Davide Risso
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/zinbwave |
| Branch: RELEASE_3_6 |
| Last Commit: ace352e |
| Last Changed Date: 2017-10-30 12:41:31 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:16:21 -0400 (Thu, 12 Apr 2018).
| Package 1471/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| zinbwave 1.0.0 Davide Risso
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: zinbwave |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings zinbwave_1.0.0.tar.gz |
| StartedAt: 2018-04-12 03:40:28 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:43:17 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 168.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: zinbwave.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings zinbwave_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/zinbwave.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’ * 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 installed files from ‘inst/doc’ ... 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: OK
zinbwave.Rcheck/00install.out
* installing *source* package ‘zinbwave’ ... ** 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 (zinbwave)
zinbwave.Rcheck/tests/testthat.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-pc-linux-gnu (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, 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
Loading required package: SingleCellExperiment
>
> test_check("zinbwave")
user system elapsed
0.028 0.000 0.027
user system elapsed
0.024 0.000 0.024
user system elapsed
0.036 0.000 0.035
user system elapsed
0.008 0.000 0.009
══ testthat results ═══════════════════════════════════════════════════════════
OK: 81 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
17.528 0.320 17.881
zinbwave.Rcheck/zinbwave-Ex.timings
| name | user | system | elapsed | |
| getAlpha_mu | 0.120 | 0.000 | 0.122 | |
| getAlpha_pi | 0.384 | 0.000 | 0.385 | |
| getBeta_mu | 0.004 | 0.000 | 0.002 | |
| getBeta_pi | 0.004 | 0.000 | 0.001 | |
| getEpsilon_W | 0.000 | 0.000 | 0.002 | |
| getEpsilon_alpha | 0.004 | 0.000 | 0.002 | |
| getEpsilon_beta_mu | 0.000 | 0.000 | 0.002 | |
| getEpsilon_beta_pi | 0.000 | 0.000 | 0.002 | |
| getEpsilon_gamma_mu | 0.004 | 0.000 | 0.001 | |
| getEpsilon_gamma_pi | 0.000 | 0.000 | 0.002 | |
| getEpsilon_zeta | 0.004 | 0.000 | 0.001 | |
| getGamma_mu | 0.000 | 0.000 | 0.002 | |
| getGamma_pi | 0.000 | 0.000 | 0.002 | |
| getLogMu | 0.004 | 0.000 | 0.002 | |
| getLogitPi | 0.000 | 0.000 | 0.002 | |
| getMu | 0.004 | 0.000 | 0.002 | |
| getPhi | 0.004 | 0.000 | 0.001 | |
| getPi | 0.000 | 0.000 | 0.002 | |
| getTheta | 0.004 | 0.000 | 0.001 | |
| getV_mu | 0.000 | 0.000 | 0.002 | |
| getV_pi | 0.000 | 0.000 | 0.002 | |
| getW | 0.004 | 0.000 | 0.002 | |
| getX_mu | 0.000 | 0.000 | 0.001 | |
| getX_pi | 0.004 | 0.000 | 0.002 | |
| getZeta | 0.004 | 0.000 | 0.001 | |
| loglik | 0.000 | 0.000 | 0.003 | |
| orthogonalizeTraceNorm | 0.000 | 0.000 | 0.002 | |
| penalty | 0.004 | 0.000 | 0.003 | |
| zinb.loglik | 0.000 | 0.000 | 0.001 | |
| zinb.loglik.dispersion | 0.004 | 0.000 | 0.001 | |
| zinbFit | 1.052 | 1.080 | 3.584 | |
| zinbInitialize | 0.160 | 0.336 | 0.909 | |
| zinbModel | 0.000 | 0.000 | 0.004 | |
| zinbOptimize | 0.160 | 0.484 | 1.275 | |
| zinbOptimizeDispersion | 0.140 | 0.316 | 0.846 | |
| zinbSim | 0.028 | 0.004 | 0.033 | |
| zinbwave | 0.480 | 0.560 | 1.764 | |