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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Rcade.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Rcade_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/Rcade.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcade/DESCRIPTION’ ... OK
* this is package ‘Rcade’ version ‘1.32.0’
* 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 ‘Rcade’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
* 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 ... NOTE
constructRcadeTable: no visible binding for global variable ‘p.DE’
constructRcadeTable: no visible binding for global variable ‘p.ChIP’
plotBBB,Rcade: no visible global function definition for ‘decorate3d’
Undefined global functions or variables:
  decorate3d p.ChIP p.DE
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
RcadeAnalysis    6.368  0.112   6.579
diffCountsBaySeq 6.148  0.000   6.152
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/Rcade.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Rcade
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘Rcade’ ...
** 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 (Rcade)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> require("Rcade") || stop("unable to load Rcade")
Loading required package: Rcade
Loading required package: GenomicRanges
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: baySeq
Loading required package: abind
Welcome to Rcade - version 1.32.0
If you are new to Rcade, please consider reading the vignette through the command: vignette("Rcade").

Attaching package: 'Rcade'

The following object is masked from 'package:BiocGenerics':

    plotPCA

[1] TRUE
> BiocGenerics:::testPackage("Rcade")
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Counting reads.


RUNIT TEST PROTOCOL -- Thu May  6 05:03:56 2021 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rcade RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
 13.200   0.392  13.658