Nicholas Clark
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/GRmetrics |
| Branch: RELEASE_3_7 |
| Last Commit: 5a7334e |
| Last Changed Date: 2018-07-28 17:48:29 -0400 (Sat, 28 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:56:59 -0400 (Wed, 17 Oct 2018).
| Package 651/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GRmetrics 1.6.1 Nicholas Clark
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GRmetrics |
| Version: 1.6.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GRmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GRmetrics_1.6.1.tar.gz |
| StartedAt: 2018-10-16 21:52:30 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:56:07 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 216.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GRmetrics.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GRmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GRmetrics_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GRmetrics.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.1’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GRbox 11.849 2.082 10.845
GRfit 13.129 0.050 16.971
GRscatter 7.797 0.045 10.895
* 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-3.7-bioc/meat/GRmetrics.Rcheck/00check.log’
for details.
GRmetrics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GRmetrics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘GRmetrics’ ... ** R ** data *** moving datasets to lazyload DB ** 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 * DONE (GRmetrics)
GRmetrics.Rcheck/tests/test.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
dirname, 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
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, 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
17.147 0.579 17.776
GRmetrics.Rcheck/GRmetrics-Ex.timings
| name | user | system | elapsed | |
| GRbox | 11.849 | 2.082 | 10.845 | |
| GRdrawDRC | 2.149 | 0.088 | 2.275 | |
| GRfit | 13.129 | 0.050 | 16.971 | |
| GRgetDefs | 1.092 | 0.037 | 1.145 | |
| GRgetGroupVars | 1.071 | 0.031 | 1.121 | |
| GRgetMetrics | 1.205 | 0.036 | 1.321 | |
| GRgetValues | 0.988 | 0.034 | 1.035 | |
| GRscatter | 7.797 | 0.045 | 10.895 | |