* using log directory 'd:/Rcompile/CRANpkg/local/3.5/nestfs.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'nestfs/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'nestfs' version '1.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'nestfs' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [5s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [11s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [111s] ERROR Running 'testthat.R' [110s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(nestfs) nestfs 1.0: using 10 cores, set 'options(mc.cores)' to change. > options(mc.cores=2) > > test_check("nestfs") -- 1. Failure: linear regression (@test_forward_selection.R#15) --------------- `fs.gauss` not equal to `fs.gauss.ok`. Component "fs": Component "vars": 2 string mismatches Component "fs": Component "fdr": Mean relative difference: 0.5444583 Component "fs": Component "llks": Mean relative difference: 0.001581259 Component "fs": Component "diffs": Mean relative difference: 0.1322846 Component "panel": 2 string mismatches Component "final.model": 1 string mismatch Component "iter1": Component "median.diff.llk": Mean relative difference: 0.1558413 Component "iter1": Component "total.diff.llk": Mean relative difference: 0.01215644 Component "iter1": Component "p.value": Mean relative difference: 0.3316292 ... -- 2. Failure: logistic regression (@test_forward_selection.R#31) ------------- `fs.binom` not equal to `fs.binom.ok`. Component "fs": Component "fdr": Mean relative difference: 0.7318001 Component "fs": Component "llks": Mean relative difference: 0.001776588 Component "fs": Component "diffs": Mean relative difference: 0.01702872 Component "iter1": Component "median.diff.llk": Mean relative difference: 0.1436064 Component "iter1": Component "total.diff.llk": Mean relative difference: 0.01428037 Component "iter1": Component "p.value": Mean relative difference: 0.1796183 Component "all.iter": Component 1: Mean relative difference: 0.0849286 Component "all.iter": Component 2: Mean relative difference: 0.1306687 Component "all.iter": Component 3: Mean relative difference: 0.1403981 -- 3. Failure: init.model (@test_forward_selection.R#43) ---------------------- fs.1$panel not equal to c("ltg", "bmi", "map"). 2/3 mismatches x[1]: "bmi" y[1]: "ltg" x[2]: "ltg" y[2]: "bmi" -- 4. Failure: init.model (@test_forward_selection.R#45) ---------------------- fs.1$final.model not equal to "ltg + bmi + map". 1/1 mismatches x[1]: "bmi + ltg + map" y[1]: "ltg + bmi + map" -- 5. Failure: init.model (@test_forward_selection.R#54) ---------------------- fs.1$panel not equal to c("ltg", "bmi", "map"). 2/3 mismatches x[1]: "bmi" y[1]: "ltg" x[2]: "ltg" y[2]: "bmi" -- 6. Failure: init.model (@test_forward_selection.R#56) ---------------------- fs.1$final.model not equal to "age + sex + ltg + bmi + map + age:sex". 1/1 mismatches x[1]: "age + sex + bmi + ltg + map + age:sex" y[1]: "age + sex + ltg + bmi + map + age:sex" -- 7. Failure: init.model (@test_forward_selection.R#61) ---------------------- summ$llks[1:4] not equal to c(NA, -2137.599696, -2056.442947, -2004.43174). 3/4 mismatches (average diff: 3.4) [2] -2136 - -2138 == 1.317 [3] -2048 - -2056 == 8.569 [4] -2004 - -2004 == 0.327 -- 8. Failure: univariate filter (@test_forward_selection.R#101) -------------- fs.1$fs not equal to fs.binom.ok$fs. Component "fdr": Mean relative difference: 0.7318001 Component "llks": Mean relative difference: 0.001776588 Component "diffs": Mean relative difference: 0.01702872 -- 9. Failure: univariate filter (@test_forward_selection.R#110) -------------- `fs.1` not equal to `fs.2`. Component "iter1": Attributes: < Component "row.names": 2 string mismatches > Component "iter1": Component "median.diff.llk": Mean relative difference: 0.4935447 Component "iter1": Component "total.diff.llk": Mean relative difference: 0.7315167 Component "iter1": Component "p.value": Mean relative difference: 0.03230231 Component "all.iter": Component 1: Attributes: < Component 2: Component 1: 2 string mismatches > Component "all.iter": Component 1: Mean relative difference: 0.01666692 -- 10. Failure: univariate filter (@test_forward_selection.R#111) ------------- fs.1$panel has length 0, not length 3. -- 11. Failure: univariate filter (@test_forward_selection.R#122) ------------- fs.1$fs not equal to fs.binom.ok$fs. Component "fdr": Mean relative difference: 0.7318001 Component "llks": Mean relative difference: 0.001776588 Component "diffs": Mean relative difference: 0.01702872 -- 12. Failure: nested forward selection (@test_nested.R#16) ------------------ `nest.gauss` not equal to `nest.gauss.ok`. Component 1: Component 1: Component 1: 2 string mismatches Component 1: Component 1: Component 2: Mean relative difference: 0.4098394 Component 1: Component 1: Component 3: Mean relative difference: 0.007496924 Component 1: Component 1: Component 4: Mean relative difference: 0.5630382 Component 1: Component 1: Component 6: Mean relative difference: 0.2587268 Component 1: Component 3: 2 string mismatches Component 1: Component 5: 1 string mismatch Component 1: Component 8: Component 1: Mean relative difference: 0.5232936 Component 1: Component 8: Component 2: Mean relative difference: 0.3151259 ... -- 13. Failure: nested forward selection (@test_nested.R#21) ------------------ summ.gauss$rank not equivalent to c(2, 1, 2, 3, 3). Lengths differ: 4 is not 5 -- 14. Failure: nested forward selection (@test_nested.R#22) ------------------ summ.gauss$coefIQR[1] not equivalent to "(28.74, 30.17)". 1/1 mismatches x[1]: "(25.50, 33.48)" y[1]: "(28.74, 30.17)" -- 15. Failure: nested forward selection (@test_nested.R#23) ------------------ summ.gauss$diffLogLikIQR[1] not equivalent to "(24.38, 40.36)". 1/1 mismatches x[1]: "(30.75, 37.11)" y[1]: "(24.38, 40.36)" -- 16. Failure: nested forward selection (@test_nested.R#28) ------------------ rownames(summ.gauss.iter1) not equal to c("bmi", "ltg", "tch", "map", "hdl", "tc", "ldl"). 2/7 mismatches x[4]: "hdl" y[4]: "map" x[5]: "map" y[5]: "hdl" -- 17. Failure: nested forward selection (@test_nested.R#30) ------------------ summ.gauss.iter1$med.pvalue not equivalent to c(0.001, 0.001, 0.004, 0.003, 0.013, 0.213, 0.199). 6/7 mismatches (average diff: 0.032) [1] 0.000 - 0.001 == -0.001 [2] 0.002 - 0.001 == 0.001 [3] 0.007 - 0.004 == 0.003 [5] 0.004 - 0.013 == -0.009 [6] 0.253 - 0.213 == 0.040 [7] 0.337 - 0.199 == 0.138 -- 18. Failure: nested forward selection (@test_nested.R#35) ------------------ `nest.binom` not equal to `nest.binom.ok`. Component 1: Component 1: Component 1: 3 string mismatches Component 1: Component 1: Component 2: Mean relative difference: 0.4198674 Component 1: Component 1: Component 3: Mean relative difference: 0.04518075 Component 1: Component 1: Component 4: Mean relative difference: 0.3275306 Component 1: Component 1: Component 6: Mean relative difference: 1.756273 Component 1: Component 3: 3 string mismatches Component 1: Component 5: 1 string mismatch Component 1: Component 8: Component 1: Mean relative difference: 0.4825096 Component 1: Component 8: Component 2: Mean relative difference: 0.4014058 ... -- 19. Failure: nested forward selection (@test_nested.R#48) ------------------ nest.cat[[1]]$panel not equal to c("bmi.cat"). Lengths differ: 2 is not 1 -- 20. Failure: nested forward selection (@test_nested.R#49) ------------------ is.na(nest.cat[[1]]$fs$coef) not equal to c(TRUE, TRUE). Lengths (3, 2) differ (comparison on first 2 components) -- 21. Failure: nested forward selection (@test_nested.R#52) ------------------ summ.cat$coef not equivalent to c(NA, -15.711). 1/2 mismatches [2] -13.5 - -15.7 == 2.24 -- 22. Failure: nested forward selection (@test_nested.R#53) ------------------ summ.cat$diffLogLik not equivalent to c(25.599, 0.009). 2/2 mismatches (average diff: 0.943) [1] 27.366 - 25.599 == 1.767 [2] 0.128 - 0.009 == 0.119 -- 23. Failure: nested forward selection old interface (@test_nested.R#61) ---- `nest.gauss` not equal to `nest.gauss.ok`. Component 1: Component 1: Component 1: 2 string mismatches Component 1: Component 1: Component 2: Mean relative difference: 0.4098394 Component 1: Component 1: Component 3: Mean relative difference: 0.007496924 Component 1: Component 1: Component 4: Mean relative difference: 0.5630382 Component 1: Component 1: Component 6: Mean relative difference: 0.2587268 Component 1: Component 3: 2 string mismatches Component 1: Component 5: 1 string mismatch Component 1: Component 8: Component 1: Mean relative difference: 0.5232936 Component 1: Component 8: Component 2: Mean relative difference: 0.3151259 ... -- 24. Failure: nested forward selection old interface (@test_nested.R#66) ---- summ.gauss$rank not equivalent to c(2, 1, 2, 3, 3). Lengths differ: 4 is not 5 -- 25. Failure: nested forward selection old interface (@test_nested.R#67) ---- summ.gauss$coefIQR[1] not equivalent to "(28.74, 30.17)". 1/1 mismatches x[1]: "(25.50, 33.48)" y[1]: "(28.74, 30.17)" -- 26. Failure: nested forward selection old interface (@test_nested.R#68) ---- summ.gauss$diffLogLikIQR[1] not equivalent to "(24.38, 40.36)". 1/1 mismatches x[1]: "(30.75, 37.11)" y[1]: "(24.38, 40.36)" -- 27. Failure: nested forward selection old interface (@test_nested.R#73) ---- rownames(summ.gauss.iter1) not equal to c("bmi", "ltg", "tch", "map", "hdl", "tc", "ldl"). 2/7 mismatches x[4]: "hdl" y[4]: "map" x[5]: "map" y[5]: "hdl" -- 28. Failure: nested forward selection old interface (@test_nested.R#75) ---- summ.gauss.iter1$med.pvalue not equivalent to c(0.001, 0.001, 0.004, 0.003, 0.013, 0.213, 0.199). 6/7 mismatches (average diff: 0.032) [1] 0.000 - 0.001 == -0.001 [2] 0.002 - 0.001 == 0.001 [3] 0.007 - 0.004 == 0.003 [5] 0.004 - 0.013 == -0.009 [6] 0.253 - 0.213 == 0.040 [7] 0.337 - 0.199 == 0.138 -- 29. Failure: nested forward selection old interface (@test_nested.R#81) ---- `nest.binom` not equal to `nest.binom.ok`. Component 1: Component 1: Component 1: 3 string mismatches Component 1: Component 1: Component 2: Mean relative difference: 0.4198674 Component 1: Component 1: Component 3: Mean relative difference: 0.04518075 Component 1: Component 1: Component 4: Mean relative difference: 0.3275306 Component 1: Component 1: Component 6: Mean relative difference: 1.756273 Component 1: Component 3: 3 string mismatches Component 1: Component 5: 1 string mismatch Component 1: Component 8: Component 1: Mean relative difference: 0.4825096 Component 1: Component 8: Component 2: Mean relative difference: 0.4014058 ... -- 30. Failure: nested forward selection old interface (@test_nested.R#96) ---- nest.cat[[1]]$panel not equal to c("bmi.cat"). Lengths differ: 2 is not 1 -- 31. Failure: nested forward selection old interface (@test_nested.R#97) ---- is.na(nest.cat[[1]]$fs$coef) not equal to c(TRUE, TRUE). Lengths (3, 2) differ (comparison on first 2 components) -- 32. Failure: nested forward selection old interface (@test_nested.R#100) --- summ.cat$coef not equivalent to c(NA, -15.711). 1/2 mismatches [2] -13.5 - -15.7 == 2.24 -- 33. Failure: nested forward selection old interface (@test_nested.R#101) --- summ.cat$diffLogLik not equivalent to c(25.599, 0.009). 2/2 mismatches (average diff: 0.943) [1] 27.366 - 25.599 == 1.767 [2] 0.128 - 0.009 == 0.119 -- 34. Failure: nested.glm (@test_nested.R#110) ------------------------------- `glm.gauss` not equal to `glm.gauss.ok`. Component 1: Component 1: Mean relative difference: 0.1129298 Component 1: Component 3: Names: 207 string mismatches Component 1: Component 3: Mean relative difference: 0.3408638 Component 1: Component 4: Mean relative difference: 0.5631371 Component 1: Component 5: Mean relative difference: 0.01137558 Component 1: Component 6: Mean relative difference: 0.0232809 Component 2: Component 1: Mean relative difference: 0.109113 Component 2: Component 3: Names: 206 string mismatches Component 2: Component 3: Mean relative difference: 0.3468208 ... -- 35. Failure: nested.glm (@test_nested.R#114) ------------------------------- `glm.binom` not equal to `glm.binom.ok`. Component 1: Component 1: Mean relative difference: 0.3823878 Component 1: Component 3: Names: 207 string mismatches Component 1: Component 3: Mean relative difference: 0.5236705 Component 1: Component 4: Mean relative difference: 1.927273 Component 1: Component 5: Mean relative difference: 0.120696 Component 1: Component 6: Mean relative difference: 0.0232809 Component 2: Component 1: Mean relative difference: 0.3970286 Component 2: Component 3: Names: 206 string mismatches Component 2: Component 3: Mean relative difference: 0.6415311 ... -- 36. Failure: nested.glm (@test_nested.R#121) ------------------------------- perf.gauss$performance not equal to 0.62174173. 1/1 mismatches [1] 0.605 - 0.622 == -0.017 -- 37. Failure: nested.glm (@test_nested.R#126) ------------------------------- perf.binom$performance not equal to 0.78288733. 1/1 mismatches [1] 0.776 - 0.783 == -0.00659 == testthat results =========================================================== [ OK: 130 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 37 ] 1. Failure: linear regression (@test_forward_selection.R#15) 2. Failure: logistic regression (@test_forward_selection.R#31) 3. Failure: init.model (@test_forward_selection.R#43) 4. Failure: init.model (@test_forward_selection.R#45) 5. Failure: init.model (@test_forward_selection.R#54) 6. Failure: init.model (@test_forward_selection.R#56) 7. Failure: init.model (@test_forward_selection.R#61) 8. Failure: univariate filter (@test_forward_selection.R#101) 9. Failure: univariate filter (@test_forward_selection.R#110) 1. ... Error: testthat unit tests failed Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR