Back to Long Tests report for BioC 3.14

This page was generated on 2022-04-09 21:00:03 -0400 (Sat, 09 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4322
riesling1Windows Server 2019 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4108
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4135
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

CHECK results for DropletUtils on riesling1


To the developers/maintainers of the DropletUtils package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 13/19HostnameOS / ArchCHECK
DropletUtils 1.14.2  (landing page)
Jonathan Griffiths
Snapshot Date: 2022-04-09 06:55:01 -0400 (Sat, 09 Apr 2022)
git_url: https://git.bioconductor.org/packages/DropletUtils
git_branch: RELEASE_3_14
git_last_commit: 945504d
git_last_commit_date: 2022-01-08 01:37:27 -0400 (Sat, 08 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK  
riesling1Windows Server 2019 Standard / x64  ERROR  
machv2macOS 10.14.6 Mojave / x86_64  OK  

Summary

Package: DropletUtils
Version: 1.14.2
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no DropletUtils_1.14.2.tar.gz
StartedAt: 2022-04-09 08:07:09 -0400 (Sat, 09 Apr 2022)
EndedAt: 2022-04-09 08:19:54 -0400 (Sat, 09 Apr 2022)
EllapsedTime: 765.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: DropletUtils.Rcheck
Warnings: NA

Tests output

DropletUtils.Rcheck/tests_i386/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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")
== Failed tests ================================================================
-- Error (test-molinfo.R:21:5): works for version 3 ----------------------------
Error: cannot allocate vector of size 451.3 Mb
Backtrace:
    x
 1. \-DropletUtils::read10xMolInfo(fname, extract.library.info = TRUE) test-molinfo.R:21:4
 2.   +-base::as.vector(h5read(sample, path))
 3.   \-rhdf5::h5read(sample, path)
 4.     \-rhdf5:::h5readDataset(...)
 5.       \-base::tryCatch(...)
 6.         \-base:::tryCatchList(expr, classes, parentenv, handlers)
 7.           \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             \-value[[3L]](cond)
-- Error (test-molinfo.R:21:5): works for version 3 ----------------------------
Error: Error in h5checktype(). H5Identifier not valid.
Backtrace:
    x
 1. \-DropletUtils::read10xMolInfo(fname, extract.library.info = TRUE) test-molinfo.R:21:4
 2.   +-base::as.vector(h5read(sample, path))
 3.   \-rhdf5::h5read(sample, path)
 4.     \-rhdf5::H5Dclose(h5dataset)
 5.       \-rhdf5:::h5checktype(h5dataset, "dataset")
-- Error (test-molinfo.R:40:5): works for version 4 ----------------------------
Error: cannot allocate vector of size 614.2 Mb
Backtrace:
    x
 1. \-DropletUtils::read10xMolInfo(fname, extract.library.info = TRUE) test-molinfo.R:40:4
 2.   +-base::as.vector(h5read(sample, "/gem_group"))
 3.   \-rhdf5::h5read(sample, "/gem_group")
 4.     \-rhdf5:::h5readDataset(...)
 5.       \-base::tryCatch(...)
 6.         \-base:::tryCatchList(expr, classes, parentenv, handlers)
 7.           \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             \-value[[3L]](cond)
-- Error (test-molinfo.R:40:5): works for version 4 ----------------------------
Error: Error in h5checktype(). H5Identifier not valid.
Backtrace:
    x
 1. \-DropletUtils::read10xMolInfo(fname, extract.library.info = TRUE) test-molinfo.R:40:4
 2.   +-base::as.vector(h5read(sample, "/gem_group"))
 3.   \-rhdf5::h5read(sample, "/gem_group")
 4.     \-rhdf5::H5Dclose(h5dataset)
 5.       \-rhdf5:::h5checktype(h5dataset, "dataset")
-- Error (test-read10x.R:11:5): read10xCounts works for version 2 matrices (tarball) --
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error: Cholmod error 'out of memory' at file ../Core/cholmod_memory.c, line 146
Backtrace:
    x
 1. \-DropletUtils::read10xCounts(file.path(tmp, "filtered_gene_bc_matrices/GRCh38")) test-read10x.R:11:4
 2.   +-BiocParallel::bplapply(...)
 3.   \-BiocParallel::bplapply(...)
-- Error (test-read10x.R:117:5): read10xCounts works for version 4 matrices (tarball) --
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error: cannot allocate vector of size 441.1 Mb
Backtrace:
    x
 1. \-DropletUtils::read10xCounts(file.path(tmp, "raw_feature_bc_matrix")) test-read10x.R:117:4
 2.   +-BiocParallel::bplapply(...)
 3.   \-BiocParallel::bplapply(...)
-- Error (test-read10x.R:149:5): read10xCounts works for version 4 matrices (HDF5) --
Error: cannot allocate vector of size 441.1 Mb
Backtrace:
     x
  1. +-testthat::expect_type(counts(out2)[1, ], "integer") test-read10x.R:149:4
  2. | \-testthat::quasi_label(enquo(object), arg = "object")
  3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
  4. +-counts(out2)[1, ]
  5. \-counts(out2)[1, ]
  6.   +-base::drop(ans)
  7.   \-DelayedArray::drop(ans)
  8.     +-base::as.array(x, drop = TRUE)
  9.     \-DelayedArray::as.array.Array(x, drop = TRUE)
 10.       \-DelayedArray:::.from_Array_to_array(x, ...)
 11.         +-DelayedArray::extract_array(x, index)
 12.         \-DelayedArray::extract_array(x, index)
 13.           +-methods::callNextMethod()
 14.           \-DelayedArray:::.nextMethod(x = x, index = index)
 15.             +-DelayedArray::extract_array(x@seed, index)
 16.             \-DelayedArray::extract_array(x@seed, index)
 17.               +-DelayedArray::extract_array(x@seed, index)
 18.               \-DelayedArray::extract_array(x@seed, index)
 19.                 +-DelayedArray::extract_array(x2@seed, x2@index)
 20.                 \-HDF5Array::extract_array(x2@seed, x2@index)
 21.                   +-DelayedArray::extract_array(sas, index)
 22.                   \-DelayedArray::extract_array(sas, index)
 23.                     \-DelayedArray:::.extract_sparse_array_from_SparseArraySeed(...)

[ FAIL 7 | WARN 0 | SKIP 0 | PASS 44 ]
Error: Test failures
Execution halted

DropletUtils.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 
 245.06   15.90  271.56 

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no DropletUtils_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 '1.14.2'
* 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 whether package 'DropletUtils' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
   13.           +-methods::callNextMethod()
   14.           \-DelayedArray:::.nextMethod(x = x, index = index)
   15.             +-DelayedArray::extract_array(x@seed, index)
   16.             \-DelayedArray::extract_array(x@seed, index)
   17.               +-DelayedArray::extract_array(x@seed, index)
   18.               \-DelayedArray::extract_array(x@seed, index)
   19.                 +-DelayedArray::extract_array(x2@seed, x2@index)
   20.                 \-HDF5Array::extract_array(x2@seed, x2@index)
   21.                   +-DelayedArray::extract_array(sas, index)
   22.                   \-DelayedArray::extract_array(sas, index)
   23.                     \-DelayedArray:::.extract_sparse_array_from_SparseArraySeed(...)
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 44 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00check.log'
for details.


Installation output

DropletUtils.Rcheck/00install.out

* installing *source* package 'DropletUtils' ...
** using staged installation
** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c downsample_run.cpp -o downsample_run.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function 'Rcpp::IntegerVector encode_sequences(Rcpp::StringVector)':
encode_sequences.cpp:8:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (size_t i=0; i<output.size(); ++i) {
                      ~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_chimeric.cpp -o find_chimeric.o
find_chimeric.cpp: In function 'Rcpp::List find_chimeric(Rcpp::StringVector, Rcpp::IntegerVector, Rcpp::IntegerVector, double, bool)':
find_chimeric.cpp:28:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
     for (size_t i=0; i<nmolecules; ++i, ++uIt) {
                      ~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_swapped.cpp -o find_swapped.o
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from find_swapped.cpp:2:
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_cell_barcodes.cpp -o get_cell_barcodes.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function 'Rcpp::List group_cells(Rcpp::StringVector, Rcpp::IntegerVector)':
group_cells.cpp:10:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     if (N!=gems.size()) {
         ~^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hashed_deltas.cpp -o hashed_deltas.o
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from hashed_deltas.cpp:2:
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/fpclassify.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/random.hpp:69,
                 from montecarlo_pval.cpp:3:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
montecarlo_pval.cpp: In function 'Rcpp::IntegerVector montecarlo_pval(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::List, Rcpp::IntegerVector)':
montecarlo_pval.cpp:99:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
             if (higher<curlen) {
                 ~~~~~~^~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rand_custom.cpp -o rand_custom.o
rand_custom.cpp: In function 'void check_pcg_vectors(Rcpp::List, Rcpp::IntegerVector, size_t, const char*)':
rand_custom.cpp:8:21: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     if (seeds.size()!=N) {
         ~~~~~~~~~~~~^~~
rand_custom.cpp:14:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     if (streams.size()!=N) {
         ~~~~~~~~~~~~~~^~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o DropletUtils.dll tmp.def 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 -LD:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00LOCK-DropletUtils/00new/DropletUtils/libs/i386

*** arch - x64
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c downsample_run.cpp -o downsample_run.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function 'Rcpp::IntegerVector encode_sequences(Rcpp::StringVector)':
encode_sequences.cpp:8:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
     for (size_t i=0; i<output.size(); ++i) {
                      ~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_chimeric.cpp -o find_chimeric.o
find_chimeric.cpp: In function 'Rcpp::List find_chimeric(Rcpp::StringVector, Rcpp::IntegerVector, Rcpp::IntegerVector, double, bool)':
find_chimeric.cpp:28:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'long long int' [-Wsign-compare]
     for (size_t i=0; i<nmolecules; ++i, ++uIt) {
                      ~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_swapped.cpp -o find_swapped.o
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from find_swapped.cpp:2:
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_cell_barcodes.cpp -o get_cell_barcodes.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function 'Rcpp::List group_cells(Rcpp::StringVector, Rcpp::IntegerVector)':
group_cells.cpp:10:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
     if (N!=gems.size()) {
         ~^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hashed_deltas.cpp -o hashed_deltas.o
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from hashed_deltas.cpp:2:
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/fpclassify.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/random.hpp:69,
                 from montecarlo_pval.cpp:3:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
montecarlo_pval.cpp: In function 'Rcpp::IntegerVector montecarlo_pval(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::List, Rcpp::IntegerVector)':
montecarlo_pval.cpp:99:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
             if (higher<curlen) {
                 ~~~~~~^~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rand_custom.cpp -o rand_custom.o
rand_custom.cpp: In function 'void check_pcg_vectors(Rcpp::List, Rcpp::IntegerVector, size_t, const char*)':
rand_custom.cpp:8:21: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     if (seeds.size()!=N) {
         ~~~~~~~~~~~~^~~
rand_custom.cpp:14:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     if (streams.size()!=N) {
         ~~~~~~~~~~~~~~^~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/scuttle/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o DropletUtils.dll tmp.def 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 -LD:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/RcppExports.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/downsample_run.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/encode_sequences.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/find_chimeric.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/find_swapped.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/get_cell_barcodes.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/group_cells.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/hashed_deltas.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/montecarlo_pval.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/rand_custom.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00_pkg_src/DropletUtils/src-x64/utils.o: file format not recognized
There were 11 warnings (use warnings() to see them)
installing to D:/biocbuild/bbs-3.14-bioc-longtests/meat/DropletUtils.Rcheck/00LOCK-DropletUtils/00new/DropletUtils/libs/x64
** 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
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (DropletUtils)