010 unpacking file1ff12b5b9cadc6.tar.gz locally unpacked file1ff12b5b9cadc6.tar.gz locally installing test.package.0005 locally test.package.0005 installed locally Extracting exported function names for test.package.0005 No exported functions from source package test.package.0005 No exported functions from Suggested packages in the DESCRIPTION file unpacking file1ff12b7fa968b8.tar.gz locally unpacked file1ff12b7fa968b8.tar.gz locally installing test.package.0006 locally test.package.0006 installed locally No R folder found in the package source path No Suggested packages in the DESCRIPTION file No Imports or Suggested packages in the DESCRIPTION file gzip: stdin: not in gzip format /usr/bin/tar: Child returned status 1 /usr/bin/tar: Error is not recoverable: exiting now traceability matrix for unsuccessful [1] "No sourceable R scripts were found in the R/ directory for package dummy_path. Make sure this was expected.\n" No top level assignments found in R folder for path The following exports were not found in R/ for path: function2 generic1 In package `path`, the R scripts (NA) are missing documentation for the following exports: function2 generic1 traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful high risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful medium risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful high risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful medium risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful high risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful medium risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful high risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful medium risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated creating traceability matrix for mockpkg creating traceability matrices for mockpkg without test coverage creating traceability matrix for mockPkg the execute_coverage parameter = TRUE but the 'function_coverage' object for mockPkg is NULL or non compliant creating traceability matrices for mockPkg with test coverage traceability matrices for mockPkg successful creating traceability matrix for mockPkg the execute_coverage parameter = TRUE but the 'function_coverage' object for mockPkg is NULL or non compliant creating traceability matrices for mockPkg with test coverage traceability matrices for mockPkg successful Error: Dependency tree in progress for pkgA package Dependency tree in progress for pkgB package Dependency tree in progress for pkgD package Finished building for pkgD Finished building for pkgB Dependency tree in progress for pkgC package Finished building for pkgC Finished building for pkgA Finished building for testpkg Dependency tree in progress for testpkg package Dependency tree in progress for pkgA package Dependency tree in progress for pkgB package Dependency tree in progress for pkgD package Finished building for pkgD Finished building for pkgB Dependency tree in progress for pkgC package Finished building for pkgC Finished building for pkgA Dependency tree in progress for pkgC package Finished building for pkgC Dependency tree in progress for pkgE package Dependency tree in progress for pkgF package Dependency tree in progress for pkgG package Finished building for pkgG Finished building for pkgF Finished building for pkgE Dependency tree in progress for unknownPkg package Finished building for unknownPkg Dependency tree in progress for basePkg package Finished building for basePkg Building dependency tree for: ggplot2 unpacking stringr locally unpacked stringr locally Some exported functions are missing help files in stringr stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has a source control stringr has vignettes stringr has examples stringr has news stringr has current news Checking for author in test Checking for author in test Checking for author in mockpkg Checking for author in test Checking for author in test unpacking here locally unpacked here locally Checking for License in here unpacking file1ff12b51974752.tar.gz locally unpacked file1ff12b51974752.tar.gz locally Checking for License in test.package.0001 unpacking file1ff12b22397c0b.tar.gz locally unpacked file1ff12b22397c0b.tar.gz locally Checking for License in test.package.0007 unpacking stringr locally unpacked stringr locally stringr has a maintainer stringr has a website stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has bug reports URL stringr has a website stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has a source control unpacking file1ff12b1c7aa431.tar.gz locally unpacked file1ff12b1c7aa431.tar.gz locally test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have bug reports URL test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control mockpkg has bug reports URL mockpkg has a website mockpkg has a website mockpkg does not have a source control Checking for author in limma Checking for author in limma unpacking stringr locally unpacked stringr locally stringr has a maintainer stringr has a website stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has bug reports URL stringr has a website stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has a source control unpacking file1ff12b33082fc8.tar.gz locally unpacked file1ff12b33082fc8.tar.gz locally test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have bug reports URL test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control Checking for author in limma Checking for author in limma unpacking here locally unpacked here locally unpacking file1ff12b2b4de9ca.tar.gz locally unpacked file1ff12b2b4de9ca.tar.gz locally unpacking here locally unpacked here locally here has examples unpacking file1ff12b7eb2c27e.tar.gz locally unpacked file1ff12b7eb2c27e.tar.gz locally test.package.0001 has no examples unpacking here locally unpacked here locally All exported functions have corresponding help files in here unpacking stringr locally unpacked stringr locally Some exported functions are missing help files in stringr unpacking file1ff12b1dbefd37.tar.gz locally unpacked file1ff12b1dbefd37.tar.gz locally installing test.package.0006 locally test.package.0006 is already installed No exported functions in test.package.0006 unpacking here locally unpacked here locally here has news unpacking file1ff12b716a06b3.tar.gz locally unpacked file1ff12b716a06b3.tar.gz locally test.package.0001 has no news unpacking here locally unpacked here locally here has current news unpacking file1ff12b321c7c.tar.gz locally unpacked file1ff12b321c7c.tar.gz locally test.package.0001 has no news path test.package.0001 has no current news test.package.0001 has no news path test.package.0001 has no current news unpacking here locally unpacked here locally here has vignettes unpacking file1ff12bdb28031.tar.gz locally unpacked file1ff12bdb28031.tar.gz locally test.package.0001 has no vignettes unpacking file1ff12b25709987.tar.gz locally unpacked file1ff12b25709987.tar.gz locally unpacking stringr locally unpacked stringr locally Using package's default risk definition. Checking stringr on CRAN... Checking SomePkg on CRAN... CRAN download failed: CRAN download failed due to timeout Checking SomePkg on Bioconductor... Checking Biobase on CRAN... Checking Biobase on Bioconductor... Checking InternalPkg on CRAN... Checking InternalPkg on Bioconductor... No InternalPkg package found on Bioconductor Attempting internal fallback download for InternalPkg Checking GhostPkg on CRAN... Checking GhostPkg on Bioconductor... No GhostPkg package found on Bioconductor Attempting internal fallback download for GhostPkg Checking GhostPkg on CRAN... Checking GhostPkg on Bioconductor... No GhostPkg package found on Bioconductor Attempting internal fallback download for GhostPkg Failed to download the package from any source. Error: couldn't find package 'GhostPkg'FALSE Checking ggplot2 on CRAN... Checking nonexistentpkg on CRAN... Checking nonexistentpkg on Bioconductor... No nonexistentpkg package found on Bioconductor Attempting internal fallback download for nonexistentpkg Checking nonexistentpkg on CRAN... Checking nonexistentpkg on Bioconductor... No nonexistentpkg package found on Bioconductor Attempting internal fallback download for nonexistentpkg Failed to download the package from any source. Error: all fallback failedFALSE Checking mockpkg on CRAN... Checking mockpkg on CRAN... No testthat or testit configuration Checking mockpkg on CRAN... url_page: https://bioconductor.org/packages/3.20/bioc/html/limma.html url_page: https://bioconductor.org/packages/3.20/bioc/html/noarchive.html Failed to fetch page: https://bioconductor.org/packages/3.20/bioc/html/noarchive.html url_page: https://bioconductor.org/packages/3.20/bioc/html/archiveonly.html url_page: https://bioconductor.org/packages/3.20/bioc/html/doesnotexist.html Checking Bioconductor version: 3.17 Checking package version: 1.38.0 Date: 2005-10-14 Checking Bioconductor version: 3.18 Checking package version: 1.38.0 Date: 2006-10-04 Checking Bioconductor version: 3.19 Checking package version: 1.38.0 Date: 2007-10-08 Checking Bioconductor version: 3.17 Checking package version: 3.40.2 Date: 2005-10-14 Checking Bioconductor version: 3.18 Checking package version: 3.40.2 Date: 2006-10-04 Checking Bioconductor version: 3.19 Checking package version: 3.40.2 Date: 2007-10-08 Checking Bioconductor version: 3.17 Checking Bioconductor version: 3.18 Checking Bioconductor version: 3.19 Package URL not found on Bioconductor Checking Bioconductor version: 3.17 Skipping Bioconductor version 3.17 due to error: Simulated error Checking Bioconductor version: 3.18 Skipping Bioconductor version 3.18 due to error: Simulated error Checking Bioconductor version: 3.19 Skipping Bioconductor version 3.19 due to error: Simulated error Package URL not found on Bioconductor No download data found or invalid format for: ggplot2 Could not fetch CRAN download data for package: ggplot2 No download data found or invalid format for: ggplot2 Could not fetch CRAN download data for package: nonexistent8package No download data found or invalid format for: nonexistent8package could not fetch download data for package: FakePackage123 No download data found for package: FakePackage123 No download data found for package: FakePackage123 could not fetch download data for package: FakePackage123 No download data found for package: EmptyDataPkg No R folder found in the package source path for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Checking GitHub data for tidyverse/ggplot2... Checking GitHub data for /ggplot2... Owner is NA or empty. Returning empty response. Checking GitHub data for tidyverse/non_existent_repo... Failed to fetch repository details: Mocked API call failure Checking GitHub data for tidyverse/ggplot2... Failed to fetch commits: Mocked commits API failure Checking GitHub data for tidyverse/non_existent_repo... Failed to fetch repository details: Mocked API call failure Repository not found: Not Found NO INTERNAL_RSPM FOUND NO INTERNAL_RSPM FOUND NO INTERNAL_RSPM FOUND Checking host package Checking host package Checking host package Checking host package Checking host package No articles found on pubmed for ggplot2 No articles found on pubmed for ggplot2 No articles found on pubmed for ggplot2 Using custom risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using custom risk definition. Using custom risk definition. Using custom risk definition. Using custom risk definition. Using custom risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. unpacking file1ff12b119ec0bd.tar.gz locally unpacked file1ff12b119ec0bd.tar.gz locally installing test.package.0001 locally test.package.0001 installed locally installing invalidPackage locally installing mock_package locally mock_package installed locally mock_package installed locally installing non_existent_directory locally No such file or directory: non_existent_directory installing mock_package locally mock_package is already installed /usr/bin/tar: Removing leading `/' from member names Saving _problems/test-parse_dcf_dependencies-111.R Saving _problems/test-parse_dcf_dependencies-181.R Starting lock file processing Starting lock file processing Finishing lock file processing Starting lock file processing Finishing lock file processing running code coverage for file1ff12b7e381419 code coverage for file1ff12b7e381419 unsuccessful R coverage for file1ff12b7e381419 failed. Read in the covr output to see what went wrong: unpacking file1ff12bbc6827c.tar.gz locally unpacked file1ff12bbc6827c.tar.gz locally unpacking file1ff12b5490801.tar.gz locally unpacked file1ff12b5490801.tar.gz locally unpacking file1ff12b489d9508.tar.gz locally unpacked file1ff12b489d9508.tar.gz locally unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking file1ff12b6135471.tar.gz locally unpacked file1ff12b6135471.tar.gz locally checking package test config checking package test config checking package test config checking package test config checking package test config checking package test config checking package test config unpacking here locally unpacked here locally unpacking empty.tar.gz locally not able to unpack empty.tar.gz locally unpacking here locally unpacked here locally [ FAIL 10 | WARN 2 | SKIP 43 | PASS 1140 ] ══ Skipped tests (43) ══════════════════════════════════════════════════════════ • On CRAN (42): 'test-assess_pkg.R:2:3', 'test-assess_pkg.R:216:3', 'test-assess_pkg.R:372:3', 'test-assess_pkg.R:451:3', 'test-assess_pkg.R:546:3', 'test-assess_pkg.R:731:3', 'test-assess_pkg.R:808:3', 'test-badges.R:44:3', 'test-check_suggested_exp_funcs.R:3:3', 'test-check_suggested_exp_funcs.R:218:3', 'test-cran_packages.R:3:3', 'test-cran_packages.R:12:3', 'test-create_traceability_matrix.R:2:3', 'test-create_traceability_matrix.R:65:3', 'test-create_traceability_matrix.R:138:3', 'test-create_traceability_matrix.R:207:3', 'test-dependency_tree.R:462:1', 'test-dependency_tree.R:466:1', 'test-dependency_tree.R:530:1', 'test-dependency_tree.R:534:1', 'test-generate_html_report.R:461:3', 'test-get_exports.R:2:3', 'test-get_exports.R:52:3', 'test-get_exports.R:141:3', 'test-get_exports.R:223:3', 'test-get_exports.R:276:3', 'test-get_exports.R:327:3', 'test-parse_dcf_dependencies.R:2:3', 'test-parse_dcf_dependencies.R:43:3', 'test-reverse_dependencies.R:2:3', 'test-risk_assess_pkg.R:10:3', 'test-risk_assess_pkg.R:130:3', 'test-risk_assess_pkg.R:154:3', 'test-run_coverage.R:2:3', 'test-run_coverage.R:49:3', 'test-run_coverage.R:93:3', 'test-run_coverage.R:137:3', 'test-run_coverage.R:182:3', 'test-run_rcmdcheck.R:2:3', 'test-run_rcmdcheck.R:61:3', 'test-run_rcmdcheck.R:136:3', 'test-run_rcmdcheck.R:206:3' • Skipping test because CRAN is available (1): 'test-parse_dcf_dependencies.R:126:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-assess_pkg.R:678:3'): assess_pkg handles error in check_suggested_exp_funcs via withCallingHandlers ── Error in `curl::curl_fetch_memory(package_url)`: Timeout was reached [cran.r-project.org]: Connection timed out after 10002 milliseconds Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-assess_pkg.R:678:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─risk.assessr::assess_pkg(pkg_source_path, rcmdcheck_args) 8. │ └─risk.assessr::get_host_package(pkg_name, pkg_ver, pkg_source_path) 9. │ └─risk.assessr::check_cran_package(pkg_name) 10. │ └─curl::curl_fetch_memory(package_url) 11. └─curl:::raise_libcurl_error(...) ── Error ('test-assess_pkg.R:723:3'): assess_pkg handles error via outer tryCatch block ── Error in `curl::curl_fetch_memory(package_url)`: Timeout was reached [cran.r-project.org]: Connection timed out after 10002 milliseconds Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-assess_pkg.R:723:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─risk.assessr::assess_pkg(pkg_source_path, rcmdcheck_args) 8. │ └─risk.assessr::get_host_package(pkg_name, pkg_ver, pkg_source_path) 9. │ └─risk.assessr::check_cran_package(pkg_name) 10. │ └─curl::curl_fetch_memory(package_url) 11. └─curl:::raise_libcurl_error(...) ── Error ('test-assess_pkg_r_package.R:34:3'): falls back to Bioconductor if CRAN download fails ── Error in `curl::curl_fetch_memory(package_url)`: Timeout was reached [cran.r-project.org]: Connection timed out after 10002 milliseconds Backtrace: ▆ 1. ├─risk.assessr::assess_pkg_r_package("SomePkg") at test-assess_pkg_r_package.R:34:3 2. │ └─risk.assessr::check_cran_package(package_name) 3. │ └─curl::curl_fetch_memory(package_url) 4. └─curl:::raise_libcurl_error(...) ── Error ('test-assess_pkg_r_package.R:68:3'): downloads a package from Bioconductor if not on CRAN ── Error in `curl::curl_fetch_memory(package_url)`: Timeout was reached [cran.r-project.org]: Connection timed out after 10002 milliseconds Backtrace: ▆ 1. ├─risk.assessr::assess_pkg_r_package("Biobase") at test-assess_pkg_r_package.R:68:3 2. │ └─risk.assessr::check_cran_package(package_name) 3. │ └─curl::curl_fetch_memory(package_url) 4. └─curl:::raise_libcurl_error(...) ── Error ('test-assess_pkg_r_package.R:116:3'): downloads a package from internal mirror if not on CRAN or Bioconductor ── Error in `curl::curl_fetch_memory(package_url)`: Timeout was reached [cran.r-project.org]: Connection timed out after 10002 milliseconds Backtrace: ▆ 1. ├─risk.assessr::assess_pkg_r_package("InternalPkg") at test-assess_pkg_r_package.R:116:3 2. │ └─risk.assessr::check_cran_package(package_name) 3. │ └─curl::curl_fetch_memory(package_url) 4. └─curl:::raise_libcurl_error(...) ── Error ('test-assess_pkg_r_package.R:140:3'): return if package not found on CRAN, Bioconductor, or internal ── Error in `curl::curl_fetch_memory(package_url)`: Timeout was reached [cran.r-project.org]: Connection timed out after 10002 milliseconds Backtrace: ▆ 1. ├─testthat::expect_message(assess_pkg_r_package("GhostPkg"), regexp = "Failed to download the package from any source") at test-assess_pkg_r_package.R:140:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─risk.assessr::assess_pkg_r_package("GhostPkg") 8. │ └─risk.assessr::check_cran_package(package_name) 9. │ └─curl::curl_fetch_memory(package_url) 10. └─curl:::raise_libcurl_error(...) ── Error ('test-assess_pkg_r_package.R:168:3'): downloads a package successfully from CRAN ── Error in `curl::curl_fetch_memory(package_url)`: Timeout was reached [cran.r-project.org]: Connection timed out after 10002 milliseconds Backtrace: ▆ 1. ├─risk.assessr::assess_pkg_r_package("ggplot2") at test-assess_pkg_r_package.R:168:3 2. │ └─risk.assessr::check_cran_package(package_name) 3. │ └─curl::curl_fetch_memory(package_url) 4. └─curl:::raise_libcurl_error(...) ── Error ('test-assess_pkg_r_package.R:190:3'): uses manually specified repos when provided ── Error in `curl::curl_fetch_memory(package_url)`: Timeout was reached [cran.r-project.org]: Connection timed out after 10002 milliseconds Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-assess_pkg_r_package.R:190:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─risk.assessr::assess_pkg_r_package("nonexistentpkg", repos = dummy_repo) 8. │ └─risk.assessr::check_cran_package(package_name) 9. │ └─curl::curl_fetch_memory(package_url) 10. └─curl:::raise_libcurl_error(...) ── Error ('test-parse_dcf_dependencies.R:111:3'): parse_dcf_dependencies extracts dependencies when CRAN is available ── Error in `value[[3L]](cond)`: Failed to download or read CRAN package metadata: cannot open URL 'https://cran.r-project.org/web/packages/packages.rds' Backtrace: ▆ 1. └─risk.assessr:::parse_dcf_dependencies(temp_dir) at test-parse_dcf_dependencies.R:111:3 2. └─risk.assessr:::remove_base_packages(deps) 3. └─base::tryCatch(...) 4. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6. └─value[[3L]](cond) ── Error ('test-parse_dcf_dependencies.R:181:3'): parse_dcf_dependencies extracts dependencies different format ── Error in `value[[3L]](cond)`: Failed to download or read CRAN package metadata: cannot open URL 'https://cran.r-project.org/web/packages/packages.rds' Backtrace: ▆ 1. └─risk.assessr:::parse_dcf_dependencies(temp_dir) at test-parse_dcf_dependencies.R:181:3 2. └─risk.assessr:::remove_base_packages(deps) 3. └─base::tryCatch(...) 4. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6. └─value[[3L]](cond) [ FAIL 10 | WARN 2 | SKIP 43 | PASS 1140 ] Error: ! Test failures. Execution halted Package: shinyGovstyle Check: tests New result: ERROR Running ‘testthat.R’ [3s/3s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(shinyGovstyle) > > test_check("shinyGovstyle") Saving _problems/test-backlink_Input-7.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 125 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-backlink_Input.R:4:3'): backlink works ─────────────────────── Expected `backlink_check$children[[1]][[2]]` to be identical to "Back". Differences: target is NULL, current is character [ FAIL 1 | WARN 0 | SKIP 0 | PASS 125 ] Error: ! Test failures. Execution halted Package: tmap Check: examples New result: ERROR Running examples in ‘tmap-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: tm_logo > ### Title: Map component: logo > ### Aliases: tm_logo > > ### ** Examples > > data(World) > > tm_shape(World) + + tm_polygons("HPI", fill.scale = tm_scale_intervals(values = "brewer.rd_yl_gn")) + + tm_logo(c("https://www.r-project.org/logo/Rlogo.png", + system.file("help", "figures", "logo.png", package = "tmap"))) + + tm_logo("http://blog.kulikulifoods.com/wp-content/uploads/2014/10/logo.png", + height=5, position = c("left", "top")) trying URL 'https://www.r-project.org/logo/Rlogo.png' Warning in download.file(file, destfile = tmpfile, mode = "wb") : URL 'https://www.r-project.org/logo/Rlogo.png': Timeout of 60 seconds was reached Error in download.file(file, destfile = tmpfile, mode = "wb") : cannot open URL 'https://www.r-project.org/logo/Rlogo.png' Calls: ... FUN -> tmap_icons -> lapply -> FUN -> download.file Execution halted