tests/testthat/_snaps/callback.md
In r-pkgs/rcmdcheck: Run 'R CMD check' from 'R' and Capture Results
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"
r-pkgs/rcmdcheck documentation built on Nov. 12, 2023, 2:53 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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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