Package check result: OK Changes to worse in reverse depends: Package: gRain Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘grain.rmd’ using knitr ** Processing: figures/grain-chest-LS-1.png 360x216 pixels, 3x8 bits/pixel, RGB Input IDAT size = 14022 bytes Input file size = 14112 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11016 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11016 Output IDAT size = 11016 bytes (3006 bytes decrease) Output file size = 11094 bytes (3018 bytes = 21.39% decrease) ** Processing: figures/grain-unnamed-chunk-35-1.png 360x216 pixels, 3x8 bits/pixel, RGB Input IDAT size = 9956 bytes Input file size = 10046 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8281 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8281 Output IDAT size = 8281 bytes (1675 bytes decrease) Output file size = 8359 bytes (1687 bytes = 16.79% decrease) ** Processing: figures/grain-unnamed-chunk-36-1.png 360x216 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10887 bytes Input file size = 10977 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8997 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8997 Output IDAT size = 8997 bytes (1890 bytes decrease) Output file size = 9075 bytes (1902 bytes = 17.33% decrease) ** Processing: figures/grain-unnamed-chunk-39-1.png 360x216 pixels, 3x8 bits/pixel, RGB Input IDAT size = 4877 bytes Input file size = 4955 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3755 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3755 Output IDAT size = 3755 bytes (1122 bytes decrease) Output file size = 3833 bytes (1122 bytes = 22.64% decrease) Quitting from lines 751-764 [unnamed-chunk-52] (grain.rmd) Error: processing vignette 'grain.rmd' failed with diagnostics: could not find function "setdiffPrim" --- failed re-building ‘grain.rmd’ SUMMARY: processing the following file failed: ‘grain.rmd’ Error: Vignette re-building failed. Execution halted Package: gRc Check: examples New result: ERROR Running examples in ‘gRc-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: add1-drop1 > ### Title: Add or drop colour classes to RCOX models > ### Aliases: add1-drop1 evalInECC evalOutECC add1.rcox drop1.rcox > ### Keywords: htest > > ### ** Examples > > > data(math) > gc.sat <- ~me:ve:al:st:an > gc.1 <- ~me+ve+al+st+an > > m.sat <- rcox(gm=gc.sat, data=math) Error in unlistPrim(lapply(gmN, length)) : could not find function "unlistPrim" Calls: rcox -> .buildStandardRepresentation Execution halted Package: gRc Check: R code for possible problems New result: NOTE .buildStandardRepresentation: no visible global function definition for ‘unlistPrim’ .buildStandardRepresentation: no visible global function definition for ‘uniquePrim’ fitNR2: no visible global function definition for ‘uniquePrim’ fitNR2: no visible global function definition for ‘setdiffPrim’ scoring: no visible global function definition for ‘unlistPrim’ update.rcox: no visible global function definition for ‘unlistPrim’ Undefined global functions or variables: setdiffPrim uniquePrim unlistPrim Package: gRim Check: examples New result: ERROR Running examples in ‘gRim-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: citest-array > ### Title: Test for conditional independence in a contingency table > ### Aliases: citest-array ciTest_table > ### Keywords: htest > > ### ** Examples > > > data(lizard) > > ## lizard is has named dimnames > names( dimnames( lizard )) [1] "diam" "height" "species" > ## checked with > is.named.array( lizard ) [1] TRUE > > ## Testing for conditional independence: > # the following are all equivalent: > ciTest(lizard, set=~diam + height + species) Testing diam _|_ height | species Statistic (DEV): 2.026 df: 2 p-value: 0.3632 method: CHISQ Slice information: statistic p.value df species 1 0.178 0.6731 1 anoli 2 1.848 0.1741 1 dist > # ciTest(lizard, set=c("diam", "height", "species")) > # ciTest(lizard, set=1:3) > # ciTest(lizard) > # (The latter because the names in lizard are as given above.) > > ## Testing for marginal independence > ciTest(lizard, set=~diam + height) Testing diam _|_ height Statistic (DEV): 0.608 df: 1 p-value: 0.4357 method: CHISQ > ciTest(lizard, set=1:2) Testing diam _|_ height Statistic (DEV): 0.608 df: 1 p-value: 0.4357 method: CHISQ > > ## Getting slice information: > ciTest(lizard, set=c("diam", "height", "species"), slice.info=TRUE)$slice statistic p.value df species 1 0.1779795 0.6731154 1 anoli 2 1.8476671 0.1740550 1 dist > > ## Do Monte Carlo test instead of usual likelihood ratio test. Different > # options: > > # 1) Do B*10 simulations divided equally over each slice: > ciTest(lizard, set=c("diam", "height", "species"), method="mc", B=400) Error in outerPrim(r.sum, c.sum) : could not find function "outerPrim" Calls: ciTest ... ciTest.table -> ciTest_table -> .CI_SMC_prim -> .CI_MC_prim Execution halted Package: gRim Check: R code for possible problems New result: NOTE .CI_MC_prim: no visible global function definition for ‘outerPrim’ .add.edge_glist: no visible global function definition for ‘intersectPrim’ .aedge_glist: no visible global function definition for ‘intersectPrim’ .dim_loglin: no visible global function definition for ‘unlistPrim’ .loglinDim: no visible global function definition for ‘unlistPrim’ .test_in_one_clique: no visible global function definition for ‘setdiffPrim’ Undefined global functions or variables: intersectPrim outerPrim setdiffPrim unlistPrim Package: gRim Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘grim.rmd’ using knitr ** Processing: figure/unnamed-chunk-8-1.png 504x504 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12011 bytes Input file size = 12101 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10549 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10549 Output IDAT size = 10549 bytes (1462 bytes decrease) Output file size = 10627 bytes (1474 bytes = 12.18% decrease) ** Processing: figure/unnamed-chunk-10-1.png 504x504 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11934 bytes Input file size = 12024 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9478 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9478 Output IDAT size = 9478 bytes (2456 bytes decrease) Output file size = 9556 bytes (2468 bytes = 20.53% decrease) Quitting from lines 197-200 [unnamed-chunk-11] (grim.rmd) Error: processing vignette 'grim.rmd' failed with diagnostics: could not find function "unlistPrim" --- failed re-building ‘grim.rmd’ SUMMARY: processing the following file failed: ‘grim.rmd’ Error: Vignette re-building failed. Execution halted Package: gRim Check: tests New result: ERROR Running ‘testhat.R’ [2s/2s] Running the tests in ‘tests/testhat.R’ failed. Complete output: > library(testthat) > > if (T){ + library(gRim) + test_check("gRim") + } Loading required package: gRain Loading required package: gRbase [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-misc.R:24:5'): dmod() ────────────────────────────────────────── Error in `setdiffPrim(hostcq, edge)`: could not find function "setdiffPrim" Backtrace: ▆ 1. └─gRim::forward(m1, criterion = "test", details = detail, type = "decomposable") at test-misc.R:24:5 2. └─gRim:::.test_out_edges(...) 3. ├─gRim::testadd(object, uv, k = k, amat = amat, ...) 4. └─gRim:::testadd.iModel(object, uv, k = k, amat = amat, ...) 5. └─gRim:::.test_in_one_clique(object, edge, hostcq, details) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted