* using log directory ‘/home/hornik/tmp/CRAN_special_clang-san/divest.Rcheck’ * using R Under development (unstable) (2024-10-18 r87246) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘divest/DESCRIPTION’ ... OK * this is package ‘divest’ version ‘1.1.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘covr’ * 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 ‘divest’ can be installed ... [67s/67s] OK * used C++ compiler: ‘Debian clang version 18.1.8 (11)’ * checking package directory ... OK * checking for future file timestamps ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [10s/10s] OK * checking Rd files ... [1s/1s] 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 line endings in shell scripts ... 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 examples ... [2s/2s] ERROR Running examples in ‘divest-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: readDicom > ### Title: Read one or more DICOM directories > ### Aliases: readDicom convertDicom sortDicom scanDicom > > ### ** Examples > > path <- system.file("extdata", "raw", package="divest") > scanDicom(path) [dcm2niix info] Found 4 DICOM file(s) label 1 T0_N_S8 2 T0_N_S9 rootPath 1 /home/hornik/tmp/CRAN_special_clang-san/divest.Rcheck/divest/extdata/raw 2 /home/hornik/tmp/CRAN_special_clang-san/divest.Rcheck/divest/extdata/raw files seriesNumber seriesDescription patientName studyDate echoTime 1 2 8 DTIb3000s5 112.00 2 2 9 fl3D_t1_sag 4.94 repetitionTime echoNumber phase diffusion 1 4100 NA FALSE TRUE 2 11 NA FALSE FALSE > readDicom(path, interactive=FALSE) [dcm2niix info] Found 4 DICOM file(s) [dcm2niix WARNING] Unable to determine manufacturer (0008,0070), so conversion is not tuned for vendor. [dcm2niix WARNING] All images appear to be a single slice - please check slice/vector orientation [dcm2niix WARNING] This diffusion series does not have a B0 (reference) volume [dcm2niix info] Convert 2 DICOM as /home/hornik/tmp/scratch/RtmpNoZFon/working_dir/RtmpbVrPst/divest_1250384_2/T0_N_S8 (96x96x1x2) [dcm2niix WARNING] Unable to determine manufacturer (0008,0070), so conversion is not tuned for vendor. [dcm2niix info] Convert 2 DICOM as /home/hornik/tmp/scratch/RtmpNoZFon/working_dir/RtmpbVrPst/divest_1250384_2/T0_N_S9 (224x256x2x1) [[1]] Internal image: "T0_N_S8" - 96 x 96 x 1 x 2 voxels - 2.5 x 2.5 x 5 mm x 4.1 s per voxel [[2]] Internal image: "T0_N_S9" - 2 x 224 x 256 voxels - 1 x 1 x 1 mm per voxel > > > > base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") > base::cat("readDicom", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > ### *