Package: leeBamViews

Version: 1.20.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:leeBamViews.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings leeBamViews_1.20.0.tar.gz

StartedAt: 2019-10-17 13:24:10 -0400 (Thu, 17 Oct 2019)

EndedAt: 2019-10-17 13:26:55 -0400 (Thu, 17 Oct 2019)

EllapsedTime: 165.0 seconds

RetCode: 0

Status:  OK

CheckDir: leeBamViews.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:leeBamViews.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings leeBamViews_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/leeBamViews.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘leeBamViews/DESCRIPTION’ ... OK
* this is package ‘leeBamViews’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
* 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 ‘leeBamViews’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.0Mb
  sub-directories of 1Mb or more:
    bam  10.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* 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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BSgenome’ ‘Biobase’ ‘Rsamtools’
  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 ... NOTE
.tabulateReads: no visible global function definition for ‘bamRanges’
.tabulateReads: no visible global function definition for
  ‘elementMetadata’
.tabulateReads : alignByFirstRange: no visible global function
  definition for ‘ScanBamParam’
.tabulateReads : alignByFirstRange: no visible global function
  definition for ‘bamRanges’
.tabulateReads : alignByFirstRange: no visible global function
  definition for ‘bamPaths’
.tabulateReads : : no visible global function definition for
  ‘as’
.tabulateReads: no visible global function definition for ‘start’
.tabulateReads: no visible global function definition for ‘bamSamples’
.tabulateReads: no visible global function definition for ‘IRanges’
.tabulateReads: no visible global function definition for ‘GRanges’
.tabulateReads: no visible global function definition for ‘seqnames’
.tabulateReads: no visible global function definition for ‘values’
.tabulateReads: no visible global function definition for ‘values<-’
.tabulateReads: no visible global function definition for ‘DataFrame’
tabulateReads,BamViews-character_OR_NULL-missing-missing: no visible
  binding for global variable ‘mclapply’
tabulateReads,BamViews-missing-missing-missing: no visible binding for
  global variable ‘mclapply’
totalReadCounts,BamViews: no visible global function definition for
  ‘bamPaths’
totalReadCounts,BamViews: no visible binding for global variable
  ‘scanBam’
totalReadCounts,BamViews: no visible global function definition for
  ‘ScanBamParam’
Undefined global functions or variables:
  DataFrame GRanges IRanges ScanBamParam as bamPaths bamRanges
  bamSamples elementMetadata mclapply scanBam seqnames start values
  values<-
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 or elapsed time > 5s
                 user system elapsed
totalReadCounts 0.933   0.02   5.533
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘lbvtest.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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-data-experiment/meat/leeBamViews.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL leeBamViews
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘leeBamViews’ ...
** 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 (leeBamViews)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> ###################################################
> ### chunk number 1: lkd
> ###################################################
> library(leeBamViews)  # bam files stored in package
Loading required package: Biobase
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, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
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: BSgenome
Loading required package: rtracklayer
> bpaths = dir(system.file("bam", package="leeBamViews"), full=TRUE, patt="bam$")
> #
> # extract genotype and lane information from filenames
> #
> gt = gsub(".*/", "", bpaths)
> gt = gsub("_.*", "", gt)
> lane = gsub(".*(.)$", "\\1", gt)
> geno = gsub(".$", "", gt)
> #
> # format the sample-level information appropriately
> #
> pd = DataFrame(geno=geno, lane=lane, row.names=paste(geno,lane,sep="."))
> prd = new("DataFrame")  # protocol data could go here
> #
> # create the views object, adding some arbitrary experiment-level information
> #
> bs1 = BamViews(bamPaths=bpaths, bamSamples=pd, 
+         bamExperiment=list(annotation="org.Sc.sgd.db"))
> bs1
BamViews dim: 0 ranges x 8 samples 
names: isowt.5 isowt.6 ... xrn.1 xrn.2 
detail: use bamPaths(), bamSamples(), bamRanges(), ... 
> #
> # get some sample-level data
> #
> bamSamples(bs1)$geno
[1] "isowt" "isowt" "rlp"   "rlp"   "ssr"   "ssr"   "xrn"   "xrn"  
> 
> 
> ###################################################
> ### chunk number 2: lkc
> ###################################################
> START=c(861250, 863000)
> END=c(862750, 864000)
> exc = GRanges(IRanges(start=START, end=END), seqnames="Scchr13", strand="+")
> bamRanges(bs1) = exc
> 
> cov2baseTrack = function(rle, start, end,
+    dp = DisplayPars(type="l", lwd=0.5, color="black"),
+    countTx=function(x)log10(x+1)) {
+  require(GenomeGraphs)
+  if (!is(rle, "Rle")) stop("requires instance of Rle")
+  dat = rle@values
+  loc = cumsum(rle@lengths)
+  ok = which(loc >= start & loc <= end)
+  makeBaseTrack(base = loc[ok], value=countTx(dat[ok]),
+     dp=dp)
+ }
> 
> library(biomaRt)
> mart = useMart("ensembl", "scerevisiae_gene_ensembl")
> 
> 
> ###################################################
> plotStrains = function(bs, query, start, end, snames, mart, martchr, seqname, strand="+") {
+  library(GenomicAlignments)  # for the readGAlignments() function
+  mm = as.matrix(findOverlaps(bamRanges(bs), query))
+  if (nrow(mm) < 1) stop("no overlap between query and input bamViews")
+  filtbs = bs[mm[,"subjectHits"], ]
+  cov = lapply(bamPaths(filtbs), function(x)coverage(readGAlignments(x))[[seqname]])
+  covtrs = lapply(cov, function(x) cov2baseTrack(x, start, end,
+    countTx = function(x) pmin(x,80)))
+  names(covtrs) = snames
+  gr = makeGeneRegion(start, end, chromosome=martchr,
+        strand=strand, biomart=mart, dp=DisplayPars(plotId=TRUE,
+        idRotation=0, idColor="black"))
+  grm = makeGeneRegion(start, end, chromosome=martchr,
+        strand="-", biomart=mart, dp=DisplayPars(plotId=TRUE,
+        idRotation=0, idColor="black"))
+  covtrs[[length(covtrs)+1]] = gr
+  covtrs[[length(covtrs)+1]] = makeGenomeAxis()
+  covtrs[[length(covtrs)+1]] = grm
+  gdPlot( covtrs, minBase=start[1], maxBase=end[1] )
+ }
> 
> 
> NN = GRanges(IRanges(start=START,end=END), seqnames="Scchr13")
> plotStrains(bs1, NN, 800000, 900000, LETTERS[1:8], mart, "XIII", seqname="Scchr13")
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    type

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

    aperm, apply, rowsum

Loading required package: GenomeGraphs
Loading required package: grid
> 
> 
> proc.time()
   user  system elapsed 
 10.554   0.494  17.811 

name	user	system	elapsed
bs1	1.100	0.040	4.506
leeRPKM	0.036	0.000	0.036
leeUnn	0.088	0.004	0.092
tabulateReads	4.339	0.072	4.525
totalReadCounts	0.933	0.020	5.533