Alejandro Reyes
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/SummarizedBenchmark |
| Branch: RELEASE_3_7 |
| Last Commit: 705ef69 |
| Last Changed Date: 2018-07-23 10:25:46 -0400 (Mon, 23 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:59:44 -0400 (Wed, 17 Oct 2018).
| Package 1445/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SummarizedBenchmark 1.0.4 Alejandro Reyes
| 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: SummarizedBenchmark |
| Version: 1.0.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SummarizedBenchmark_1.0.4.tar.gz |
| StartedAt: 2018-10-17 00:19:48 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:22:51 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 183.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SummarizedBenchmark.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:SummarizedBenchmark.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SummarizedBenchmark_1.0.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SummarizedBenchmark.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 ‘SummarizedBenchmark/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SummarizedBenchmark’ version ‘1.0.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘tidyr’ ‘SummarizedExperiment’ ‘S4Vectors’ ‘BiocGenerics’ ‘UpSetR’
‘rlang’ ‘stringr’ ‘BiocParallel’ ‘ggplot2’ ‘mclust’ ‘dplyr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘SummarizedBenchmark’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
data 8.9Mb
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::replaceSlots’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.list2mat : <anonymous>: no visible binding for global variable
‘.method’
.list2mat : <anonymous>: no visible binding for global variable ‘.val’
.list2mat : <anonymous>: no visible binding for global variable ‘.id’
plotROC: no visible binding for global variable ‘FDR’
plotROC: no visible binding for global variable ‘TPR’
plotROC: no visible binding for global variable ‘method’
Undefined global functions or variables:
.id .method .val FDR TPR method
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/SummarizedBenchmark.Rcheck/00check.log’
for details.
SummarizedBenchmark.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SummarizedBenchmark ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘SummarizedBenchmark’ ... ** R ** data *** moving datasets to lazyload DB ** 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 (SummarizedBenchmark)
SummarizedBenchmark.Rcheck/tests/testthat.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.
> library("testthat")
> library("SummarizedBenchmark")
Loading required package: tidyr
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:tidyr':
expand
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
Loading required package: UpSetR
Loading required package: rlang
Attaching package: 'rlang'
The following object is masked from 'package:Biobase':
exprs
The following objects are masked from 'package:testthat':
is_false, is_null, is_true
Loading required package: stringr
Loading required package: ggplot2
Loading required package: mclust
Package 'mclust' version 5.4.1
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:matrixStats':
count
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:GenomicRanges':
intersect, setdiff, union
The following object is masked from 'package:GenomeInfoDb':
intersect
The following objects are masked from 'package:IRanges':
collapse, desc, intersect, setdiff, slice, union
The following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, union
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> test_check("SummarizedBenchmark")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 134 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
15.640 0.854 16.716
SummarizedBenchmark.Rcheck/SummarizedBenchmark-Ex.timings
| name | user | system | elapsed | |
| Accessors | 0.112 | 0.024 | 0.138 | |
| BenchDesign | 0.004 | 0.000 | 0.005 | |
| SummarizedBenchmark-class | 0.744 | 0.062 | 0.815 | |
| SummarizedBenchmark | 0.208 | 0.005 | 0.214 | |
| addMethod | 0.032 | 0.003 | 0.036 | |
| addPerformanceMetric | 0.060 | 0.004 | 0.064 | |
| availableMetrics | 0.008 | 0.000 | 0.007 | |
| buildBench | 0.225 | 0.030 | 0.259 | |
| dropMethod | 0.005 | 0.000 | 0.005 | |
| estimateMetrics | 0.454 | 0.011 | 0.468 | |
| expandMethod | 0.014 | 0.001 | 0.016 | |
| is.BenchDesign | 0.003 | 0.000 | 0.003 | |
| modifyMethod | 0.005 | 0.000 | 0.005 | |
| performanceMetrics | 0.069 | 0.003 | 0.072 | |
| plotMethodsOverlap | 0.004 | 0.003 | 0.007 | |
| plotROC | 0.004 | 0.002 | 0.006 | |
| print.BenchDesign | 0.003 | 0.000 | 0.003 | |
| printMethod | 0.006 | 0.001 | 0.007 | |
| tdat | 0.003 | 0.002 | 0.005 | |
| tidyUpMetrics | 0.140 | 0.001 | 0.142 | |