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CHECK report for GRmetrics on veracruz1

This page was generated on 2018-04-12 13:43:27 -0400 (Thu, 12 Apr 2018).

Package 619/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRmetrics 1.4.1
Nicholas Clark , Mario Medvedovic
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GRmetrics
Branch: RELEASE_3_6
Last Commit: 3bbbb3a
Last Changed Date: 2017-11-03 22:44:40 -0400 (Fri, 03 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GRmetrics
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GRmetrics_1.4.1.tar.gz
StartedAt: 2018-04-12 04:47:17 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 04:51:01 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 224.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GRmetrics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GRmetrics_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GRmetrics.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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     16.326  0.249  16.368
GRfit     10.388  0.038  10.683
GRscatter  5.745  0.036   5.910
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/GRmetrics.Rcheck/00check.log’
for details.



Installation output

GRmetrics.Rcheck/00install.out

* 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)

Tests output

GRmetrics.Rcheck/tests/test.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> # 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 
 17.368   0.310  17.989 

Example timings

GRmetrics.Rcheck/GRmetrics-Ex.timings

nameusersystemelapsed
GRbox16.326 0.24916.368
GRdrawDRC3.5180.0723.661
GRfit10.388 0.03810.683
GRgetDefs0.9800.0401.045
GRgetGroupVars0.8960.0200.938
GRgetMetrics0.9450.0250.998
GRgetValues0.9100.0240.950
GRscatter5.7450.0365.910