- using R version 4.3.3 (2024-02-29)
- using platform: aarch64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘ieegio/DESCRIPTION’ ... OK
- this is package ‘ieegio’ version ‘0.0.2’
- package encoding: UTF-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 ‘ieegio’ can be installed ... [4s/5s] OK
See the install log for details.
- 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 R 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 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 ... [4s/4s] OK
- checking Rd files ... [0s/0s] 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 ... [4s/4s] ERROR
Running examples in ‘ieegio-Ex.R’ failed
The error most likely occurred in:
> ### Name: imaging-volume
> ### Title: Read and write volume data
> ### Aliases: imaging-volume read_volume write_volume io_read_mgz
> ### io_write_mgz io_write_mgz.ieegio_volume io_write_mgz.ieegio_mgh
> ### io_write_mgz.nifti io_write_mgz.niftiImage
> ### io_write_mgz.ants.core.ants_image.ANTsImage io_write_mgz.array
> ### io_read_nii io_write_nii io_write_nii.ieegio_nifti
> ### io_write_nii.ants.core.ants_image.ANTsImage io_write_nii.niftiImage
> ### io_write_nii.nifti io_write_nii.ieegio_mgh io_write_nii.array
>
> ### ** Examples
>
>
>
> library(ieegio)
>
> nifti_file <- "brain.demosubject.nii.gz"
>
> # Use `ieegio_sample_data(nifti_file)`
> # to download sample data
>
>
> if( ieegio_sample_data(nifti_file, test = TRUE) ) {
+
+ # ---- NIfTI examples ---------------------------------------------
+
+ file <- ieegio_sample_data(nifti_file)
+
+ # basic read
+ vol <- read_volume(file)
+
+ # voxel to scanner RAS
+ vol$transforms$vox2ras
+
+ # to freesurfer surface
+ vol$transforms$vox2ras_tkr
+
+ # to FSL
+ vol$transforms$vox2fsl
+
+ image(vol$data[,,128], asp = 1, axes = FALSE)
+
+ # ---- using other methods --------------------------------------
+ # default
+ vol <- read_volume(file, method = "oro", format = "nifti")
+ vol$header
+
+ # lazy-load nifti
+ vol2 <- read_volume(file, method = "rnifti", format = "nifti")
+ vol2$header
+
+ # Using ANTsPyx
+ vol3 <- read_volume(file, method = "ants", format = "nifti")
+ vol3$header
+
+ # ---- write --------------------------------------------------------
+
+ # write as NIfTI
+ f <- tempfile(fileext = ".nii.gz")
+
+ write_volume(vol, f, format = "nifti")
+
+ # alternative method
+ write_volume(vol$header, f, format = "nifti")
+
+ # write to mgz/mgh
+ f2 <- tempfile(fileext = ".mgz")
+
+ write_volume(vol, f, format = "mgh")
+
+ # clean up
+ unlink(f)
+ unlink(f2)
+
+ }
<simpleWarning in check_forbidden_install("Miniconda"): cannot install Miniconda during R CMD check>
Warning in check_forbidden_install("Conda Environments") :
cannot install Conda Environments during R CMD check
Error: Unable to find conda binary. Is Anaconda installed?
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [3s/3s] OK
Running ‘testthat.R’ [3s/3s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking re-building of vignette outputs ... [8s/9s] OK
- checking PDF version of manual ... [4s/5s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '