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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CexoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CexoR_1.30.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CexoR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CexoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CexoR’ version ‘1.30.1’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
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 ‘CexoR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'CexoR' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CexoR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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 ... NOTE
cexor: no visible global function definition for ‘subsetByOverlaps’
Undefined global functions or variables:
  subsetByOverlaps
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘CexoR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CexoR-package
> ### Title: An R package to uncover high-resolution protein-DNA interactions
> ###   in ChIP-exo replicates
> ### Aliases: CexoR-package CexoR
> 
> ### ** Examples
> 
> 
> ## hg19. chr2:1-1,000,000. CTCF data from Rhee and Pugh (2011)
> 
> owd <- setwd(tempdir())
> 
> rep1 <- "CTCF_rep1_chr2_1-1e6.bam"
> rep2 <- "CTCF_rep2_chr2_1-1e6.bam"
> rep3 <- "CTCF_rep3_chr2_1-1e6.bam"
> r1 <- system.file("extdata", rep1, package="CexoR",mustWork = TRUE)
> r2 <- system.file("extdata", rep2, package="CexoR",mustWork = TRUE)
> r3 <- system.file("extdata", rep3, package="CexoR",mustWork = TRUE)
> 
> chipexo <- cexor(bam=c(r1,r2,r3), chrN="chr2", chrL=1e6, idr=0.01, p=1e-18, N=3e4)
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iPlus], lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Warning in pskellam(q = k[iMinus] - 1, lambda1 = lambda1[w], lambda2 = lambda2[w],  :
  NaNs produced
Error in names(x) <- value : 
  'names' attribute [8] must be the same length as the vector [0]
Calls: cexor -> colnames<- -> colnames<-
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
   
  1 Test Suite : 
  CexoR RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in test_cexor: Error in names(x) <- value : 
    'names' attribute [8] must be the same length as the vector [0]
  
  Test files with failing tests
  
     test_cexor.R 
       test_cexor 
  
  
  Error in BiocGenerics:::testPackage("CexoR") : 
    unit tests failed for package CexoR
  Execution halted
* 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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/CexoR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CexoR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CexoR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
Warning: Package 'CexoR' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
Warning: Package 'CexoR' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package keeps a record of temporary installation path
* DONE (CexoR)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("CexoR") || stop("unable to load CexoR")
Loading required package: CexoR
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
[1] TRUE
Warning messages:
1: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' 
2: Package 'CexoR' is deprecated and will be removed from Bioconductor
  version 3.14 
> BiocGenerics:::testPackage("CexoR")
Timing stopped at: 1.621 0.068 1.69
Error in names(x) <- value : 
  'names' attribute [8] must be the same length as the vector [0]
In addition: There were 50 or more warnings (use warnings() to see the first 50)


RUNIT TEST PROTOCOL -- Thu Oct 14 17:19:33 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
CexoR RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test_cexor: Error in names(x) <- value : 
  'names' attribute [8] must be the same length as the vector [0]

Test files with failing tests

   test_cexor.R 
     test_cexor 


Error in BiocGenerics:::testPackage("CexoR") : 
  unit tests failed for package CexoR
Execution halted