• using R Under development (unstable) (2025-02-21 r87787)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 ... [21s/51s] OK See the install log for details.
• used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
• used Fortran compiler: ‘GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
• 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 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 ... [39s/92s] 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 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 for GNU extensions in Makefiles ... OK
• checking include directives 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 ... [12s/28s] ERROR Running examples in ‘qMRI-Ex.R’ failed The error most likely occurred in: > ### 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 ... [28s/164s] 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 '/data/gannet/ripley/R/packages/tests-devel/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 2024) (preloaded format=pdflatex)  restricted \write18 enabled. entering extended mode (./IRMRI-Example.tex LaTeX2e <2024-11-01> patch level 2 L3 programming layer <2025-01-18> (/data/gannet2/ripley/2024/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/06/29 v1.4n Standard LaTeX document class (/data/gannet2/ripley/2024/texmf-dist/tex/latex/base/size10.clo)) (/data/gannet2/ripley/2024/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'. (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/biblatex.sty (/data/gannet2/ripley/2024/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/data/gannet2/ripley/2024/texmf-dist/tex/generic/infwarerr/infwarerr.sty) (/data/gannet2/ripley/2024/texmf-dist/tex/generic/iftex/iftex.sty) (/data/gannet2/ripley/2024/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/graphics/keyval.sty) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/data/gannet2/ripley/2024/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/logreq/logreq.sty (/data/gannet2/ripley/2024/texmf-dist/tex/latex/logreq/logreq.def)) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/base/ifthen.sty) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/url/url.sty) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/blx-dm.def) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/blx-compat.def) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/blx-bibtex.def Package biblatex Warning: Using fall-back bibtex backend: (biblatex) functionality may be reduced/unavailable. ) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/biblatex.def) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/bbx/authoryear.bbx (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/bbx/standard.bbx)) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/cbx/authoryear.cbx) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/biblatex.cfg) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/l3kernel/expl3.sty (/data/gannet2/ripley/2024/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) ) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/blx-case-expl3.sty (/data/gannet2/ripley/2024/texmf-dist/tex/latex/l3packages/xparse/xparse.sty)))  (/data/gannet/ripley/R/R-devel/share/texmf/tex/latex/Sweave.sty (/data/gannet2/ripley/2024/texmf-dist/tex/latex/graphics/graphicx.sty (/data/gannet2/ripley/2024/texmf-dist/tex/latex/graphics/graphics.sty (/data/gannet2/ripley/2024/texmf-dist/tex/latex/graphics/trig.sty) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/base/textcomp.sty) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/base/fontenc.sty)) No file IRMRI-Example.aux. (/data/gannet2/ripley/2024/texmf-dist/tex/latex/biblatex/lbx/english.lbx) No file IRMRI-Example.bbl. (/data/gannet2/ripley/2024/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/data/gannet2/ripley/2024/texmf-dist/tex/latex/grfext/grfext.sty (/data/gannet2/ripley/2024/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty )) (/data/gannet2/ripley/2024/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg )) ! 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 '/data/gannet/ripley/R/packages/tests-devel/qMRI.Rcheck/vign_test/qMRI/vignettes' Error in tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/qMRI.Rcheck/vign_test/qMRI", :   running 'make' failed Execution halted
• checking PDF version of manual ... [9s/18s] 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, 1 WARNING