Andrea Rau
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/coseq |
| Branch: RELEASE_3_8 |
| Last Commit: 169b805 |
| Last Changed Date: 2019-01-04 13:04:49 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:16 -0400 (Tue, 16 Apr 2019).
| Package 333/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| coseq 1.6.1 Andrea Rau
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: coseq |
| Version: 1.6.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:coseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings coseq_1.6.1.tar.gz |
| StartedAt: 2019-04-15 23:16:04 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:20:28 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 264.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: coseq.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:coseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings coseq_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/coseq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coseq’ 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 ‘coseq’ 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 ... OK
* 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
compareARI 5.035 0.044 5.119
coseq 4.866 0.028 5.080
* 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: OK
coseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL coseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘coseq’ ... ** 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 * DONE (coseq)
coseq.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("coseq")
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
> test_check("coseq")
****************************************
coseq analysis: kmeans approach & logclr transformation
K = 0 to 3
Use set.seed() prior to running coseq for reproducible results.****************************************
****************************************
coseq analysis: Gamma approach & logclr transformation
K = 2 to 4
Use set.seed() prior to running coseq for reproducible results.****************************************
****************************************
coseq analysis: kmeans approach & other transformation
K = 2 to 4
Use set.seed() prior to running coseq for reproducible results.****************************************
****************************************
coseq analysis: kmeans approach & other transformation
K = 2 to 4
Use set.seed() prior to running coseq for reproducible results.****************************************
****************************************
coseq analysis: Normal approach & none transformation
K = 2 to 4
Use set.seed() prior to running coseq for reproducible results.****************************************
****************************************
coseq analysis: Normal approach & logMedianRef transformation
K = 2 to 4
Use set.seed() prior to running coseq for reproducible results.****************************************
══ testthat results ═══════════════════════════════════════════════════════════
OK: 30 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
12.879 0.703 13.712
coseq.Rcheck/coseq-Ex.timings
| name | user | system | elapsed | |
| NormMixClus | 1.065 | 0.045 | 1.120 | |
| NormMixClusK | 0.407 | 0.002 | 0.410 | |
| NormMixParam | 0.215 | 0.002 | 0.217 | |
| clusterEntropy | 0.001 | 0.000 | 0.001 | |
| clusterInertia | 0.526 | 0.011 | 0.539 | |
| compareARI | 5.035 | 0.044 | 5.119 | |
| compareICL | 4.542 | 0.030 | 4.626 | |
| coseq-package | 4.531 | 0.037 | 4.621 | |
| coseq | 4.866 | 0.028 | 5.080 | |
| coseqHelpers | 4.339 | 0.032 | 4.403 | |
| coseqRun | 1.809 | 0.017 | 1.839 | |
| kmeansProbaPost | 0.005 | 0.000 | 0.005 | |
| matchContTable | 0.003 | 0.001 | 0.003 | |
| plot | 4.083 | 0.031 | 4.175 | |
| summary | 3.799 | 0.027 | 3.852 | |
| transformRNAseq | 0.013 | 0.000 | 0.014 | |