* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/rSHAPE.Rcheck’
* using R Under development (unstable) (2024-03-16 r86144)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
    GNU Fortran (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
* running under: Fedora Linux 38 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘rSHAPE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rSHAPE’ version ‘0.3.2’
* 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 ‘rSHAPE’ can be installed ... [12s/12s] OK
* checking package 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 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 ... [20s/20s] 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 LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* checking examples ... OK
* checking examples with --run-donttest ... [17m/18m] ERROR
Running examples in ‘rSHAPE-Ex.R’ failed
The error most likely occurred in:

> ### Name: shapeExperiment
> ### Title: This is a function used to read the SHAPE_experimentalDesign
> ###   type input file and then build a SHAPE experiment by creating all the
> ###   folder structure, .R and .sh scripts required to programatically run
> ###   your experiment - excluding post-analysis, that's a you problem.
> ### Aliases: shapeExperiment
> 
> ### ** Examples
> 
> # This function relies on script templates which can be found at:
> # 'https://github.com/JDench/SHAPE_library/tree/master/SHAPE_templates'
> # Once these have been downloaded you can pass the appropriate filepath values
> # to the first two arguments. For this example, I'll assume you've installed
> # them to a folder position that is now just under the root of your
> # R-environment working directory.
> # However, before runing the function we need to parameterise your run of SHAPE,
> # here I call the default parameters:
> defineSHAPE()
> # Now using the default templates we design an experiment folder complete with
> # shell scripts to submit our work programatically.
> # NOTE: Again, this example assumes you've downloaded the templates and placed
> #        them at the next filepath and directory-path locations
> ## No test: 
> shapeExperiment(func_filepath_toDesign = "~/SHAPE_templates/SHAPE_experimentalDesign.v.1.r",
+                              func_templateDir = "~/SHAPE_templates/")
Error in stopError(paste("Could not find the experimental design file at: ",  : 
  Could not find the experimental design file at: ~/SHAPE_templates/SHAPE_experimentalDesign.v.1.r
Calls: shapeExperiment -> stopError
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/rSHAPE.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 18:58.48, 1052.20 + 26.99