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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Chicago.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Chicago_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Chicago.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Chicago/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Chicago’ version ‘1.30.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Chicago’ 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ‘Chicago-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: normaliseOtherEnds
> ### Title: Normalise Other Ends
> ### Aliases: normaliseOtherEnds
> 
> ### ** Examples
> 
> ##FIXME: example can be run by loading data package if it is installed, once it exists
> 
> if("PCHiCdata" %in% rownames(installed.packages()))
+ {
+   library(PCHiCdata)
+   data(smESC)
+   
+   ##modifiy smESC to use correct design directory
+   designDir <- file.path(system.file("extdata", package="PCHiCdata"), "mm9TestDesign")
+   smESC <- modifySettings(cd=smESC, designDir=designDir)
+   
+   ##normalise here...
+   normaliseOtherEnds(smESC)
+   
+ } else {
+   warning("Please install the PCHiCdata package to run this example.")
+ }
Warning: settings are not checked for consistency with the original ones.
Locating <baitmapfile>.baitmap in /home/biocbuild/R/R-4.3.1/site-library/PCHiCdata/extdata/mm9TestDesign...
Found mm9_chr18and19.baitmap
Locating <rmapfile>.rmap in /home/biocbuild/R/R-4.3.1/site-library/PCHiCdata/extdata/mm9TestDesign...
Found mm9_chr18and19.rmap
Locating <nperbinfile>.npb in /home/biocbuild/R/R-4.3.1/site-library/PCHiCdata/extdata/mm9TestDesign...
Found mm9_chr18and19.npb
Locating <nbaitsperbinfile>.nbpb in /home/biocbuild/R/R-4.3.1/site-library/PCHiCdata/extdata/mm9TestDesign...
Found mm9_chr18and19.nbpb
Locating <proxOEfile>.poe in /home/biocbuild/R/R-4.3.1/site-library/PCHiCdata/extdata/mm9TestDesign...
Found mm9_chr18and19.poe
Checking the design files...
Reading the settings from NPB file header...
Checking the integrity of the NPB file...
Reading NPerBin file...
Checking the integrity of the NBPB file...
Reading NBaitsPerBin file...
Preprocessing input...
Computing trans-counts...
Filtering out 5 other ends with top 0.01% number of trans-interactions
Binning...
Computing total bait counts...
Reading NBaitsPerBin file...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/Chicago.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL Chicago
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘Chicago’ ...
** 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 (Chicago)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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.

> library(testthat)
> library(Chicago)
Loading required package: data.table

Welcome to CHiCAGO - version 1.30.0
If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").
NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")
> 
> test_check("Chicago")
Read 4 items
Read 4 items
Read 4 items
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  2.864   0.238   3.183