Davide Risso
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/zinbwave |
| Branch: RELEASE_3_9 |
| Last Commit: a2ef508 |
| Last Changed Date: 2019-05-02 11:54:07 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:00:23 -0400 (Wed, 16 Oct 2019).
| Package 1740/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| zinbwave 1.6.0 Davide Risso
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: zinbwave |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2019-10-16 07:50:14 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:56:48 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 394.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: zinbwave.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:zinbwave.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings zinbwave_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/zinbwave.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
zinbFit 22.997 12.888 29.232
zinbsurf 11.749 6.754 15.522
zinbwave 10.699 6.630 14.071
zinbOptimize 10.045 6.016 13.467
zinbInitialize 6.857 4.214 9.114
zinbOptimizeDispersion 6.626 3.979 8.992
* 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/3.6/Resources/library’ * installing *source* package ‘zinbwave’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (zinbwave)
zinbwave.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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, rowsum
Loading required package: SingleCellExperiment
>
> test_check("zinbwave")
user system elapsed
0.038 0.000 0.038
user system elapsed
0.030 0.000 0.031
user system elapsed
0.046 0.000 0.046
user system elapsed
0.012 0.000 0.013
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 158 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
90.687 4.965 95.618
zinbwave.Rcheck/zinbwave-Ex.timings
| name | user | system | elapsed | |
| getAlpha_mu | 0.004 | 0.000 | 0.003 | |
| getAlpha_pi | 0.002 | 0.000 | 0.002 | |
| getBeta_mu | 0.002 | 0.000 | 0.003 | |
| getBeta_pi | 0.002 | 0.001 | 0.003 | |
| getEpsilon_W | 0.002 | 0.000 | 0.002 | |
| getEpsilon_alpha | 0.002 | 0.001 | 0.003 | |
| getEpsilon_beta_mu | 0.002 | 0.000 | 0.002 | |
| getEpsilon_beta_pi | 0.002 | 0.000 | 0.003 | |
| getEpsilon_gamma_mu | 0.002 | 0.000 | 0.002 | |
| getEpsilon_gamma_pi | 0.002 | 0.000 | 0.002 | |
| getEpsilon_zeta | 0.002 | 0.000 | 0.003 | |
| getGamma_mu | 0.002 | 0.000 | 0.002 | |
| getGamma_pi | 0.002 | 0.000 | 0.003 | |
| getLogMu | 0.003 | 0.001 | 0.003 | |
| getLogitPi | 0.003 | 0.000 | 0.003 | |
| getMu | 0.002 | 0.000 | 0.003 | |
| getPhi | 0.002 | 0.001 | 0.003 | |
| getPi | 0.003 | 0.000 | 0.003 | |
| getTheta | 0.002 | 0.000 | 0.003 | |
| getV_mu | 0.002 | 0.000 | 0.002 | |
| getV_pi | 0.002 | 0.000 | 0.003 | |
| getW | 0.002 | 0.001 | 0.002 | |
| getX_mu | 0.002 | 0.000 | 0.002 | |
| getX_pi | 0.002 | 0.001 | 0.003 | |
| getZeta | 0.003 | 0.000 | 0.003 | |
| loglik | 0.004 | 0.000 | 0.004 | |
| orthogonalizeTraceNorm | 0.002 | 0.001 | 0.003 | |
| penalty | 0.003 | 0.001 | 0.003 | |
| zinb.loglik | 0.001 | 0.000 | 0.001 | |
| zinb.loglik.dispersion | 0.000 | 0.000 | 0.001 | |
| zinbFit | 22.997 | 12.888 | 29.232 | |
| zinbInitialize | 6.857 | 4.214 | 9.114 | |
| zinbModel | 0.004 | 0.002 | 0.005 | |
| zinbOptimize | 10.045 | 6.016 | 13.467 | |
| zinbOptimizeDispersion | 6.626 | 3.979 | 8.992 | |
| zinbSim | 0.058 | 0.017 | 0.074 | |
| zinbsurf | 11.749 | 6.754 | 15.522 | |
| zinbwave | 10.699 | 6.630 | 14.071 | |