R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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Platform: x86_64-apple-darwin20 (64-bit)

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> 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 0 | WARN 0 | SKIP 0 | PASS 78 ]
> 
> 
> proc.time()
   user  system elapsed 
345.762  34.064 403.149 

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no DropletUtils_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-longtests/meat/DropletUtils.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘DropletUtils/DESCRIPTION’ ... OK
* this is package ‘DropletUtils’ version ‘1.20.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package 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 ... SKIPPED
* 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 ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-longtests/meat/DropletUtils.Rcheck/00check.log’
for details.

* installing *source* package ‘DropletUtils’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c downsample_run.cpp -o downsample_run.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c encode_sequences.cpp -o encode_sequences.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c find_chimeric.cpp -o find_chimeric.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c find_swapped.cpp -o find_swapped.o
In file included from find_swapped.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
8 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c get_cell_barcodes.cpp -o get_cell_barcodes.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c group_cells.cpp -o group_cells.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hashed_deltas.cpp -o hashed_deltas.o
In file included from hashed_deltas.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
8 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c montecarlo_pval.cpp -o montecarlo_pval.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rand_custom.cpp -o rand_custom.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scuttle/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-longtests/meat/DropletUtils.Rcheck/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)