##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings DropletUtils_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DropletUtils.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘DropletUtils/DESCRIPTION’ ... OK
* this is package ‘DropletUtils’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DropletUtils’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
* 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 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 ... 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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.0/site-library/DropletUtils/libs/DropletUtils.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  The following objects are masked from 'package:matrixStats':
  
      anyMissing, rowMedians
  
  > test_check("DropletUtils")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 1003 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-hashing.R:244:9'): edge cases are handled correctly with combinatorial barcodes ──
  out$LogFC not identical to .compute_expected_lfc(SCALING, PSEUDO).
  Objects equal but not identical
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 1003 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘DropletUtils.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/DropletUtils.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL DropletUtils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘DropletUtils’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c downsample_run.cpp -o downsample_run.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c encode_sequences.cpp -o encode_sequences.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c find_chimeric.cpp -o find_chimeric.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c find_swapped.cpp -o find_swapped.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c get_cell_barcodes.cpp -o get_cell_barcodes.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c group_cells.cpp -o group_cells.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c hashed_deltas.cpp -o hashed_deltas.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c montecarlo_pval.cpp -o montecarlo_pval.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c rand_custom.cpp -o rand_custom.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.3.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o DropletUtils.so RcppExports.o downsample_run.o encode_sequences.o find_chimeric.o find_swapped.o get_cell_barcodes.o group_cells.o hashed_deltas.o montecarlo_pval.o rand_custom.o utils.o /home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-DropletUtils/00new/DropletUtils/libs
** R
** 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 (DropletUtils)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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(DropletUtils)
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 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

> test_check("DropletUtils")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 1003 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-hashing.R:244:9'): edge cases are handled correctly with combinatorial barcodes ──
out$LogFC not identical to .compute_expected_lfc(SCALING, PSEUDO).
Objects equal but not identical

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 1003 ]
Error: Test failures
Execution halted