Check results for 'pkgload'

using R version 4.5.0 beta (2025-03-29 r88069)
using platform: aarch64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.4
using session charset: UTF-8
checking for file ‘pkgload/DESCRIPTION’ ... OK
this is package ‘pkgload’ version ‘1.4.0’
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 executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘pkgload’ can be installed ... [2s/2s] OK See the install log for details.
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 code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [0s/0s] OK
checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
checking whether the package can be unloaded cleanly ... [0s/0s] OK
checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
checking loading without being on the library search path ... [0s/0s] OK
checking whether startup messages can be suppressed ... [0s/0s] 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 ... [3s/3s] OK
checking Rd files ... [0s/0s] 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 examples ... [0s/1s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [103s/147s] ERROR Running ‘testthat.R’ [103s/146s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(pkgload) > > # Needed so that install.packages works correctly > Sys.setenv("R_TESTS" = "") > > test_check("pkgload") Starting 2 test processes [ FAIL 1 | WARN 0 | SKIP 15 | PASS 344 ] ══ Skipped tests (15) ══════════════════════════════════════════════════════════ • "pkgload" %in% dev_packages() is not TRUE (1): 'test-shim.R:126:3' • On CRAN (14): 'test-depend.R:5:3', 'test-depend.R:15:3', 'test-depend.R:43:3', 'test-load-hooks.R:155:3', 'test-load.R:44:3', 'test-namespace.R:140:3', 'test-shim.R:59:3', 'test-shim.R:135:3', 'test-source.R:2:3', 'test-help.R:57:3', 'test-help.R:117:3', 'test-help.R:128:3', 'test-help.R:141:3', 'test-help.R:162:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-help.R:48:3'): shim_question behaves like util::? for searches ── shim_question(`?`(lm)) (`actual`) not identical to utils::`?`(`?`(lm)) (`expected`). attr(actual$matches, 'row.names')[18948:19009] vs attr(expected$matches, 'row.names')[18948:18950] 18948 18949 18950 - 18951 - 18952 - 18953 - 18954 - 18955 - 18956 - 18957 and 52 more ... actual$matches vs expected$matches Topic Title Name ID Package LibPath Type Field Entry actual$matches[4021, ] eight_elman the original SNNS eight elman example, using the RSNNS high-level api (rsnns) eight_elman 4917/86 RSNNS /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RSNNS demo Title the original SNNS eight elman example, using the RSNNS high-level api (rsnns) actual$matches[4022, ] eight_elmanSnnsR the original SNNS eight elman example, using the RSNNS low-level api (SnnsR) eight_elmanSnnsR 4917/87 RSNNS /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RSNNS demo alias eight_elmanSnnsR actual$matches[4023, ] eight_elmanSnnsR the original SNNS eight elman example, using the RSNNS low-level api (SnnsR) eight_elmanSnnsR 4917/87 RSNNS /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RSNNS demo Title the original SNNS eight elman example, using the RSNNS low-level api (SnnsR) - actual$matches[4024, ] LogisticRegressionFast Logistic Regression implementation that uses R's glm LogisticRegressionFast 4920/23 RSSL /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RSSL help Title Logistic Regression implementation that uses R's glm + expected$matches[4024, ] LogisticRegressionFast Logistic Regression implementation that uses R's glm LogisticRegressionFast 4921/23 RSSL /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RSSL help Title Logistic Regression implementation that uses R's glm - actual$matches[4025, ] CalculateLModeCCFI Calculates L-Mode CCFI CalculateLModeCCFI 4952/10 RTaxometrics /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RTaxometrics help alias CalculateLModeCCFI + expected$matches[4025, ] CalculateLModeCCFI Calculates L-Mode CCFI CalculateLModeCCFI 4953/10 RTaxometrics /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RTaxometrics help alias CalculateLModeCCFI - actual$matches[4026, ] EstimateLMode Estimates L-Mode base rate EstimateLMode 4952/26 RTaxometrics /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RTaxometrics help alias EstimateLMode + expected$matches[4026, ] EstimateLMode Estimates L-Mode base rate EstimateLMode 4953/26 RTaxometrics /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RTaxometrics help alias EstimateLMode - actual$matches[4027, ] RunLMode Performs L-Mode RunLMode 4952/37 RTaxometrics /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RTaxometrics help alias RunLMode + expected$matches[4027, ] RunLMode Performs L-Mode RunLMode 4953/37 RTaxometrics /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RTaxometrics help alias RunLMode - actual$matches[4028, ] Anova.clm Anova Tables for Cumulative Link (Mixed) Models Anova.clm 4957/1 RVAideMemoire /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RVAideMemoire help alias Anova.clm + expected$matches[4028, ] Anova.clm Anova Tables for Cumulative Link (Mixed) Models Anova.clm 4958/1 RVAideMemoire /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RVAideMemoire help alias Anova.clm - actual$matches[4029, ] Anova.clm Anova Tables for Cumulative Link (Mixed) Models Anova.clm 4957/1 RVAideMemoire /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RVAideMemoire help alias Anova.clmm + expected$matches[4029, ] Anova.clm Anova Tables for Cumulative Link (Mixed) Models Anova.clm 4958/1 RVAideMemoire /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RVAideMemoire help alias Anova.clmm - actual$matches[4030, ] logis.noise Creating a nls model for logistic regression from fitted values of a glm model logis.noise 4957/66 RVAideMemoire /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RVAideMemoire help Title Creating a nls model for logistic regression from fitted values of a glm model + expected$matches[4030, ] logis.noise Creating a nls model for logistic regression from fitted values of a glm model logis.noise 4958/66 RVAideMemoire /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RVAideMemoire help Title Creating a nls model for logistic regression from fitted values of a glm model and 1491 more ... actual$matches vs expected$matches Topic Title Name ID Package LibPath Type Field Entry actual$matches[11790, ] lmboot-package Bootstrap in Linear Models lmboot-package 13967/4 lmboot /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lmboot help alias lmboot actual$matches[11791, ] lmds Landmark MDS lmds 13968/2 lmds /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lmds help alias lmds actual$matches[11792, ] lmds Landmark MDS lmds 13968/2 lmds /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lmds help alias lmds-package - actual$matches[11793, ] confint.merMod Compute Confidence Intervals for Parameters of a [ng]lmer Fit confint.merMod 13969/17 lme4 /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4 help Title Compute Confidence Intervals for Parameters of a [ng]lmer Fit + expected$matches[11793, ] getMME Build the mixed model equations from a lmebreed object getMME 13969/27 lme4breeding /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4breeding help Title Build the mixed model equations from a lmebreed object - actual$matches[11794, ] glmFamily-class Class '"glmFamily"' - a reference class for 'family' glmFamily-class 13969/29 lme4 /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4 help alias glmFamily-class + expected$matches[11794, ] lme4breeding *L*inear *m*ixed *e*quations *4* *B*reeding lme4breeding-package 13969/30 lme4breeding /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4breeding help alias lme4breeding - actual$matches[11795, ] glmFamily-class Class '"glmFamily"' - a reference class for 'family' glmFamily-class 13969/29 lme4 /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4 help Title Class '"glmFamily"' - a reference class for 'family' + expected$matches[11795, ] lmebreed-class Relationship-based mixed-effects model fits lmebreed-class 13969/31 lme4breeding /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4breeding help alias lmebreed-class - actual$matches[11796, ] glmFamily Generator object for the 'glmFamily' class glmFamily 13969/30 lme4 /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4 help alias glmFamily + expected$matches[11796, ] lmebreed-class Relationship-based mixed-effects model fits lmebreed-class 13969/31 lme4breeding /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4breeding help alias fitted,lmebreed-method - actual$matches[11797, ] glmFamily Generator object for the 'glmFamily' class glmFamily 13969/30 lme4 /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4 help Title Generator object for the 'glmFamily' class + expected$matches[11797, ] lmebreed-class Relationship-based mixed-effects model fits lmebreed-class 13969/31 lme4breeding /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4breeding help alias ranef,lmebreed-method - actual$matches[11798, ] glmer Fitting Generalized Linear Mixed-Effects Models glmer 13969/31 lme4 /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4 help alias glmer + expected$matches[11798, ] lmebreed-class Relationship-based mixed-effects model fits lmebreed-class 13969/31 lme4breeding /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4breeding help alias residuals,lmebreed-method - actual$matches[11799, ] glmer Fitting Generalized Linear Mixed-Effects Models glmer 13969/31 lme4 /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4 help concept GLMM + expected$matches[11799, ] lmebreed Fit mixed-effects models incorporating relationships lmebreed 13969/32 lme4breeding /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4breeding help alias lmebreed and 7210 more ... actual$matches$Topic | expected$matches$Topic [11790] "lmboot-package" | "lmboot-package" [11790] [11791] "lmds" | "lmds" [11791] [11792] "lmds" | "lmds" [11792] [11793] "confint.merMod" - [11794] "glmFamily-class" - [11795] "glmFamily-class" - [11796] "glmFamily" - [11797] "glmFamily" - [11798] "glmer" - [11799] "glmer" - ... ... ... and 55 more ... actual$matches$Title[11790:11854] vs expected$matches$Title[11790:11795] "Bootstrap in Linear Models" "Landmark MDS" "Landmark MDS" - "Compute Confidence Intervals for Parameters of a [ng]lmer Fit" - "Class '\"glmFamily\"' - a reference class for 'family'" - "Class '\"glmFamily\"' - a reference class for 'family'" - "Generator object for the 'glmFamily' class" - "Generator object for the 'glmFamily' class" - "Fitting Generalized Linear Mixed-Effects Models" - "Fitting Generalized Linear Mixed-Effects Models" and 55 more ... actual$matches$Name | expected$matches$Name [11790] "lmboot-package" | "lmboot-package" [11790] [11791] "lmds" | "lmds" [11791] [11792] "lmds" | "lmds" [11792] [11793] "confint.merMod" - [11794] "glmFamily-class" - [11795] "glmFamily-class" - [11796] "glmFamily" - [11797] "glmFamily" - [11798] "glmer" - [11799] "glmer" - ... ... ... and 55 more ... actual$matches$ID | expected$matches$ID [4021] "4917/86" | "4917/86" [4021] [4022] "4917/87" | "4917/87" [4022] [4023] "4917/87" | "4917/87" [4023] [4024] "4920/23" - "4921/23" [4024] [4025] "4952/10" - "4953/10" [4025] [4026] "4952/26" - "4953/26" [4026] [4027] "4952/37" - "4953/37" [4027] [4028] "4957/1" - "4958/1" [4028] [4029] "4957/1" - "4958/1" [4029] [4030] "4957/66" - "4958/66" [4030] ... ... ... and 1491 more ... actual$matches$ID | expected$matches$ID [11790] "13967/4" | "13967/4" [11790] [11791] "13968/2" | "13968/2" [11791] [11792] "13968/2" | "13968/2" [11792] [11793] "13969/17" - "13969/27" [11793] [11794] "13969/29" - "13969/30" [11794] [11795] "13969/29" - "13969/31" [11795] [11796] "13969/30" - "13969/31" [11796] [11797] "13969/30" - "13969/31" [11797] [11798] "13969/31" | "13969/31" [11798] [11799] "13969/31" - "13969/32" [11799] ... ... ... and 7210 more ... actual$matches$Package | expected$matches$Package [11790] "lmboot" | "lmboot" [11790] [11791] "lmds" | "lmds" [11791] [11792] "lmds" | "lmds" [11792] [11793] "lme4" - [11794] "lme4" - [11795] "lme4" - [11796] "lme4" - [11797] "lme4" - [11798] "lme4" - [11799] "lme4" - ... ... ... and 55 more ... actual$matches$LibPath[11790:11854] vs expected$matches$LibPath[11790:11795] "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lmboot" "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lmds" "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lmds" - "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4" - "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4" - "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4" - "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4" - "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4" - "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4" - "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/lme4" and 55 more ... actual$matches$Type | expected$matches$Type [11797] "help" | "help" [11797] [11798] "help" | "help" [11798] [11799] "help" | "help" [11799] [11800] "help" - [11801] "help" - [11802] "help" - [11803] "help" - [11804] "help" - [11805] "help" - [11806] "help" - ... ... ... and 55 more ... actual$matches$Field | expected$matches$Field [11792] "alias" | "alias" [11792] [11793] "Title" | "Title" [11793] [11794] "alias" | "alias" [11794] [11795] "Title" - [11796] "alias" - [11797] "Title" - [11798] "alias" - [11799] "concept" - [11800] "alias" | "alias" [11795] [11801] "concept" - ... ... ... and 56 more ... actual$matches$Field | expected$matches$Field [11861] "alias" | "alias" [11820] [11862] "Title" | "Title" [11821] [11863] "alias" | "alias" [11822] [11864] "Title" - [11865] "alias" | "alias" [11823] [11866] "Title" - [11867] "Title" - [11868] "alias" | "alias" [11824] [11869] "alias" | "alias" [11825] [11870] "alias" | "alias" [11826] ... ... ... and 20 more ... actual$matches$Entry[11790:11854] vs expected$matches$Entry[11790:11795] "lmboot" "lmds" "lmds-package" - "Compute Confidence Intervals for Parameters of a [ng]lmer Fit" - "glmFamily-class" - "Class '\"glmFamily\"' - a reference class for 'family'" - "glmFamily" - "Generator object for the 'glmFamily' class" - "glmer" - "GLMM" and 55 more ... [ FAIL 1 | WARN 0 | SKIP 15 | PASS 344 ] Error: Test failures Execution halted
checking PDF version of manual ... [4s/5s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '