Check results for 'pema'

using R version 4.4.1 (2024-06-14)
using platform: aarch64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.4
using session charset: UTF-8
checking for file ‘pema/DESCRIPTION’ ... OK
this is package ‘pema’ version ‘0.1.3’
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 ‘pema’ can be installed ... [238s/238s] OK See the install log for details.
used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
used SDK: ‘MacOSX11.3.sdk’
checking C++ specification ... OK Not all R platforms support C++17
checking installed package size ... NOTE installed size is 151.6Mb sub-directories of 1Mb or more: libs 150.6Mb
checking package directory ... OK
checking ‘build’ 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 ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
checking loading without being on the library search path ... [2s/2s] OK
checking whether startup messages can be suppressed ... [1s/1s] 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 contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [0s/0s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking line endings in shell scripts ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking line endings in Makefiles ... OK
checking compilation flags in Makevars ... OK
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
checking use of PKG_*FLAGS in Makefiles ... OK
checking compiled code ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [2s/1s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [16s/16s] ERROR Running ‘testthat.R’ [16s/16s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(pema) > > test_check("pema") SAMPLING FOR MODEL 'lasso_MA' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 6.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.66 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 10 [ 10%] (Warmup) Chain 1: Iteration: 2 / 10 [ 20%] (Warmup) Chain 1: Iteration: 3 / 10 [ 30%] (Warmup) Chain 1: Iteration: 4 / 10 [ 40%] (Warmup) Chain 1: Iteration: 5 / 10 [ 50%] (Warmup) Chain 1: Iteration: 6 / 10 [ 60%] (Sampling) Chain 1: Iteration: 7 / 10 [ 70%] (Sampling) Chain 1: Iteration: 8 / 10 [ 80%] (Sampling) Chain 1: Iteration: 9 / 10 [ 90%] (Sampling) Chain 1: Iteration: 10 / 10 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 0.011 seconds (Warm-up) Chain 1: 0 seconds (Sampling) Chain 1: 0.011 seconds (Total) Chain 1: SAMPLING FOR MODEL 'lasso_MA' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 3.6e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.36 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 10 [ 10%] (Warmup) Chain 2: Iteration: 2 / 10 [ 20%] (Warmup) Chain 2: Iteration: 3 / 10 [ 30%] (Warmup) Chain 2: Iteration: 4 / 10 [ 40%] (Warmup) Chain 2: Iteration: 5 / 10 [ 50%] (Warmup) Chain 2: Iteration: 6 / 10 [ 60%] (Sampling) Chain 2: Iteration: 7 / 10 [ 70%] (Sampling) Chain 2: Iteration: 8 / 10 [ 80%] (Sampling) Chain 2: Iteration: 9 / 10 [ 90%] (Sampling) Chain 2: Iteration: 10 / 10 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 0.013 seconds (Warm-up) Chain 2: 0 seconds (Sampling) Chain 2: 0.013 seconds (Total) Chain 2: SAMPLING FOR MODEL 'lasso_MA' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 3.5e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: WARNING: No variance estimation is Chain 3: performed for num_warmup < 20 Chain 3: Chain 3: Iteration: 1 / 10 [ 10%] (Warmup) Chain 3: Iteration: 2 / 10 [ 20%] (Warmup) Chain 3: Iteration: 3 / 10 [ 30%] (Warmup) Chain 3: Iteration: 4 / 10 [ 40%] (Warmup) Chain 3: Iteration: 5 / 10 [ 50%] (Warmup) Chain 3: Iteration: 6 / 10 [ 60%] (Sampling) Chain 3: Iteration: 7 / 10 [ 70%] (Sampling) Chain 3: Iteration: 8 / 10 [ 80%] (Sampling) Chain 3: Iteration: 9 / 10 [ 90%] (Sampling) Chain 3: Iteration: 10 / 10 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 0.013 seconds (Warm-up) Chain 3: 0 seconds (Sampling) Chain 3: 0.013 seconds (Total) Chain 3: SAMPLING FOR MODEL 'lasso_MA' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 3.5e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds. Chain 4: Adjust your expectations accordingly! Chain 4: Chain 4: Chain 4: WARNING: No variance estimation is Chain 4: performed for num_warmup < 20 Chain 4: Chain 4: Iteration: 1 / 10 [ 10%] (Warmup) Chain 4: Iteration: 2 / 10 [ 20%] (Warmup) Chain 4: Iteration: 3 / 10 [ 30%] (Warmup) Chain 4: Iteration: 4 / 10 [ 40%] (Warmup) Chain 4: Iteration: 5 / 10 [ 50%] (Warmup) Chain 4: Iteration: 6 / 10 [ 60%] (Sampling) Chain 4: Iteration: 7 / 10 [ 70%] (Sampling) Chain 4: Iteration: 8 / 10 [ 80%] (Sampling) Chain 4: Iteration: 9 / 10 [ 90%] (Sampling) Chain 4: Iteration: 10 / 10 [100%] (Sampling) Chain 4: Chain 4: Elapsed Time: 0.016 seconds (Warm-up) Chain 4: 0 seconds (Sampling) Chain 4: 0.016 seconds (Total) Chain 4: [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-multiple_imp.R:8:1'): (code run outside of `test_that()`) ────── Error: package or namespace load failed for 'mice' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'pan' Backtrace: ▆ 1. └─base::library(mice) at test-multiple_imp.R:8:1 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ] Error: Test failures Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [5s/5s] OK
checking PDF version of manual ... [2s/2s] OK
DONE Status: 1 ERROR, 2 NOTEs
using check arguments '--no-clean-on-error '