* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/intePareto.Rcheck’
* using R Under development (unstable) (2023-01-30 r83727)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
    GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
* running under: Fedora 34 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘intePareto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘intePareto’ version ‘0.1.2’
* 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 ‘intePareto’ can be installed ... [32s/32s] 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 ... 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 ... [10s/10s] 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 ... [39s/39s] 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 data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [19s/19s] ERROR
Running examples in ‘intePareto-Ex.R’ failed
The error most likely occurred in:

> ### Name: doMatch
> ### Title: Match the RNA-Seq and ChIP-Seq data on the gene level
> ### Aliases: doMatch
> 
> ### ** Examples
> 
> data(test_rna_meta)
> data(test_chip_meta)
> ## No test: 
> for(i in test_rna_meta$SRR){
+ test_rna_meta$files <- system.file("extdata",paste0(i,".tsv"),
+ package = "intePareto")
+ }
> for(i in test_chip_meta$SRR){
+ test_chip_meta$files <- system.file("extdata", paste0(i,".bam"),
+ package = "intePareto")
+ }
> doMatch(rnaMeta = test_rna_meta,
+ chipMeta = test_chip_meta,
+ region = "promoter",
+ method = "weighted.mean",
+ host = "http://aug2017.archive.ensembl.org",
+ ensemblDataset = "mmusculus_gene_ensembl")
get RNA counts
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Error: Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://aug2017.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [14s/14s] 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/intePareto.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 4:30.74, 249.17 + 19.66