Multiple platform build/check report for BioC 3.12 - CHECK report for BASiCS on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BASiCS_2.2.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BASiCS.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.2.4’
* 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 10.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.4Mb
* 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 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_TestDE                    9.812  0.016   9.845
BASiCS_MCMC                      7.500  0.024   7.545
BASiCS_VarThresholdSearchHVG_LVG 6.304  0.008   6.333
newBASiCS_Chain                  4.960  0.152   5.126
BASiCS_DivideAndConquer          2.976  0.276  19.479
* 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-3.12-bioc/meat/BASiCS.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BASiCS
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BASiCS’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c BASiCS.cpp -o BASiCS.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/armadillo:355:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from libraries.h:11,
                 from utils.h:4,
                 from updates.h:4,
                 from BASiCS.cpp:1:
In static member function ‘static void arma::memory::release(eT*) [with eT = const int]’,
    inlined from ‘arma::Mat<eT>::~Mat() [with eT = int]’ at /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:30:20,
    inlined from ‘arma::Col<int>::~Col()’ at /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/Col_bones.hpp:23:7,
    inlined from ‘Rcpp::List BASiCS_MCMCcppNoSpikes(int, int, int, arma::mat, arma::mat, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, double, double, double, double, double, double, double, double, double, double, arma::vec, int, arma::vec, arma::vec, arma::vec, int, double, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int, int, int, const double&, const double&, const double&, const double&, const double&, const double&, int)’ at MCMCNoSpikes.h:241:20:
/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:115:9: warning: attempt to free a non-heap object ‘<anonymous>’ [-Wfree-nonheap-object]
     free( (void *)(mem) );
     ~~~~^~~~~~~~~~~~~~~~~
In static member function ‘static void arma::memory::release(eT*) [with eT = const int]’,
    inlined from ‘arma::Mat<eT>::~Mat() [with eT = int]’ at /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:30:20,
    inlined from ‘arma::Col<int>::~Col()’ at /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/Col_bones.hpp:23:7,
    inlined from ‘Rcpp::List BASiCS_MCMCcppRegNoSpikes(int, int, int, arma::mat, arma::mat, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, double, double, double, double, double, int, arma::vec, arma::mat, double, double, arma::vec, double, double, arma::vec, const double&, double, arma::vec, int, arma::vec, arma::vec, arma::vec, int, double, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, int, int, int, bool, bool, arma::vec, const double&, const double&, const double&, const double&, const double&, const double&, int)’ at MCMCRegNoSpikes.h:280:37:
/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:115:9: warning: attempt to free a non-heap object ‘<anonymous>’ [-Wfree-nonheap-object]
     free( (void *)(mem) );
     ~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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 version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 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")'.


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 0 | SKIP 0 | PASS 403 ]
> 
> proc.time()
   user  system elapsed 
253.140   1.284 255.037

Example timings

name	user	system	elapsed
BASiCS_Chain-methods	2.716	0.092	2.812
BASiCS_Chain	4.280	0.016	4.310
BASiCS_CorrectOffset	0.012	0.004	0.017
BASiCS_DenoisedCounts	2.832	0.000	2.842
BASiCS_DenoisedRates	2.62	0.00	2.63
BASiCS_DetectVG	1.768	0.040	1.814
BASiCS_DiagHist	1.748	0.020	1.767
BASiCS_DiagPlot	1.044	0.004	1.058
BASiCS_DivideAndConquer	2.976	0.276	19.479
BASiCS_Draw	0.444	0.044	0.488
BASiCS_EffectiveSize	0.372	0.036	0.412
BASiCS_Filter	0.000	0.000	0.003
BASiCS_LoadChain	2.256	0.124	2.388
BASiCS_MCMC	7.500	0.024	7.545
BASiCS_MockSCE	0.300	0.000	0.304
BASiCS_PlotDE	4.968	0.016	4.991
BASiCS_PlotOffset	1.372	0.000	1.373
BASiCS_PlotVG	0.724	0.000	0.725
BASiCS_PriorParam	0.268	0.000	0.266
BASiCS_ShowFit	0.392	0.000	0.395
BASiCS_Sim	0.920	0.004	0.925
BASiCS_Summary-methods	0.008	0.000	0.007
BASiCS_Summary	2.580	0.008	2.601
BASiCS_TestDE	9.812	0.016	9.845
BASiCS_VarThresholdSearchHVG_LVG	6.304	0.008	6.333
BASiCS_VarianceDecomp	0.308	0.000	0.307
Summary-BASiCS_Chain-method	0.100	0.004	0.106
dim-BASiCS_Chain-method	0.004	0.004	0.010
dimnames-BASiCS_Chain-method	0.012	0.000	0.010
displayChainBASiCS-BASiCS_Chain-method	0.200	0.072	1.421
displaySummaryBASiCS-BASiCS_Summary-method	0.176	0.060	0.244
makeExampleBASiCS_Data	0.216	0.024	0.244
newBASiCS_Chain	4.960	0.152	5.126
plot-BASiCS_Chain-method	0.112	0.036	0.154
plot-BASiCS_Summary-method	0.168	0.068	0.243
show-BASiCS_ResultDE-method	0.176	0.056	0.237
show-BASiCS_ResultVG-method	0.164	0.076	0.262
show-BASiCS_ResultsDE-method	0.180	0.076	0.268
subset-BASiCS_Chain-method	1.324	0.108	1.448

CHECK report for BASiCS on malbec1

Summary

Command output

Installation output

Tests output

Example timings