* using log directory ‘/srv/hornik/tmp/CRAN/runMCMCbtadjust.Rcheck’ * using R Under development (unstable) (2024-05-27 r86634) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘runMCMCbtadjust/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘runMCMCbtadjust’ version ‘1.1.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] Note_to_CRAN_maintainers Maintainer: ‘Frédéric Gosselin ’ * 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 serialization versions ... OK * checking whether package ‘runMCMCbtadjust’ can be installed ... [4s/4s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [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 use of S3 registration ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘nimble’ ‘nimbleAPT’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [7s/7s] OK * checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [4s/4s] OK Running ‘testthat.R’ [4s/4s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [9m/14m] ERROR Error(s) in re-building vignettes: ... --- re-building ‘runMCMCbtadjust_Nimble_variations.Rmd’ using knitr ** Processing: figure/Analysis of correlations - bis-1.png 504x504 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 14088 bytes Input file size = 14958 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12984 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 12803 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 = 1 f = 0 IDAT size = 12803 Output IDAT size = 12803 bytes (1285 bytes decrease) Output file size = 12881 bytes (2077 bytes = 13.89% decrease) ** Processing: figure/Analysis of correlations - traceplot-1.png 504x504 pixels, 3x8 bits/pixel, RGB Input IDAT size = 57906 bytes Input file size = 58068 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 57686 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 IDAT size = 54400 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 = 5 IDAT size = 54400 Output IDAT size = 54400 bytes (3506 bytes decrease) Output file size = 54478 bytes (3590 bytes = 6.18% decrease) ** Processing: figure/Nimble second run, with RW_block - traceplot-1.png 504x504 pixels, 3x8 bits/pixel, RGB Input IDAT size = 46185 bytes Input file size = 46323 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41180 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 = 41180 Output IDAT size = 41180 bytes (5005 bytes decrease) Output file size = 41258 bytes (5065 bytes = 10.93% decrease) # Hamiltonian Monte Carlo sampler We will in the sequel try two other possibilities provided by Nimble. The first one is to use an Hamiltonian approach - similar in principle to the one provided by `STAN` - which is a priori well suited to such badly behaving cases. This will require rather numerous steps to do so. First, this will require the loading of the new `nimbleHMC` library as well as modifications of `nimbleOptions` in the component `parallelizeInitExpr` of parameter `control.MCMC`; this is done in what follows in the variable `newParallelizeInitExpr`. Second, we need to refer to the HMC sampler in the `confModel.expression.toadd` component. Third, we need to turn to TRUE the `buildDerivs` component of parameter `control.MCMC`. This actually means that the log posterior density should be derivable relative to all the parameters to use this sampler - or at least relative to the parameters on which this sampler is applied. This is what we now perform: Quitting from lines 7-29 [Nimble second run, with HMC] (./../man/fragments/Nimble_samplers_HMC_fragment.Rmd) Quitting from lines 64-64 [unnamed-chunk-3] (runMCMCbtadjust_Nimble_variations.Rmd) Error: processing vignette 'runMCMCbtadjust_Nimble_variations.Rmd' failed with diagnostics: error reading from connection --- failed re-building ‘runMCMCbtadjust_Nimble_variations.Rmd’ --- re-building ‘runMCMCbtadjust_Presentation.Rmd’ using knitr --- finished re-building ‘runMCMCbtadjust_Presentation.Rmd’ --- re-building ‘runMCMCbtadjust_extraCalculations.Rmd’ using knitr --- finished re-building ‘runMCMCbtadjust_extraCalculations.Rmd’ SUMMARY: processing the following file failed: ‘runMCMCbtadjust_Nimble_variations.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE