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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPXpress.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ChIPXpress_1.43.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPXpress.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ChIPXpress/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPXpress’ version ‘1.43.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPXpress’ 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 ... NOTE
Package in Depends field not imported from: ‘ChIPXpressData’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ‘ChIPXpress-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ChIPXpress
> ### Title: ChIPXpress Ranking
> ### Aliases: ChIPXpress
> ### Keywords: ChIPXpress
> 
> ### ** Examples
> 
> ## Example analyses of real Oct4 bound genes predicted
> ## from ChIP-seq data in ESC using pre-built GPL1261 
> ## database
> 
> ## Load predicted Oct4-bound genes from ChIPx data
> data(Oct4ESC_ChIPgenes)
> 
> ## Load example GPL1261 Database
> library(bigmemory)
> path <- system.file("extdata",package="ChIPXpressData")
> DB_GPL1261 <- attach.big.matrix("DB_GPL1261.bigmemory.desc",path=path)
> ## To load the human GPL570 data, replace 'DB_GPL1261' with 'DB_GPL570'.
> 
> ## Run ChIPXpress ("18999" is Entrez GeneID of Oct4)
> out <- ChIPXpress(TFID="18999",ChIP=Oct4ESC_ChIPgenes$EntrezID,DB=DB_GPL1261)
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ChIPXpress.Rnw’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘ChIPXpress.Rnw’
  ...
> path <- system.file("extdata", package = "ChIPXpressData")

> DB_GPL1261 <- attach.big.matrix("DB_GPL1261.bigmemory.desc", 
+     path = path)

> Output <- ChIPXpress(TFID = "18999", ChIP = Oct4ESC_ChIPgenes$EntrezID, 
+     DB = DB_GPL1261)
Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘ChIPXpress.Rnw’ using Sweave
Loading required package: ChIPXpressData
Loading required package: bigmemory
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Killed

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

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPXpress.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChIPXpress
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘ChIPXpress’ ...
** 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 (ChIPXpress)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> require("ChIPXpress") || stop("unable to load ChIPXpress")
Loading required package: ChIPXpress
Loading required package: ChIPXpressData
Loading required package: bigmemory
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
[1] TRUE
> BiocGenerics:::testPackage("ChIPXpress")


RUNIT TEST PROTOCOL -- Mon Feb  6 21:06:08 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChIPXpress RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 11.224   0.460  12.711