* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qMRI.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘qMRI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qMRI’ version ‘1.2.7.8’
* 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 ‘qMRI’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/qMRI-00install.html' for details.
* used C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 14.2.0-16) 14.2.0’
* 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
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* checking loading without being on the library search path ... [1s/1s] OK
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* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] ERROR
Running examples in ‘qMRI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimateIRfluid
> ### Title: Estimate parameters in Inversion Recovery MRI experiments model
> ###   for CSF voxel
> ### Aliases: estimateIRfluid
> ### Keywords: models regression
> 
> ### ** Examples
> 
> dataDir0 <- system.file("extdataIR", package = "qMRI")
> dataDir <- tempdir("IRdata")
Error in tempdir(check) : NA in coercion to Rboolean
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [7s/27s] WARNING
Error(s) in re-building vignettes:
  ...
--- re-building ‘IRMRI-Example.Rnw’ using Sweave

Error: processing vignette 'IRMRI-Example.Rnw' failed with diagnostics:
 chunk 2 (label = 0b) 
Error in tempdir(check) : NA in coercion to Rboolean

--- failed re-building ‘IRMRI-Example.Rnw’

--- re-building ‘qMRI-Example.Rnw’ using Sweave
Loading required package: awsMethods

Use the function setCores() to change the number of CPU cores.

Loading required package: parallel
Reading RAW images requires to install dcraw, see 

    http://cybercom.net/~dcoffin/dcraw/ for LINUX and http://www.insflug.org/raw/
    for macOS and Windows 

Use awsMethods::setCores(ncores) to specify number of cores for openMP
oro.nifti 0.11.4
--- finished re-building ‘qMRI-Example.Rnw’

make[1]: Entering directory '/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qMRI.Rcheck/vign_test/qMRI/vignettes'
pdflatex -interaction nonstopmode IRMRI-Example.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./IRMRI-Example.tex
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Document Class: article 2024/06/29 v1.4n Standard LaTeX document class
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(/usr/share/texlive/texmf-dist/tex/latex/filecontents/filecontents.sty

Package filecontents Warning: This package is obsolete. Disabling it and
(filecontents)                passing control to the filecontents environment
(filecontents)                defined by the LaTeX kernel.

)

LaTeX Info: Writing file `./qmriIR.bib'.


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Package biblatex Warning: Using fall-back bibtex backend:
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(/usr/share/texlive/texmf-dist/tex/latex/l3packages/xparse/xparse.sty)))
(/home/hornik/tmp/R.check/r-devel-gcc/Work/build/share/texmf/tex/latex/Sweave.s
ty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
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(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty)
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No file IRMRI-Example.aux.
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(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
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! LaTeX Error: File `IRMRI-Example-concordance.tex' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: tex)

Enter file name: 
! Emergency stop.
<read *> 
         
l.54 \input{IRMRI-Example-concordance}
                                      ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on IRMRI-Example.log.
make[1]: *** [Makefile:3: all] Error 1
make[1]: Leaving directory '/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qMRI.Rcheck/vign_test/qMRI/vignettes'
Error in tools::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qMRI.Rcheck/vign_test/qMRI",  : 
  running 'make' failed
Execution halted

* checking PDF version of manual ... [4s/5s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR, 1 WARNING