##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings EnMCB_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/EnMCB.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘EnMCB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnMCB’ version ‘1.10.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘EnMCB’ can be installed ... OK
* 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 ... 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 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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘EnMCB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IdentifyMCB
> ### Title: Identification of methylation correlated blocks
> ### Aliases: IdentifyMCB
> 
> ### ** Examples
> 
> data('demo_data',package = "EnMCB")
> 
> #import the demo TCGA data with 10000+ CpGs site and 455 samples
> #remove # to run
> res<-IdentifyMCB(demo_data$realdata)
Start calculating the correlation, this may take a while...
Warning in gzfile(file, "rb") :
  cannot open compressed file '/home/biocbuild/.cache/R/BiocFileCache/13ce7b4c1d6151_file13ce7b2394bb31', probable reason 'No such file or directory'
Error in gzfile(file, "rb") : cannot open the connection
Calls: IdentifyMCB -> get450kAnno -> readRDS -> gzfile
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-hello.R:5'): multiplication works ──────────────────────────────
  Error in `gzfile(file, "rb")`: cannot open the connection
  Backtrace:
      ▆
   1. └─EnMCB::IdentifyMCB(demo_data$realdata) at test-hello.R:5:2
   2.   └─EnMCB:::get450kAnno()
   3.     └─base::readRDS(rev(q$rpath)[1])
   4.       └─base::gzfile(file, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in gzfile(file, "rb") :
  cannot open compressed file '/home/biocbuild/.cache/R/BiocFileCache/13ce7b4c1d6151_file13ce7b2394bb31', probable reason 'No such file or directory'
Quitting from lines 42-49 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/EnMCB.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL EnMCB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘EnMCB’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EnMCB)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(EnMCB)
> 
> test_check("EnMCB")
Start calculating the correlation, this may take a while...
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-hello.R:5'): multiplication works ──────────────────────────────
Error in `gzfile(file, "rb")`: cannot open the connection
Backtrace:
    ▆
 1. └─EnMCB::IdentifyMCB(demo_data$realdata) at test-hello.R:5:2
 2.   └─EnMCB:::get450kAnno()
 3.     └─base::readRDS(rev(q$rpath)[1])
 4.       └─base::gzfile(file, "rb")

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted