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This page was generated on 2021-09-22 15:04:46 -0400 (Wed, 22 Sep 2021).

CHECK results for BASiCS on nebbiolo1

To the developers/maintainers of the BASiCS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCS.git to
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raw results

Package 121/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BASiCS 2.4.0  (landing page)
Alan O'Callaghan
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/BASiCS
git_branch: RELEASE_3_13
git_last_commit: 385fa3d
git_last_commit_date: 2021-05-19 12:30:39 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BASiCS
Version: 2.4.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BASiCS_2.4.0.tar.gz
StartedAt: 2021-09-21 08:55:18 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:05:05 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 586.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BASiCS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BASiCS_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BASiCS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BASiCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BASiCS’ version ‘2.4.0’
* package encoding: UTF-8
* 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 ‘BASiCS’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   5.0Mb
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
BASiCS_MCMC             8.896  0.020   8.917
newBASiCS_Chain         6.436  0.020   6.456
BASiCS_TestDE           5.985  0.008   5.993
BASiCS_Chain            5.638  0.072   5.711
BASiCS_DivideAndConquer 3.015  0.014  15.726
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/BASiCS.Rcheck/00check.log’
for details.



Installation output

BASiCS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BASiCS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘BASiCS’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c BASiCS.cpp -o BASiCS.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-BASiCS/00new/BASiCS/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BASiCS)

Tests output

BASiCS.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(BASiCS)
Loading required package: SingleCellExperiment
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
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.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

    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
> 
> test_check("BASiCS")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 402 ]
> 
> proc.time()
   user  system elapsed 
317.342   4.396 321.841 

Example timings

BASiCS.Rcheck/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods3.6420.1483.794
BASiCS_Chain5.6380.0725.711
BASiCS_CorrectOffset0.0170.0040.021
BASiCS_DenoisedCounts3.5670.0003.566
BASiCS_DenoisedRates3.5150.0123.527
BASiCS_DetectVG0.5210.0040.524
BASiCS_DiagHist0.9320.0080.939
BASiCS_DiagPlot0.5480.0000.549
BASiCS_DivideAndConquer 3.015 0.01415.726
BASiCS_Draw0.6800.0070.687
BASiCS_EffectiveSize0.2020.0080.210
BASiCS_Filter0.0020.0000.002
BASiCS_LoadChain3.2860.0123.298
BASiCS_MCMC8.8960.0208.917
BASiCS_MockSCE0.6930.0000.693
BASiCS_PlotDE2.9960.0363.032
BASiCS_PlotOffset0.7690.0000.769
BASiCS_PlotVG0.2900.0160.305
BASiCS_PriorParam0.5360.0000.537
BASiCS_ShowFit0.1980.0040.202
BASiCS_Sim1.4220.0081.431
BASiCS_Summary-methods0.0050.0000.005
BASiCS_Summary3.4210.0203.441
BASiCS_TestDE5.9850.0085.993
BASiCS_VarThresholdSearchHVG_LVG1.6810.0201.701
BASiCS_VarianceDecomp0.1670.0000.167
Summary-BASiCS_Chain-method0.0450.0000.045
dim-BASiCS_Chain-method0.0040.0040.008
dimnames-BASiCS_Chain-method0.0010.0070.009
displayChainBASiCS-BASiCS_Chain-method0.0870.0260.125
displaySummaryBASiCS-BASiCS_Summary-method0.0960.0060.102
makeExampleBASiCS_Data0.5620.0000.563
newBASiCS_Chain6.4360.0206.456
plot-BASiCS_Chain-method0.0770.0230.101
plot-BASiCS_Summary-method0.0980.0040.103
show-BASiCS_ResultDE-method0.0890.0280.116
show-BASiCS_ResultVG-method0.0960.0060.101
show-BASiCS_ResultsDE-method0.0970.0000.097
subset-BASiCS_Chain-method0.8770.0040.881