Davide Risso
| Snapshot Date: 2019-03-17 17:02:07 -0400 (Sun, 17 Mar 2019) |
| URL: https://git.bioconductor.org/packages/zinbwave |
| Branch: RELEASE_3_8 |
| Last Commit: fe932f7 |
| Last Changed Date: 2019-03-11 11:31:23 -0400 (Mon, 11 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-03-18 11:33:35 -0400 (Mon, 18 Mar 2019).
| Package 1648/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| zinbwave 1.4.2 Davide Risso
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | |||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | |
| Package: zinbwave |
| Version: 1.4.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings zinbwave_1.4.2.tar.gz |
| StartedAt: 2019-03-18 03:34:37 -0400 (Mon, 18 Mar 2019) |
| EndedAt: 2019-03-18 03:39:19 -0400 (Mon, 18 Mar 2019) |
| EllapsedTime: 282.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: zinbwave.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings zinbwave_1.4.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/zinbwave.Rcheck’
* using R version 3.5.2 Patched (2018-12-20 r75875)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zinbwave/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘zinbwave’ version ‘1.4.2’
* 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 ‘zinbwave’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
zinbFit 3.293 3.738 3.372
* 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
zinbwave.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL zinbwave ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘zinbwave’ ... ** 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 (zinbwave)
zinbwave.Rcheck/tests/testthat.Rout
R version 3.5.2 Patched (2018-12-20 r75875) -- "Eggshell Igloo"
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(zinbwave)
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
Loading required package: SingleCellExperiment
>
> test_check("zinbwave")
user system elapsed
0.032 0.000 0.032
user system elapsed
0.026 0.000 0.027
user system elapsed
0.04 0.00 0.04
user system elapsed
0.010 0.000 0.011
══ testthat results ═══════════════════════════════════════════════════════════
OK: 159 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
88.608 2.736 91.322
zinbwave.Rcheck/zinbwave-Ex.timings
| name | user | system | elapsed | |
| getAlpha_mu | 0.003 | 0.000 | 0.003 | |
| getAlpha_pi | 0.002 | 0.000 | 0.002 | |
| getBeta_mu | 0.002 | 0.000 | 0.002 | |
| getBeta_pi | 0.002 | 0.000 | 0.001 | |
| getEpsilon_W | 0.002 | 0.000 | 0.002 | |
| getEpsilon_alpha | 0.001 | 0.000 | 0.002 | |
| getEpsilon_beta_mu | 0.002 | 0.000 | 0.002 | |
| getEpsilon_beta_pi | 0.002 | 0.000 | 0.002 | |
| getEpsilon_gamma_mu | 0.001 | 0.000 | 0.002 | |
| getEpsilon_gamma_pi | 0.002 | 0.001 | 0.002 | |
| getEpsilon_zeta | 0.002 | 0.000 | 0.002 | |
| getGamma_mu | 0.002 | 0.000 | 0.002 | |
| getGamma_pi | 0.002 | 0.000 | 0.002 | |
| getLogMu | 0.002 | 0.001 | 0.002 | |
| getLogitPi | 0.002 | 0.000 | 0.002 | |
| getMu | 0.002 | 0.000 | 0.002 | |
| getPhi | 0.002 | 0.000 | 0.002 | |
| getPi | 0.002 | 0.000 | 0.003 | |
| getTheta | 0.002 | 0.000 | 0.002 | |
| getV_mu | 0.002 | 0.001 | 0.002 | |
| getV_pi | 0.002 | 0.000 | 0.002 | |
| getW | 0.002 | 0.000 | 0.002 | |
| getX_mu | 0.002 | 0.000 | 0.002 | |
| getX_pi | 0.001 | 0.000 | 0.002 | |
| getZeta | 0.002 | 0.000 | 0.001 | |
| loglik | 0.003 | 0.000 | 0.003 | |
| orthogonalizeTraceNorm | 0.001 | 0.001 | 0.002 | |
| penalty | 0.002 | 0.000 | 0.002 | |
| zinb.loglik | 0 | 0 | 0 | |
| zinb.loglik.dispersion | 0.001 | 0.001 | 0.001 | |
| zinbFit | 3.293 | 3.738 | 3.372 | |
| zinbInitialize | 0.983 | 1.312 | 1.052 | |
| zinbModel | 0.003 | 0.001 | 0.005 | |
| zinbOptimize | 1.167 | 1.537 | 1.336 | |
| zinbOptimizeDispersion | 0.784 | 1.110 | 0.988 | |
| zinbSim | 0.052 | 0.016 | 0.068 | |
| zinbsurf | 1.997 | 2.053 | 2.241 | |
| zinbwave | 1.837 | 2.200 | 1.887 | |