* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/KFAS.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘KFAS/DESCRIPTION’ ... OK
* this is package ‘KFAS’ version ‘1.5.1’
* 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 ‘KFAS’ can be installed ... [42s/81s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/KFAS-00install.html' for details.
* used C compiler: ‘clang version 20.1.0-rc3’
* used Fortran compiler: ‘flang version 20.1.0-rc3’
* checking installed package size ... OK
* 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 ... 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 whether startup messages can be suppressed ... 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 ... [32s/57s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking usage of KIND in Fortran files ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/31s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [30s/59s] ERROR
Running ‘test-all.R’ [30s/58s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("KFAS")
Loading required package: KFAS
Please cite KFAS in publications by using:
Jouni Helske (2017). KFAS: Exponential Family State Space Models in R. Journal of Statistical Software, 78(10), 1-39. doi:10.18637/jss.v078.i10.
Call:
SSModel(formula = t12 ~ SSMcycle(period = 10, type = "common",
Q = 2) + SSMcycle(period = 10, type = "distinct", P1 = diag(c(1,
1, 2, 2)), Q = diag(1:2)) + SSMtrend(2, type = "common",
Q = diag(c(1, 0.5))) + SSMtrend(2, type = "distinct", Q = list(diag(0.1,
2), diag(0.01, 2)), P1 = diag(c(0.1, 0.01, 0.1, 0.01))) +
SSMseasonal(period = 4, type = "common") + SSMseasonal(period = 4,
type = "distinct", Q = diag(c(2, 3)), P1 = diag(c(2, 2, 2,
3, 3, 3))) + SSMseasonal(period = 5, type = "common",
sea.type = "trig") + SSMseasonal(period = 5, type = "distinct",
sea.type = "trig", Q = diag(c(0.1, 0.2)), P1 = diag(rep(c(0.1,
0.2), each = 4))) + SSMarima(ar = 0.9, ma = 0.2) + SSMregression(~-1 +
x, index = 1, Q = 1, data = d))
State space model object of class SSModel
Dimensions:
[1] Number of time points: 100
[1] Number of time series: 2
[1] Number of disturbances: 25
[1] Number of states: 38
Names of the states:
[1] x.t1 level slope level.t1 slope.t1
[6] level.t2 slope.t2 sea_dummy1 sea_dummy2 sea_dummy3
[11] sea_dummy1.t1 sea_dummy2.t1 sea_dummy3.t1 sea_dummy1.t2 sea_dummy2.t2
[16] sea_dummy3.t2 sea_trig1 sea_trig*1 sea_trig2 sea_trig*2
[21] sea_trig1.t1 sea_trig*1.t1 sea_trig2.t1 sea_trig*2.t1 sea_trig1.t2
[26] sea_trig*1.t2 sea_trig2.t2 sea_trig*2.t2 cycle cycle*
[31] cycle.t1 cycle*.t1 cycle.t2 cycle*.t2 arima1.t1
[36] arima2.t1 arima1.t2 arima2.t2
Distributions of the time series:
[1] gaussian
Object is a valid object of class SSModel.[ FAIL 1 | WARN 3 | SKIP 0 | PASS 574 ]
â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
── Failure ('testLMM.R:32:3'): lmms works properly ─────────────────────────────
logLik(fit_lmm$model) not equivalent to unclass(logLik(fm1)).
1/1 mismatches
[1] -872 - -Inf == Inf
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 574 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [67s/138s] OK
* checking PDF version of manual ... [9s/13s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR