* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/htrSPRanalysis.Rcheck’
* using R Under development (unstable) (2025-06-27 r88363)
* 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
* checking for file ‘htrSPRanalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘htrSPRanalysis’ version ‘0.1.0’
* 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 ‘htrSPRanalysis’ can be installed ... 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 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [1s/61s] ERROR
Running examples in ‘htrSPRanalysis-Ex.R’ failed
The error most likely occurred in:

> ### Name: process_input
> ### Title: Process user input files and obtain options for fitting.
> ### Aliases: process_input
> 
> ### ** Examples
> 
> # set up file paths for example
> 
> ## No test: 
>  sample_sheet_path <- system.file("extdata",
+  "sample_sheet.xlsx", package="htrSPRanalysis")
> 
> fn <- paste0("https://gitlab.oit.duke.edu/janice/htrspranalysis/",
+         "-/raw/master/inst/extdata/titration_data.xlsx?ref_type=heads")
> 
> download.file(fn,
+       destfile = paste0(tempdir(),"/titration_data.xlsx"),
+       mode = "wb")
trying URL 'https://gitlab.oit.duke.edu/janice/htrspranalysis/-/raw/master/inst/extdata/titration_data.xlsx?ref_type=heads'
Content type 'application/octet-stream' length 4816423 bytes (4.6 MB)
=================================
downloaded 3.1 MB

Warning in download.file(fn, destfile = paste0(tempdir(), "/titration_data.xlsx"),  :
  downloaded length 3227648 != reported length 4816423
Warning in download.file(fn, destfile = paste0(tempdir(), "/titration_data.xlsx"),  :
  URL 'https://gitlab.oit.duke.edu/janice/htrspranalysis/-/raw/master/inst/extdata/titration_data.xlsx?ref_type=heads': Timeout of 60 seconds was reached
Error in download.file(fn, destfile = paste0(tempdir(), "/titration_data.xlsx"),  : 
  download from 'https://gitlab.oit.duke.edu/janice/htrspranalysis/-/raw/master/inst/extdata/titration_data.xlsx?ref_type=heads' failed
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [35s/74s] OK
* 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
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/htrSPRanalysis.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:44.76, 81.40 + 44.64