Build/check report for BioC 3.17 - CHECK results for BASiCS on kunpeng1

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"	4259
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*

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BASiCS_2.11.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BASiCS.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 ‘BASiCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BASiCS’ version ‘2.11.5’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   8.2Mb
* 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             9.408  0.403   9.815
BASiCS_TestDE           8.929  0.123   9.054
newBASiCS_Chain         5.745  0.120   5.868
BASiCS_Chain            5.228  0.034   5.263
BASiCS_DivideAndConquer 3.735  0.320  45.440
* 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 ...
  ‘BASiCS.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/BASiCS.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BASiCS
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘BASiCS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -fopenmp -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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


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(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

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

    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
> 
> test_check("BASiCS")
Starting 2 test processes
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 455 ]
> 
> proc.time()
   user  system elapsed 
332.821 170.602 358.058

Example timings

name	user	system	elapsed
BASiCS_Chain-methods	3.201	0.085	3.291
BASiCS_Chain	5.228	0.034	5.263
BASiCS_CorrectOffset	0.013	0.009	0.027
BASiCS_DenoisedCounts	3.224	0.003	3.227
BASiCS_DenoisedRates	3.163	0.058	3.222
BASiCS_DetectVG	1.054	0.048	1.104
BASiCS_DiagHist	1.392	0.015	1.413
BASiCS_DiagPlot	2.706	0.044	2.753
BASiCS_DivideAndConquer	3.735	0.320	45.440
BASiCS_Draw	0.603	0.009	0.613
BASiCS_EffectiveSize	0.312	0.008	0.320
BASiCS_Filter	0.002	0.001	0.003
BASiCS_LoadChain	2.907	0.196	3.104
BASiCS_MCMC	9.408	0.403	9.815
BASiCS_MockSCE	0.555	0.004	0.559
BASiCS_PlotDE	4.546	0.156	4.704
BASiCS_PlotOffset	1.340	0.008	1.348
BASiCS_PlotVG	0.539	0.012	0.550
BASiCS_PriorParam	0.424	0.008	0.432
BASiCS_ShowFit	0.35	0.00	0.35
BASiCS_Sim	1.185	0.032	1.217
BASiCS_Summary-methods	0.006	0.000	0.006
BASiCS_Summary	2.968	0.072	3.042
BASiCS_TestDE	8.929	0.123	9.054
BASiCS_VarThresholdSearchHVG_LVG	3.123	0.007	3.132
BASiCS_VarianceDecomp	0.295	0.004	0.300
Summary-BASiCS_Chain-method	0.071	0.001	0.071
dim-BASiCS_Chain-method	0.004	0.003	0.008
dimnames-BASiCS_Chain-method	0.007	0.001	0.008
displayChainBASiCS-BASiCS_Chain-method	0.132	0.034	0.268
displaySummaryBASiCS-BASiCS_Summary-method	0.129	0.009	0.137
makeExampleBASiCS_Data	0.432	0.012	0.444
newBASiCS_Chain	5.745	0.120	5.868
plot-BASiCS_Chain-method	0.132	0.013	0.169
plot-BASiCS_Summary-method	0.133	0.005	0.138
show-BASiCS_ResultDE-method	0.120	0.016	0.136
show-BASiCS_ResultVG-method	0.129	0.008	0.137
show-BASiCS_ResultsDE-method	0.113	0.024	0.139
subset-BASiCS_Chain-method	1.325	0.020	1.345

CHECK results for BASiCS on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings