| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:35 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the zinbwave package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zinbwave.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2163/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| zinbwave 1.21.0 (landing page) Davide Risso
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | TIMEOUT | |||||||||
| Package: zinbwave |
| Version: 1.21.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings zinbwave_1.21.0.tar.gz |
| StartedAt: 2023-02-07 19:11:47 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 19:51:47 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 2400.0 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: zinbwave.Rcheck |
| Warnings: NA |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings zinbwave_1.21.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/zinbwave.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘zinbwave/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘zinbwave’ version ‘1.21.0’
* 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 LazyData ... 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 ...
‘intro.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ...
zinbwave.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL zinbwave ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, 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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: SingleCellExperiment
>
> test_check("zinbwave")
user system elapsed
0.050 0.000 0.049
user system elapsed
0.049 0.000 0.049
user system elapsed
0.069 0.000 0.069
user system elapsed
0.048 0.000 0.049
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 219 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 219 ]
>
> proc.time()
user system elapsed
122.465 1.544 126.294
zinbwave.Rcheck/zinbwave-Ex.timings
| name | user | system | elapsed | |
| computeDevianceResiduals | 0.642 | 0.012 | 0.656 | |
| computeObservationalWeights | 1.923 | 0.080 | 2.003 | |
| getAlpha_mu | 0.003 | 0.000 | 0.004 | |
| getAlpha_pi | 0.004 | 0.000 | 0.004 | |
| getBeta_mu | 0.003 | 0.000 | 0.003 | |
| getBeta_pi | 0.003 | 0.000 | 0.004 | |
| getEpsilon_W | 0.004 | 0.000 | 0.004 | |
| getEpsilon_alpha | 0.003 | 0.000 | 0.003 | |
| getEpsilon_beta_mu | 0.000 | 0.004 | 0.003 | |
| getEpsilon_beta_pi | 0.004 | 0.000 | 0.004 | |
| getEpsilon_gamma_mu | 0.004 | 0.000 | 0.003 | |
| getEpsilon_gamma_pi | 0.004 | 0.000 | 0.005 | |
| getEpsilon_zeta | 0.004 | 0.000 | 0.003 | |
| getGamma_mu | 0.003 | 0.000 | 0.003 | |
| getGamma_pi | 0.004 | 0.000 | 0.004 | |
| getLogMu | 0.000 | 0.003 | 0.003 | |
| getLogitPi | 0.004 | 0.000 | 0.004 | |
| getMu | 0.003 | 0.000 | 0.003 | |
| getPhi | 0.004 | 0.000 | 0.004 | |
| getPi | 0.004 | 0.000 | 0.004 | |
| getTheta | 0.000 | 0.004 | 0.004 | |
| getV_mu | 0.001 | 0.001 | 0.004 | |
| getV_pi | 0.004 | 0.000 | 0.003 | |
| getW | 0.000 | 0.003 | 0.003 | |
| getX_mu | 0.003 | 0.000 | 0.003 | |
| getX_pi | 0.003 | 0.000 | 0.004 | |
| getZeta | 0.003 | 0.000 | 0.004 | |
| imputeZeros | 0.394 | 0.012 | 0.406 | |
| loglik | 0.003 | 0.000 | 0.004 | |
| nFactors | 0.003 | 0.000 | 0.004 | |
| nFeatures | 0.003 | 0.000 | 0.003 | |
| nParams | 0.003 | 0.000 | 0.003 | |
| nSamples | 0.003 | 0.000 | 0.003 | |
| orthogonalizeTraceNorm | 0.002 | 0.000 | 0.003 | |
| penalty | 0.003 | 0.000 | 0.004 | |
| zinb.loglik | 0.001 | 0.000 | 0.001 | |
| zinb.loglik.dispersion | 0.001 | 0.000 | 0.000 | |
| zinbAIC | 0.379 | 0.000 | 0.379 | |
| zinbFit | 0.731 | 0.004 | 0.735 | |
| zinbInitialize | 0.150 | 0.000 | 0.152 | |
| zinbModel | 0.003 | 0.000 | 0.004 | |
| zinbOptimize | 0.228 | 0.000 | 0.227 | |
| zinbOptimizeDispersion | 0.123 | 0.000 | 0.123 | |
| zinbSim | 0.033 | 0.004 | 0.038 | |
| zinbsurf | 1.044 | 0.000 | 1.045 | |
| zinbwave | 1.218 | 0.012 | 1.230 | |