MidnightBSD Magus

math/R-cran-SQUAREM

Squared Extrapolation Methods for Accelerating EM-Like Algorithms

License Permissions: dist-mirror dist-sell pkg-mirror pkg-sell auto-accept

Events

Build Log

===>  Testing for R-cran-SQUAREM-2026.1
* using log directory '/magus/work/usr/mports/math/R-cran-SQUAREM/work/SQUAREM.Rcheck'
* using R version 4.4.0 (2024-04-24)
* using platform: amd64-portbld-midnightbsd4.0
* R was compiled by
    MidnightBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)
    GNU Fortran (MidnightBSD Ports Collection) 14.2.0
* running under: MidnightBSD m4064 4.0.5 MidnightBSD 4.0.5 stable/4.0-n13794-ebf9c891ff GENERIC amd64
* using session charset: ASCII
* using options '--no-manual --no-build-vignettes'
* checking for file 'SQUAREM/DESCRIPTION' ... OK
* this is package 'SQUAREM' version '2026.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'setRNG', 'interval'
* 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 'SQUAREM' can be installed ... OK
* 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 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'SQUAREM-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fpiter
> ### Title: Fixed-Point Iteration Scheme
> ### Aliases: fpiter
> 
> ### ** Examples
> 
> 
> ##############################################################################
> # Example 1:  EM algorithm for Poisson mixture estimation 
> poissmix.em <- function(p,y) {
+ # The fixed point mapping giving a single E and M step of the EM algorithm
+ # 
+ pnew <- rep(NA,3)
+ i <- 0:(length(y)-1)
+ zi <- p[1]*exp(-p[2])*p[2]^i / (p[1]*exp(-p[2])*p[2]^i + (1 - p[1])*exp(-p[3])*p[3]^i)
+ pnew[1] <- sum(y*zi)/sum(y)
+ pnew[2] <- sum(y*i*zi)/sum(y*zi)
+ pnew[3] <- sum(y*i*(1-zi))/sum(y*(1-zi))
+ p <- pnew
+ return(pnew)
+ }
> 
> poissmix.loglik <- function(p,y) {
+ # Objective function whose local minimum is a fixed point \
+ # negative log-likelihood of binary poisson mixture
+ i <- 0:(length(y)-1)
+ loglik <- y*log(p[1]*exp(-p[2])*p[2]^i/exp(lgamma(i+1)) + 
+ 		(1 - p[1])*exp(-p[3])*p[3]^i/exp(lgamma(i+1)))
+ return ( -sum(loglik) )
+ }
> 
> # Real data from Hasselblad (JASA 1969)
> poissmix.dat <- data.frame(death=0:9, freq=c(162,267,271,185,111,61,27,8,3,1))
> y <- poissmix.dat$freq
> tol <- 1.e-08
> 
> # Use a preset seed so the example is reproducible. 
> require("setRNG")
Loading required package: setRNG
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'setRNG'
> old.seed <- setRNG(list(kind="Mersenne-Twister", normal.kind="Inversion",
+     seed=54321))
Error in setRNG(list(kind = "Mersenne-Twister", normal.kind = "Inversion",  : 
  could not find function "setRNG"
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'Hasselblad1969.R'
 ERROR
Running the tests in 'tests/Hasselblad1969.R' failed.
Last 13 lines of output:
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'setRNG'
  > 
  > # data for Poisson mixture estimation  from Hasselblad (JASA 1969)
  > poissmix.dat <- data.frame(death=0:9, freq=c(162,267,271,185,111,61,27,8,3,1))
  > 
  > y <- poissmix.dat$freq
  > tol <- 1.e-08
  > 
  > # generate a random initial guess for 3 parameters
  > setRNG(list(kind="Wichmann-Hill", normal.kind="Box-Muller", seed=123))
  Error in setRNG(list(kind = "Wichmann-Hill", normal.kind = "Box-Muller",  : 
    could not find function "setRNG"
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ...
  'SQUAREM.Rnw' using 'UTF-8'... failed
 WARNING
Errors in running code in vignettes:
when running code in 'SQUAREM.Rnw'
  ...
Loading required package: setRNG
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'setRNG'

> setRNG(list(kind = "Wichmann-Hill", normal.kind = "Box-Muller", 
+     seed = 123))

  When sourcing 'SQUAREM.R':
Error: could not find function "setRNG"
Execution halted

* checking re-building of vignette outputs ... SKIPPED
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  '/magus/work/usr/mports/math/R-cran-SQUAREM/work/SQUAREM.Rcheck/00check.log'
for details.

*** Error code 1

Stop.
make: stopped in /usr/mports/math/R-cran-SQUAREM