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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pipeFrame.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings pipeFrame_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pipeFrame.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘pipeFrame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pipeFrame’ version ‘1.15.0’
* 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 ‘pipeFrame’ 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 ... NOTE
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘pipeFrame-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Step-class
> ### Title: Methods for Step objects
> ### Aliases: Step-class Step init,Step-method init stepName,Step-method
> ###   stepName stepType,Step-method stepType pipeName,Step-method pipeName
> ###   input,Step-method input input<-,Step-method input<-
> ###   output,Step-method output output<-,Step-method output<-
> ###   param,Step-method param param<-,Step-method param<-
> ###   property,Step-method property property<-,Step-method property<-
> ###   report,Step-method report report<-,Step-method report<-
> ###   argv,Step-method argv $,Step-method $ $<-,Step-method $<-
> ###   getParam,Step-method getParam getParamItems,Step-method getParamItems
> ###   isReady,Step-method isReady clearStepCache,Step-method clearStepCache
> ###   getAutoPath,Step-method getAutoPath checkRequireParam,Step-method
> ###   checkRequireParam checkAllPath,Step-method checkAllPath
> ###   getParamMD5Path,Step-method getParamMD5Path
> ###   getStepWorkDir,Step-method getStepWorkDir stepID,Step-method stepID
> ###   writeLog,Step-method writeLog processing genReport
> 
> ### ** Examples
> 
> 
> 
> library(BSgenome)
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, aperm, 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
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

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

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: rtracklayer
> library(rtracklayer)
> library(magrittr)

Attaching package: ‘magrittr’

The following object is masked from ‘package:GenomicRanges’:

    subtract

> 
> # generate new Step : RandomRegionOnGenome
> setClass(Class = "RandomRegionOnGenome",
+          contains = "Step"
+ )
> 
> setMethod(
+     f = "init",
+     signature = "RandomRegionOnGenome",
+     definition = function(.Object,prevSteps = list(),...){
+         # All arguments in function randomRegionOnGenome
+         # will be passed from "..."
+         # so get the arguments from "..." first.
+         allparam <- list(...)
+         sampleNumb <- allparam[["sampleNumb"]]
+         regionLen <- allparam[["regionLen"]]
+         genome <- allparam[["genome"]]
+         outputBed <- allparam[["outputBed"]]
+         # no previous steps for this step so ingnore the "prevSteps"
+         # begin to set input parameters
+         # no input for this step
+         # begin to set output parameters
+         if(is.null(outputBed)){
+             output(.Object)$outputBed <-
+                 getStepWorkDir(.Object,"random.bed")
+         }else{
+             output(.Object)$outputBed <- outputBed
+         }
+         # begin to set other parameters
+         param(.Object)$regionLen <-  regionLen
+         param(.Object)$sampleNumb <- sampleNumb
+         if(is.null(genome)){
+             param(.Object)$bsgenome <-  getBSgenome(getGenome())
+         }else{
+             param(.Object)$bsgenome <-  getBSgenome(genome)
+         }
+         # don't forget to return .Object
+         .Object
+     }
+ )
> 
> setMethod(
+     f = "processing",
+     signature = "RandomRegionOnGenome",
+     definition = function(.Object,...){
+         # All arguments are set in .Object
+         # so we can get them from .Object
+         allparam <- list(...)
+         sampleNumb <- getParam(.Object,"sampleNumb")
+         regionLen <- getParam(.Object,"regionLen")
+         bsgenome <- getParam(.Object,"bsgenome")
+         outputBed <- getParam(.Object,"outputBed")
+         # begin the calculation
+         chrlens <-seqlengths(bsgenome)
+         selchr <- grep("_|M",names(chrlens),invert=TRUE)
+         chrlens <- chrlens[selchr]
+         startchrlens <- chrlens - regionLen
+         spchrs <- sample(x = names(startchrlens),
+         size =  sampleNumb, replace = TRUE,
+         prob = startchrlens / sum(startchrlens))
+         gr <- GRanges()
+         for(chr in names(startchrlens)){
+             startpt <- sample(x = 1:startchrlens[chr],
+             size = sum(spchrs == chr),replace = FALSE)
+             gr <- c(gr,GRanges(seqnames = chr,
+             ranges = IRanges(start = startpt, width = 1000)))
+         }
+         result <- sort(gr,ignore.strand=TRUE)
+         rtracklayer::export.bed(object = result, con =  outputBed)
+         # don't forget to return .Object
+         .Object
+     }
+ )
> 
> 
> 
> setMethod(
+     f = "genReport",
+     signature = "RandomRegionOnGenome",
+     definition = function(.Object, ...){
+         .Object
+     }
+ )
> 
> 
> 
> 
> 
> 
> # This function is exported in NAMESPACE for user to use
> randomRegionOnGenome <- function(sampleNumb, regionLen = 1000,
+                                  genome = NULL, outputBed = NULL, ...){
+     allpara <- c(list(Class = "RandomRegionOnGenome", prevSteps = list()),
+                  as.list(environment()),list(...))
+     step <- do.call(new,allpara)
+     invisible(step)
+ }
> 
> 
> # generate another new Step : OverlappedRandomRegion
> setClass(Class = "OverlappedRandomRegion",
+          contains = "Step"
+ )
> 
> setMethod(
+     f = "init",
+     signature = "OverlappedRandomRegion",
+     definition = function(.Object,prevSteps = list(),...){
+         # All arguments in function overlappedRandomRegion and
+         # runOerlappedRandomRegion will be passed from "..."
+         # so get the arguments from "..." first.
+         allparam <- list(...)
+         inputBed <- allparam[["inputBed"]]
+         randomBed <- allparam[["randomBed"]]
+         outputBed <- allparam[["outputBed"]]
+         # inputBed can obtain from previous step object when running
+         # runOerlappedRandomRegion
+         if(length(prevSteps)>0){
+             prevStep <- prevSteps[[1]]
+             input(.Object)$randomBed <-  getParam(prevStep,"outputBed")
+         }
+         # begin to set input parameters
+         if(!is.null(inputBed)){
+             input(.Object)$inputBed <- inputBed
+         }
+         if(!is.null(randomBed)){
+             input(.Object)$randomBed <- randomBed
+         }
+         # begin to set output parameters
+         # the output is recemended to set under the step work directory
+         if(!is.null(outputBed)){
+             output(.Object)$outputBed <-  outputBed
+         }else{
+             output(.Object)$outputBed <-
+                 getAutoPath(.Object, getParam(.Object, "inputBed"),
+                             "bed", suffix = "bed")
+             # the path can also be generate in this way
+             # ib <- getParam(.Object,"inputBed")
+             # output(.Object)$outputBed <-
+             #    file.path(getStepWorkDir(.Object),
+             #    paste0(substring(ib,1,nchar(ib)-3), "bed"))
+         }
+         # begin to set other parameters
+         # no other parameters
+         # don't forget to return .Object
+ 
+ 
+         .Object
+     }
+ )
> setMethod(
+     f = "processing",
+     signature = "OverlappedRandomRegion",
+     definition = function(.Object,...){
+         # All arguments are set in .Object
+         # so we can get them from .Object
+         allparam <- list(...)
+         inputBed <- getParam(.Object,"inputBed")
+         randomBed <- getParam(.Object,"randomBed")
+         outputBed <- getParam(.Object,"outputBed")
+ 
+         # begin the calculation
+         gr1 <- import.bed(con = inputBed)
+         gr2 <- import.bed(con = randomBed)
+         gr <- second(findOverlapPairs(gr1,gr2))
+         export.bed(gr,con = outputBed)
+         # don't forget to return .Object
+         .Object
+     }
+ )
> 
> 
> setMethod(
+     f = "genReport",
+     signature = "OverlappedRandomRegion",
+     definition = function(.Object, ...){
+         .Object
+     }
+ )
> 
> 
> 
> 
> # This function is exported in NAMESPACE for user to use
> overlappedRandomRegion <- function(inputBed, randomBed,
+                                    outputBed = NULL, ...){
+     allpara <- c(list(Class = "OverlappedRandomRegion",
+         prevSteps = list()),as.list(environment()),list(...))
+     step <- do.call(new,allpara)
+     invisible(step)
+ }
> 
> setGeneric("runOverlappedRandomRegion",
+            function(prevStep,
+                     inputBed,
+                     randomBed = NULL,
+                     outputBed = NULL,
+                     ...) standardGeneric("runOverlappedRandomRegion"))
[1] "runOverlappedRandomRegion"
> 
> 
> 
> setMethod(
+     f = "runOverlappedRandomRegion",
+     signature = "Step",
+     definition = function(prevStep,
+                           inputBed,
+                           randomBed = NULL,
+                           outputBed = NULL,
+                           ...){
+         allpara <- c(list(Class = "OverlappedRandomRegion",
+             prevSteps = list(prevStep)),as.list(environment()),list(...))
+         step <- do.call(new,allpara)
+         invisible(step)
+     }
+ )
> 
> # add to graph
> addEdges(edges = c("RandomRegionOnGenome","OverlappedRandomRegion"),
+          argOrder = 1)
> # begin to test pipeline
> setGenome("hg19")
> # generate test BED file
> test_bed <- file.path(tempdir(),"test.bed")
> library(rtracklayer)
> export.bed(GRanges("chr7:1-127473000"),test_bed)
> 
> 
> rd <- randomRegionOnGenome(10000)
>>>>>>==========================================================
Step Name:pipe_RandomRegionOnGenome
Error in .stopOnAvailablePkg(genome) : 
  BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
  You first need to install it, which you can do with:
      library(BiocManager)
      install("BSgenome.Hsapiens.UCSC.hg19")
Calls: randomRegionOnGenome ... .getInstalledPkgnameFromGenome -> .stopOnAvailablePkg
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:
    2.   ├─base::do.call(new, allpara) at test-StepOpr.R:95:8
    3.   └─methods (local) `<fn>`(...)
    4.     ├─methods::initialize(value, ...)
    5.     └─pipeFrame (local) initialize(value, ...)
    6.       └─pipeFrame (local) .local(.Object, ...)
    7.         ├─base::do.call(init, argv)
    8.         ├─pipeFrame (local) `<nnstndGF>`(...)
    9.         └─pipeFrame (local) `<nnstndGF>`(...)
   10.           └─BSgenome::getBSgenome(getGenome()) at test-StepOpr.R:40:16
   11.             └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   12.               └─BSgenome:::.stopOnAvailablePkg(genome)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 22 ]
  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 ...
  ‘pipeFrame.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘pipeFrame.Rmd’ using rmarkdown
Quitting from lines 714-724 (pipeFrame.Rmd) 
Error: processing vignette 'pipeFrame.Rmd' failed with diagnostics:
error in evaluating the argument 'prevStep' in selecting a method for function 'runOverlappedRandomRegion': BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
  You first need to install it, which you can do with:
      library(BiocManager)
      install("BSgenome.Hsapiens.UCSC.hg19")
--- failed re-building ‘pipeFrame.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/pipeFrame.Rcheck/00check.log’
for details.

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

R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
Copyright (C) 2023 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(pipeFrame)
> 
> test_check("pipeFrame")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 22 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-StepOpr.R:227:5'): test basic operation of class Step  ─────────
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
  You first need to install it, which you can do with:
      library(BiocManager)
      install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
     ▆
  1. └─pipeFrame (local) randomRegionOnGenome(10000) at test-StepOpr.R:227:4
  2.   ├─base::do.call(new, allpara) at test-StepOpr.R:95:8
  3.   └─methods (local) `<fn>`(...)
  4.     ├─methods::initialize(value, ...)
  5.     └─pipeFrame (local) initialize(value, ...)
  6.       └─pipeFrame (local) .local(.Object, ...)
  7.         ├─base::do.call(init, argv)
  8.         ├─pipeFrame (local) `<nnstndGF>`(...)
  9.         └─pipeFrame (local) `<nnstndGF>`(...)
 10.           └─BSgenome::getBSgenome(getGenome()) at test-StepOpr.R:40:16
 11.             └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
 12.               └─BSgenome:::.stopOnAvailablePkg(genome)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 22 ]
Error: Test failures
Execution halted