Package: GRmetrics

Version: 1.4.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GRmetrics_1.4.1.tar.gz

StartedAt: 2018-04-12 00:06:49 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:09:47 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 178.8 seconds

RetCode: 0

Status:  OK

CheckDir: GRmetrics.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GRmetrics_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GRmetrics.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRmetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRmetrics’ version ‘1.4.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GRmetrics’ 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 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
.GRcalculate: no visible binding for global variable
  ‘treatment_duration’
.GRlogisticFit: no visible binding for global variable ‘experiment’
GRdrawDRC: no visible binding for global variable ‘GRvalue’
Undefined global functions or variables:
  GRvalue experiment treatment_duration
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
GRbox 12.868  0.060  13.950
GRfit  7.140  0.004   7.152
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.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 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/GRmetrics.Rcheck/00check.log’
for details.

* installing *source* package ‘GRmetrics’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GRmetrics)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

> # Case C (example 4) test
> #install.packages('readr')      # un-comment and install these packages if necessary
> #install.packages('devtools')   # un-comment and install these packages if necessary
> ## try http:// if https:// URLs are not supported
> #source("https://bioconductor.org/biocLite.R")
> #biocLite("SummarizedExperiment")
> 
> # Load GRmetrics functions
> library(GRmetrics)
Loading required package: SummarizedExperiment
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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: Biobase
Welcome to Bioconductor

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

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

> # Load Case C (example 4) input
> data("inputCaseC")
> # Run GRfit function with case = "C"
> output4 = GRfit(inputData = inputCaseC, groupingVariables = c('cell_line','agent', 'perturbation','replicate', 'time'), case = "C")
There were 50 or more warnings (use warnings() to see the first 50)
> 
> # Load Case A (example 1) input
> data("inputCaseA")
> # Run GRfit function with case = "A"
> output1 = GRfit(inputData = inputCaseA, groupingVariables = c('cell_line','agent', 'perturbation','replicate', 'time'), case = "A")
There were 50 or more warnings (use warnings() to see the first 50)
> 
> # change type integer to numeric for the sake of testing
> metadata(output1)[[1]]$replicate = as.numeric(metadata(output1)[[1]]$replicate)
> all.equal(output1, output4)
[1] TRUE
> #[1] TRUE
> # Test passed - output from Case C matches output from Case A
> 
> proc.time()
   user  system elapsed 
 13.996   0.144  14.150 

name	user	system	elapsed
GRbox	12.868	0.060	13.950
GRdrawDRC	2.492	0.008	2.588
GRfit	7.140	0.004	7.152
GRgetDefs	0.696	0.000	0.693
GRgetGroupVars	0.656	0.000	0.659
GRgetMetrics	0.652	0.000	0.654
GRgetValues	0.648	0.000	0.649
GRscatter	4.116	0.028	4.151