Package: DataFakeR Check: tests New result: ERROR Running ‘testthat.R’ [5s/5s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(mockery) > library(DataFakeR) > > test_check("DataFakeR") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-lint_check.R:3:3'): Linting package ──────────────────────────── Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead. Backtrace: ▆ 1. └─lintr::with_defaults(...) at test-lint_check.R:3:3 2. └─lintr:::lintr_deprecated(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ] Error: Test failures Execution halted Package: demic Check: tests New result: ERROR Running ‘testthat.R’ [22s/22s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(demic) > > test_check("demic") $all_ptr est_ptr coefficient pValue cor correctY Akk0_001 1.946931 0.3840328 7.840437e-25 0.9970041 3.260867 Akk1_001 2.763177 0.5858478 1.476701e-26 0.9979485 3.321042 Akk2_001 3.449088 0.7136534 5.229909e-31 0.9992274 3.361187 $contigs_ptr est_ptr coefficient pValue cor correctY Akk0_001 1.798694 0.3946267 1.017910e-14 0.9963922 3.241897 Akk1_001 2.410111 0.5802927 2.564956e-13 0.9960962 3.295741 Akk2_001 2.936096 0.7122483 2.063295e-16 0.9986812 3.312708 $samples_ptr NULL est_ptr coefficient pValue cor correctY Bfrag0_002 2.061760 0.3699599 1.470163e-36 0.9918912 2.216383 Bfrag1_002 3.043483 0.5690839 3.576654e-49 0.9981767 2.222179 Bfrag2_002 4.204818 0.7343522 1.049070e-51 0.9986483 2.208119 est_ptr coefficient pValue cor correctY Ecoli0_003 1.991885 0.3716124 4.875530e-30 0.9823685 2.292568 Ecoli1_003 2.839380 0.5629711 6.072941e-40 0.9945473 2.214114 Ecoli2_003 3.928690 0.7381452 2.262995e-42 0.9961262 2.148132 $all_ptr est_ptr coefficient pValue cor correctY Sample1 1.577167 0.3978371 8.111920e-37 0.7637339 1.481230 Sample2 2.354320 0.7476431 1.453821e-88 0.9410749 1.588319 Sample3 1.838580 0.5317476 1.621567e-46 0.8202775 1.417947 $contigs_ptr est_ptr coefficient pValue cor correctY Sample1 1.572593 0.3965031 1.620183e-26 0.7885387 1.483148 Sample2 2.304554 0.7323414 8.817124e-57 0.9357828 1.585934 Sample3 1.877752 0.5526271 1.092737e-31 0.8339565 1.419581 $samples_ptr NULL $all_ptr est_ptr coefficient pValue cor correctY Sample1 2.281308 0.6319368 5.251404e-62 0.9775760 0.3235725 Sample2 1.748664 0.4282018 4.980528e-39 0.9244302 0.3799434 Sample3 2.323527 0.6459869 1.588855e-64 0.9803428 0.3075130 $contigs_ptr est_ptr coefficient pValue cor correctY Sample1 2.284582 0.6341423 1.671337e-37 0.9739948 0.3949256 Sample2 1.755248 0.4312617 7.905802e-22 0.9136081 0.4137077 Sample3 2.305551 0.6411114 1.441915e-41 0.9795860 0.3931166 $samples_ptr NULL structure(list(`(Intercept)` = c(0.122133753095513, 0.112468233560288, 0.0372788404325122, 0.177304339887256, 0.0270507610681736, 0.0842232868459067, 0.106812647682803, 0.162034499737329, 0.14194349045613, 0.138951868657145 ), GC_content = c(-0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212), s_c = c("a:1", "a:2", "b:3", "b:4", "c:5", "c:6", "d:7", "d:8", "e:9", "e:10")), row.names = c("a:1", "a:2", "b:3", "b:4", "c:5", "c:6", "d:7", "d:8", "e:9", "e:10"), class = "data.frame") [ FAIL 1 | WARN 9 | SKIP 0 | PASS 42 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-est_ptr.R:48:3'): DEMIC main function produces correct output on sourceforge data cluster 2 ── O$contigs_ptr (`actual`) not equal to `EO2` (`expected`). actual vs expected correctY - actual[1, ] 0.3949256 + expected[1, ] 0.3099378 - actual[2, ] 0.4137077 + expected[2, ] 0.3779174 - actual[3, ] 0.3931166 + expected[3, ] 0.3044411 `actual$correctY`: 0.39 0.41 0.39 `expected$correctY`: 0.31 0.38 0.30 [ FAIL 1 | WARN 9 | SKIP 0 | PASS 42 ] Error: Test failures Execution halted Package: logrx Check: tests New result: ERROR Running ‘testthat.R’ [26s/25s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(logrx) > > test_check("logrx") [1] "hello logrx" hello logrx this is outputhello logrx this is outputhello logrx this is outputhello logrx this is output processing file: ex1.Rmd [1] "print" output file: ex1.knit.md /usr/bin/pandoc +RTS -K512m -RTS ex1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output ex1.html --lua-filter /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /home/hornik/tmp/scratch/RtmpWxgwx2/rmarkdown-str2e80604ea3bc2c.html Output created: ex1.html Warning in for (i in 1L:d2) { : closing unused connection 4 (/home/hornik/tmp/scratch/RtmpWxgwx2/log_out_nested.Rds) processing file: ref/ex1.Rmd output file: /home/hornik/tmp/scratch/RtmpWxgwx2/file2e8060195c91ba.R Rows: 3 Columns: 2 $ cyl 4, 6, 8 $ mean 26.66364, 19.74286, 15.10000 [1] "hello logrx" Error: ref/ex4.R:5:0: unexpected end of input 3: 4: print("hello logrx" ^ [1] 1 [1] 1 processing file: ref/ex1.Rmd output file: /home/hornik/tmp/scratch/RtmpWxgwx2/file2e806075b60b01.R [1] "print" [1] "log print" [1] "log print 2" log catlog cat 2log inform log inform 2 log message log message 2 Error: log error Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not [1] "hello logrx" hello logrx this is outputhello again logrx this is outputhello logrx this is output[1] "log print" [1] "log print 2" log catlog cat 2log inform log inform 2 log message log message 2 Error: log error [1] "log print" [1] "log print 2" log catlog cat 2log inform log inform 2 log message log message 2 Error: log error [1] 1 [1] 1 [ FAIL 2 | WARN 9 | SKIP 0 | PASS 113 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get.R:191:4'): library lint returns expected result when multiple linters are set ── write_lint_results() (`actual`) not identical to `expected` (`expected`). lines(actual)[1:6] vs lines(expected)[1:6] "Line 6 [library_call_linter] Move all library calls to the top of the script." "" - "Line 8 [undesirable_operator_linter] Avoid undesirable operator `<<-`. It" + "Line 8 [undesirable_operator_linter] Operator `<<-` is undesirable. It" "assigns outside the current environment in a way that can be hard to reason" "about. Prefer fully-encapsulated functions wherever possible, or, if" "necessary, assign to a specific environment with assign(). Recall that you" ── Failure ('test-writer.R:196:4'): write_lint_results will return a formatted lint results element ── write_lint_results() (`actual`) not identical to paste0(...) (`expected`). lines(actual)[1:10] vs lines(expected)[1:10] - "Line 3 [undesirable_operator_linter] Avoid undesirable operator `<<-`. It" + "Line 3 [undesirable_operator_linter] Operator `<<-` is undesirable. It" "assigns outside the current environment in a way that can be hard to reason" "about. Prefer fully-encapsulated functions wherever possible, or, if" "necessary, assign to a specific environment with assign(). Recall that you" "can create an environment at the desired scope with new.env()." "" - "Line 4 [undesirable_operator_linter] Avoid undesirable operator `<<-`. It" + "Line 4 [undesirable_operator_linter] Operator `<<-` is undesirable. It" "assigns outside the current environment in a way that can be hard to reason" "about. Prefer fully-encapsulated functions wherever possible, or, if" "necessary, assign to a specific environment with assign(). Recall that you" [ FAIL 2 | WARN 9 | SKIP 0 | PASS 113 ] Error: Test failures Execution halted Package: shiny.info Check: tests New result: ERROR Running ‘testthat.R’ [1s/1s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(shiny.info) > > test_check("shiny.info") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-lintr.R:1:1'): (code run outside of `test_that()`) ───────────── Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead. Backtrace: ▆ 1. └─lintr::with_defaults(...) at test-lintr.R:1:1 2. └─lintr:::lintr_deprecated(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ] Error: Test failures Execution halted