##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SingleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SingleR_2.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SingleR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SingleR/DESCRIPTION’ ... OK
* this is package ‘SingleR’ version ‘2.7.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SingleR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 code 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/SingleR/libs/SingleR.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plotScoreDistribution 10.574  0.141  10.753
plotDeltaDistribution  5.741  0.112   5.881
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SingleR.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c find_classic_markers.cpp -o find_classic_markers.o
In file included from find_classic_markers.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from find_classic_markers.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
    bool remaining = true;
         ^
2 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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c grouped_medians.cpp -o grouped_medians.o
In file included from grouped_medians.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from grouped_medians.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
    bool remaining = true;
         ^
2 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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c integrate_build.cpp -o integrate_build.o
In file included from integrate_build.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from integrate_build.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
    bool remaining = true;
         ^
2 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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c integrate_run.cpp -o integrate_run.o
In file included from integrate_run.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from integrate_run.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
    bool remaining = true;
         ^
2 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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c prebuild.cpp -o prebuild.o
In file included from prebuild.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from prebuild.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
    bool remaining = true;
         ^
2 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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c run.cpp -o run.o
In file included from run.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from run.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
    bool remaining = true;
         ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SingleR.so RcppExports.o find_classic_markers.o grouped_medians.o integrate_build.o integrate_run.o prebuild.o run.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-SingleR/00new/SingleR/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 (SingleR)

R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(SingleR)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

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

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> test_check("SingleR")
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 301 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 301 ]
> 
> proc.time()
   user  system elapsed 
 75.248   1.536 131.731