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This page was generated on 2024-03-28 11:37:16 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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

Package 2268/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zinbwave 1.25.2  (landing page)
Davide Risso
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/zinbwave
git_branch: devel
git_last_commit: 0835b7d
git_last_commit_date: 2024-03-13 16:20:15 -0400 (Wed, 13 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for zinbwave on nebbiolo1


To the developers/maintainers of the zinbwave package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: zinbwave
Version: 1.25.2
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings zinbwave_1.25.2.tar.gz
StartedAt: 2024-03-28 03:50:53 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 03:57:14 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 380.4 seconds
RetCode: 0
Status:   OK  
CheckDir: zinbwave.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings zinbwave_1.25.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/zinbwave.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘zinbwave/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘zinbwave’ version ‘1.25.2’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) zinbSim.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) zinbSim.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) zinbSim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) zinbSim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/zinbwave.Rcheck/00check.log’
for details.


Installation output

zinbwave.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL zinbwave
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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)

Tests output

zinbwave.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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 
  0.029   0.000   0.029 
   user  system elapsed 
  0.029   0.000   0.029 
   user  system elapsed 
   0.04    0.00    0.04 
   user  system elapsed 
  0.028   0.000   0.028 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 222 ]
> 
> proc.time()
   user  system elapsed 
 81.906   1.463  83.361 

Example timings

zinbwave.Rcheck/zinbwave-Ex.timings

nameusersystemelapsed
computeDevianceResiduals0.9200.0640.984
computeObservationalWeights0.7380.0990.838
getAlpha_mu0.0030.0000.002
getAlpha_pi0.0020.0000.002
getBeta_mu0.0020.0000.002
getBeta_pi0.0020.0000.002
getEpsilon_W0.0020.0000.002
getEpsilon_alpha0.0020.0000.002
getEpsilon_beta_mu0.0010.0000.002
getEpsilon_beta_pi0.0020.0000.002
getEpsilon_gamma_mu0.0020.0000.002
getEpsilon_gamma_pi0.0020.0000.002
getEpsilon_zeta0.0020.0000.002
getGamma_mu0.0000.0020.002
getGamma_pi0.0010.0010.002
getLogMu0.0020.0010.002
getLogitPi0.0000.0020.002
getMu0.0010.0010.002
getPhi0.0020.0010.002
getPi0.0020.0000.002
getTheta0.0020.0000.002
getV_mu0.0020.0000.002
getV_pi0.0020.0000.002
getW0.0020.0000.001
getX_mu0.0020.0000.002
getX_pi0.0020.0000.002
getZeta0.0020.0000.002
imputeZeros0.2290.0080.237
loglik0.0030.0000.002
nFactors0.0020.0000.002
nFeatures0.0020.0000.002
nParams0.0020.0000.002
nSamples0.0020.0000.002
orthogonalizeTraceNorm0.0020.0000.002
penalty0.0020.0000.002
zinb.loglik0.0000.0000.001
zinb.loglik.dispersion000
zinbAIC0.2440.0020.246
zinbFit0.4510.0320.483
zinbInitialize0.0910.0240.116
zinbModel0.0030.0000.003
zinbOptimize0.1490.0070.156
zinbOptimizeDispersion0.0820.0010.082
zinbSim0.0200.0110.032
zinbsurf0.6810.0050.685
zinbwave0.7480.0080.755