##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:screenCounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings screenCounter_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/screenCounter.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘screenCounter/DESCRIPTION’ ... OK
* this is package ‘screenCounter’ version ‘1.0.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘screenCounter’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/screenCounter.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL screenCounter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘screenCounter’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_combo_barcodes_paired.cpp -o count_combo_barcodes_paired.o
In file included from count_combo_barcodes_paired.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesPairedEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:465:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_combo_barcodes_paired.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesPairedEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_combo_barcodes_single.cpp -o count_combo_barcodes_single.o
In file included from count_combo_barcodes_single.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:5:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:465:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_combo_barcodes_single.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:5:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
In file included from count_combo_barcodes_single.cpp:3:
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:69:24: warning: unused variable 'len' [-Wunused-variable]
                size_t len = current.second - current.first;
                       ^
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:78:24: warning: unused variable 'len' [-Wunused-variable]
                size_t len = current.second - current.first;
                       ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_dual_barcodes.cpp -o count_dual_barcodes.o
In file included from count_dual_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:465:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_dual_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_random_barcodes.cpp -o count_random_barcodes.o
In file included from count_random_barcodes.cpp:3:
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:111:14: warning: unused variable 'found' [-Wunused-variable]
        bool found = false;
             ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_single_barcodes.cpp -o count_single_barcodes.o
In file included from count_single_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/SingleBarcodeSingleEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:465:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_single_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/SingleBarcodeSingleEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o screenCounter.so RcppExports.o count_combo_barcodes_paired.o count_combo_barcodes_single.o count_dual_barcodes.o count_random_barcodes.o count_single_barcodes.o utils.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-screenCounter/00new/screenCounter/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (screenCounter)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(screenCounter)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: 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: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("screenCounter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 264 ]
> 
> proc.time()
   user  system elapsed 
 18.225   0.916  34.899