# block_callback by line Code for (line in chk) cb(paste0(line, "\n")) Output - using log directory '/tmp/RtmpoYWa4I/file31fc5a857856/mlr.Rcheck' - using R version 3.5.0 (2017-01-27) - using platform: x86_64-pc-linux-gnu (64-bit) - using session charset: UTF-8 v checking for file 'mlr/DESCRIPTION' - this is package 'mlr' version '2.13' - package encoding: UTF-8 v checking package namespace information N checking package dependencies Package suggested but not available for checking: 'elmNN' v checking if this is a source package v checking if there is a namespace v checking for executable files v checking for hidden files and directories v checking for portable file names v checking for sufficient/correct file permissions - checking whether package 'mlr' can be installed ... [22s/22s] OK N checking installed package size installed size is 6.5Mb sub-directories of 1Mb or more: data 3.3Mb R 2.0Mb v checking package directory v checking 'build' directory v checking DESCRIPTION meta-information v checking top-level files v checking for left-over files v checking index information v checking package subdirectories v checking R files for non-ASCII characters v checking R files for syntax errors v checking whether the package can be loaded v checking whether the package can be loaded with stated dependencies v checking whether the package can be unloaded cleanly v checking whether the namespace can be loaded with stated dependencies v checking whether the namespace can be unloaded cleanly v checking loading without being on the library search path N checking dependencies in R code Picked up _JAVA_OPTIONS: -Xmx2048m -Xms512m v checking S3 generic/method consistency v checking replacement functions v checking foreign function calls - checking R code for possible problems ... [34s/34s] OK v checking Rd files v checking Rd metadata v checking Rd cross-references v checking for missing documentation entries v checking for code/documentation mismatches v checking Rd \usage sections v checking Rd contents v checking for unstated dependencies in examples v checking contents of 'data' directory v checking data for non-ASCII characters v checking data for ASCII and uncompressed saves v checking line endings in C/C++/Fortran sources/headers v checking compiled code v checking installed files from 'inst/doc' v checking files in 'vignettes' - checking examples ... [18s/28s] OK v checking for unstated dependencies in 'tests' - checking tests Running the tests in 'tests/run-classif1.R' failed. Last 999 lines of output: burning and aggregating chains from all threads... done building BART with mem-cache speedup... done building BART in 0.013 sec burning and aggregating chains from all threads... done building BART with mem-cache speedup... Iteration 100/1250 Iteration 200/1250 Iteration 300/1250 Iteration 400/1250 Iteration 500/1250 Iteration 600/1250 Iteration 700/1250 Iteration 800/1250 Iteration 900/1250 Iteration 1000/1250 Iteration 1100/1250 Iteration 1200/1250 done building BART in 0.551 sec burning and aggregating chains from all threads... done building BART with mem-cache speedup... done building BART in 0.028 sec burning and aggregating chains from all threads... done building BART with mem-cache speedup... done building BART in 0.014 sec burning and aggregating chains from all threads... done -- 1. Error: classif_blackboost (@test_classif_blackboost.R#32) --------------- no method for assigning subsets of this S4 class 1: do.call(mboost::blackboost, pars) at testthat/test_classif_blackboost.R:32 2: (function (formula, data = list(), weights = NULL, na.action = na.pass, offset = NULL, family = Gaussian(), control = boost_control(), oobweights = NULL, tree_controls = partykit::ctree_control(teststat = "quad", testtype = "Teststatistic", mincriterion = 0, minsplit = 10, minbucket = 4, maxdepth = 2, saveinfo = FALSE), ...) { cl <- match.call() mf <- match.call(expand.dots = FALSE) m <- match(c("formula", "data", "weights", "na.action"), names(mf), 0L) mf <- mf[c(1L, m)] mf$drop.unused.levels <- TRUE mf[[1L]] <- quote(stats::model.frame) mf <- eval(mf, parent.frame()) response <- model.response(mf) weights <- model.weights(mf) mf <- mf[, -1, drop = FALSE] mf$"(weights)" <- NULL bl <- list(btree(mf, tree_controls = tree_controls)) ret <- mboost_fit(bl, response = response, weights = weights, offset = offset, family = family, control = control, oobweights = oobweights, ...) ret$call <- cl Error: testthat unit tests failed Execution halted v checking for unstated dependencies in vignettes v checking package vignettes in 'inst/doc' - checking running R code from vignettes 'mlr.Rmd' using 'UTF-8' ... [0s/0s] OK NONE - checking re-building of vignette outputs ... [3s/4s] OK v checking PDF version of manual # block_callback by chunks Code for (ch in chunks) cb(ch) Output - using log directory '/tmp/RtmpoYWa4I/file31fc5a857856/mlr.Rcheck' - using R version 3.5.0 (2017-01-27) - using platform: x86_64-pc-linux-gnu (64-bit) - using session charset: UTF-8 v checking for file 'mlr/DESCRIPTION' - this is package 'mlr' version '2.13' - package encoding: UTF-8 v checking package namespace information N checking package dependencies Package suggested but not available for checking: 'elmNN' v checking if this is a source package v checking if there is a namespace v checking for executable files v checking for hidden files and directories v checking for portable file names v checking for sufficient/correct file permissions - checking whether package 'mlr' can be installed ... [22s/22s] OK N checking installed package size installed size is 6.5Mb sub-directories of 1Mb or more: data 3.3Mb R 2.0Mb v checking package directory v checking 'build' directory v checking DESCRIPTION meta-information v checking top-level files v checking for left-over files v checking index information v checking package subdirectories v checking R files for non-ASCII characters v checking R files for syntax errors v checking whether the package can be loaded v checking whether the package can be loaded with stated dependencies v checking whether the package can be unloaded cleanly v checking whether the namespace can be loaded with stated dependencies v checking whether the namespace can be unloaded cleanly v checking loading without being on the library search path chec N checking dependencies in R code Picked up _JAVA_OPTI Picked up _JAVA_OPTIONS: -Xmx2048m -Xms512m v checking S3 generic/method consistency v checking replacement functions checking foreign func v checking foreign function calls - checking R code for possible problems ... [34s/34s] OK checking Rd files ... O v checking Rd files v checking Rd metadata v checking Rd cross-references v checking for missing documentation entries v checking for code/documentation mismatches v checking Rd \usage sections v checking Rd contents v checking for unstated dependencies in examples v checking contents of 'data' directory v checking data for non-ASCII characters v checking data for ASCII and uncompressed saves checking line endings in C/C++/Fortran s v checking line endings in C/C++/Fortran sources/headers checking compiled code ... OK v checking compiled code v checking installed files from 'inst/doc' v checking files in 'vignettes' - checking examples ... [18s/28s] OK v checking for unstated dependencies in 'tests' - checking tests Running the tests in 't Running the tests in 'tests/run-classif1.R' failed. Last 999 lines of output: burning and aggregating chains from all threads... done building BART with mem-cache speedup... done building BART in 0.013 sec burning and aggregating chains from all threads... done building building BART with mem-cache speedup... Iteration 100/1250 Iteration 200/1250 Iteration 300/1250 Iteration 400/1250 Iteration 5 Iteration 500/1250 Iteration 600/1250 Iterat Iteration 700/1250 Iteration 800/1250 Iteration 900/1250 Iteration 1000/1250 Iteration 1100/1250 Iteration 1200/1250 done building BART in 0.551 sec burning and aggregating ch burning and aggregating chains from all threads... done building BART with mem-cache speedup... done building BART in 0.028 sec burning and aggregating chains from all threads... done building BART with mem-cache speedup... done building B done building BART in 0.014 sec burning and aggregating chains from all threads... done -- 1. Error: classif_blackboost (@test_classif_blackboost.R#32) --------------- no method for assigning subsets of this S4 class 1: do.call(mboost::blackboost, pars) 1: do.call(mboost::blackboost, pars) at testthat/test_classif_blackboost.R:32 2: (function (formula, data = list(), weights = NULL, na.action = na.pass, offset = NULL, family = Gaussian(), control = boost_control(), oobweights = NULL, tree_controls = partykit::ctree_control(teststat = "quad", testtype = "Teststatistic", mincriterion = 0, minsplit = 10, minbucket = 4, maxdepth = 2, saveinfo = FALSE), ...) { cl <- ma cl <- match.call() mf <- match.call(expand.dots = FALSE) m <- match(c("formula", "data", "weights", "na.action"), names(mf), 0L) mf <- mf[c(1L, m)] mf$drop.unu mf$drop.unused.levels <- TRUE mf[[1L]] <- quote(stats::model.frame) mf <- eval(mf, parent.frame()) response <- model.response(mf) weights <- model.weights(mf) mf <- mf[, -1, drop = FALSE] mf$"(weights)" <- NULL bl <- list(btree(mf, tree_controls bl <- list(btree(mf, tree_controls = tree_controls)) re ret <- mboost_fit(bl, response = response, weights = weights, offset = offset, family = family, control = control, oobweights = oobweights, ...) ret$call ret$call <- cl Error: testthat unit tests failed Execution halted v checking for unstated dependencies in vignettes v checking package vignettes in 'inst/doc' - checking running R code from vignettes 'mlr.Rmd' using 'UTF-8' ... [0s/0s] OK NONE - checking re-building of vignette outputs ... [3s/4s] OK checking PDF vers v checking PDF version of manual # notes, errors, warnings Code for (line in out) cb(line) Output N Step one More note text. W Step two More warning text. E Step three More error text. # tests Code for (line in txt) cb(paste0(line, "\n")) Output v checking for unstated dependencies in 'tests' E checking tests Running 'testthat.R' Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(lpirfs) > > test_check("lpirfs") Error in parse(con, n = -1, srcfile = srcfile, encoding = "UTF-8") : test-diagnost_ols.R:19:8: unexpected $end 18: 19: lm_mode ^ Calls: test_check ... doWithOneRestart -> force -> lapply -> FUN -> source_file -> parse Execution halted v checking for unstated dependencies in vignettes # multi-arch tests Code for (line in txt) cb(paste0(line, "\n")) Output v checking for unstated dependencies in 'tests' - checking tests -- running tests for arch 'i386' ... [2s] ERROR Running the tests in 'tests/testthat.R' failed. Complete output: > library("testthat") > library("GMSE") > > test_check("GMSE") -- running tests for arch 'x64' ... [3s] OK * checking for unstated dependencies in vignettes ... OK # multiple test file run times are measured properly Code out Output [1] " \r checking examples ... \r \rv checking examples (5s)" [2] "\r \rv checking for unstated dependencies in 'tests'" [3] "\r \r- checking tests" [4] "\r \r Running 'first_edition.R'\r \r\r \rv Running 'first_edition.R' (13.2s)" [5] " Running 'second_edition.R'\r \r\r \rv Running 'second_edition.R' (14.3s)" [6] "\r \rv checking for unstated dependencies in vignettes" [7] "\r \rv checking package vignettes in 'inst/doc'" [8] "\r" # multi-arch test cases Code out Output [1] " \r- using log directory 'C:/Users/csard/works/ps.Rcheck'" [2] "\r \r- using R version 4.1.1 (2021-08-10)" [3] "\r \r- using platform: x86_64-w64-mingw32 (64-bit)" [4] "\r \r- using session charset: ISO8859-1" [5] "\r \rv checking for file 'ps/DESCRIPTION'" [6] "\r \r- this is package 'ps' version '1.3.2.9000'" [7] "\r \rv checking for unstated dependencies in 'tests'" [8] "\r \r- checking tests" [9] "\r \r-- running tests for arch 'i386' " [10] "\r \r\r \rv Running 'testthat.R'" [11] "\r \r-- running tests for arch 'x64' " [12] "\r \r\r \rv Running 'testthat.R'" [13] "\r \rv checking PDF version of manual" [14] "\r \r\r" # failed test case Code out Output [1] " \rv checking for unstated dependencies in 'tests'" [2] "\r \r- checking tests" [3] "\r \r\r \rE Running 'testthat.R'" [4] "\r \r Running the tests in 'tests/testthat.R' failed." [5] "\r \r Last 13 lines of output:" [6] "\r \r / | 0 | windows " [7] "\r \r / | 0 | winver " [8] "\r \r / | 0 | winver " [9] "\r \r v | 6 | winver" [10] "\r \r " [11] "\r \r == Results =====================================================================" [12] "\r \r Duration: 13.5 s" [13] "\r \r " [14] "\r \r -- Skipped tests --------------------------------------------------------------" [15] "\r \r * Needs working IPv6 connection (2)" [16] "\r \r * On CRAN (13)" [17] "\r \r " [18] "\r \r [ FAIL 1 | WARN 0 | SKIP 15 | PASS 367 ]" [19] "\r \r Error: Test failures" [20] "\r \r Execution halted" [21] "\r \rv checking PDF version of manual" [22] "\r \r\r" # comparing test output Code out Output [1] " \rv checking for unstated dependencies in 'tests'" [2] "\r \r- checking tests" [3] "\r \r\r \rv Running 'first_edition.R'" [4] "\r \rv Running 'second_edition.R'" [5] "\r \rv Running 'spelling.R'" [6] "X Comparing 'spelling.Rout' to 'spelling.Rout.save'" [7] " 6,8d5" [8] "\r \r < Potential spelling errors:" [9] "\r \r < WORD FOUND IN" [10] "\r \r < programatically NEWS.md:14" [11] "\r \r\r \rv checking for unstated dependencies in vignettes" [12] "\r \rv checking package vignettes in 'inst/doc'" [13] "\r" # partial comparing line Code out Output [1] " \r- checking tests" [2] "\r \r\r \rv Running 'test-1.R'" [3] " Comparing 'test-1.Rout' to \r \rv Comparing 'test-1.Rout' to 'test-1.Rout.save'" [4] "\r \r\r \rv Running 'test-2.R'" [5] "v Comparing 'test-2.Rout' to 'test-2.Rout.save'" [6] "\r \r\r \rv checking PDF version of manual" [7] "\r \r\r" # multiple comparing blocks Code out Output [1] " \rv checking examples" [2] "\r \rv checking for unstated dependencies in 'tests'" [3] "\r \r- checking tests" [4] "\r \r\r \rv Running 'test-1.R'" [5] "v Comparing 'test-1.Rout' to 'test-1.Rout.save'" [6] "\r \r\r \rv Running 'test-2.R'" [7] "v Comparing 'test-2.Rout' to 'test-2.Rout.save'" [8] "\r \r\r \rv Running 'test.R'" [9] "X Comparing 'test.Rout' to 'test.Rout.save'" [10] " 1,4d0" [11] "\r \r <" [12] "\r \r <" [13] "\r \r < >" [14] "\r \r < > cat(\"This is the output.\\n\")" [15] "\r \r 6d1" [16] "\r \r < >" [17] "\r \r\r \r " [18] "\r \rE" [19] "\r \r Running the tests in 'tests/testthat.R' failed." [20] "\r \r Last 13 lines of output:" [21] "\r \r + ## ps does not support this platform" [22] "\r \r + reporter <- \"progress\"" [23] "\r \r + }" [24] "\r \r >" [25] "\r \r > if (ps_is_supported()) test_check(\"ps\", reporter = reporter)" [26] "\r \r cleanup-reporter:" [27] "\r \r cleanup testthat reporter: ......................................................................................................................................" [28] "\r \r common:" [29] "\r \r common: ...................................................................................................................................................." [30] "\r \r connections:" [31] "\r \r connections: ................................................................S............S............" [32] "\r \r finished:" [33] "\r \r process finished: ..................................................................................." [34] "\r \r kill-tree:" [35] "\r \r kill-tree: ..............................................." [36] "\r \rv checking PDF version of manual" [37] "\r" # simple_callback Code out Output [1] "* using log directory '/private/tmp/readr.Rcheck'" [2] "* using R version 4.1.0 (2021-05-18)" [3] "* using platform: x86_64-apple-darwin17.0 (64-bit)" [4] "* using session charset: UTF-8" [5] "* checking for file 'readr/DESCRIPTION' ... OK" [6] "* this is package 'readr' version '2.0.1.9000'" [7] "* package encoding: UTF-8" [8] "* checking package namespace information ... OK" [9] "* checking package dependencies ... OK" [10] "* checking if this is a source package ... OK" [11] "* checking if there is a namespace ... OK" [12] "* checking for executable files ... OK" [13] "* checking for hidden files and directories ... OK" [14] "* checking for portable file names ... OK" [15] "* checking for sufficient/correct file permissions ... OK" [16] "* checking whether package 'readr' can be installed ... OK" [17] "* checking installed package size ... OK" [18] "* checking package directory ... OK" [19] "* checking 'build' directory ... OK" [20] "* checking DESCRIPTION meta-information ... OK" [21] "* checking top-level files ... OK" [22] "* checking for left-over files ... OK" [23] "* checking index information ... OK" [24] "* checking package subdirectories ... OK" [25] "* checking R files for non-ASCII characters ... OK" [26] "* checking R files for syntax errors ... OK" [27] "* checking whether the package can be loaded ... OK" [28] "* checking whether the package can be loaded with stated dependencies ... OK" [29] "* checking whether the package can be unloaded cleanly ... OK" [30] "* checking whether the namespace can be loaded with stated dependencies ... OK" [31] "* checking whether the namespace can be unloaded cleanly ... OK" [32] "* checking loading without being on the library search path ... OK" [33] "* checking dependencies in R code ... OK" [34] "* checking S3 generic/method consistency ... OK" [35] "* checking replacement functions ... OK" [36] "* checking foreign function calls ... OK" [37] "* checking R code for possible problems ... OK" [38] "* checking Rd files ... OK" [39] "* checking Rd metadata ... OK" [40] "* checking Rd cross-references ... OK" [41] "* checking for missing documentation entries ... OK" [42] "* checking for code/documentation mismatches ... OK" [43] "* checking Rd \\usage sections ... OK" [44] "* checking Rd contents ... OK" [45] "* checking for unstated dependencies in examples ... OK" [46] "* checking R/sysdata.rda ... OK" [47] "* checking line endings in C/C++/Fortran sources/headers ... OK" [48] "* checking compiled code ... OK" [49] "* checking installed files from 'inst/doc' ... OK" [50] "* checking files in 'vignettes' ... OK" [51] "* checking examples ... OK" [52] "* checking for unstated dependencies in 'tests' ... OK" [53] "* checking tests ..." [54] " Running 'first_edition.R'" [55] " Running 'second_edition.R'" [56] " Running 'spelling.R'" [57] " Comparing 'spelling.Rout' to 'spelling.Rout.save' ...6,8d5" [58] "< Potential spelling errors:" [59] "< WORD FOUND IN" [60] "< programatically NEWS.md:14" [61] " OK" [62] "* checking for unstated dependencies in vignettes ... OK" [63] "* checking package vignettes in 'inst/doc' ... OK" [64] "* checking running R code from vignettes ..." [65] " 'locales.Rmd' using 'UTF-8'... OK" [66] " 'readr.Rmd' using 'UTF-8'... OK" [67] " NONE" [68] "* checking re-building of vignette outputs ... OK" [69] "* checking PDF version of manual ... OK" [70] "* DONE" [71] "" [72] "Status: OK" # multiple tests Code out Output [1] " \r- checking examples ... NONE" [2] "\r \rv checking for unstated dependencies in 'tests'" [3] "\r \r- checking tests" [4] "\r \r\r \r- Running 'a.R'" [5] "\r \r- Running 'b.R'" [6] "\r \r- Running 'c.R'" [7] "E Some test files failed" [8] "\r \r Running the tests in 'tests/b.R' failed." [9] "\r \r Complete output:" [10] "\r \r > stop(\"error\")" [11] "\r \r Error: error" [12] "\r \r Execution halted" [13] "\r \rv checking PDF version of manual" [14] "\r" --- Code out Output [1] " \r- checking examples ... NONE" [2] "\r \rv checking for unstated dependencies in 'tests'" [3] "\r \r- checking tests" [4] "\r \r\r \rv Running 'a.R'" [5] "\r \rE Running 'b.R'" [6] "\r \r Running the tests in 'tests/b.R' failed." [7] "\r \r Complete output:" [8] "\r \r > stop(\"error\")" [9] "\r \r Error: error" [10] "\r \r Execution halted" [11] "\r \rv checking PDF version of manual" [12] "\r"
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