##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miloR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miloR_2.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/miloR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miloR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miloR’ version ‘2.0.0’
* 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 ‘miloR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDAbeeswarm: no visible binding for global variable ‘SpatialFDR’
plotDAbeeswarm: no visible binding for global variable ‘logFC’
plotDAbeeswarm: no visible binding for global variable ‘is_signif’
plotDAbeeswarm: no visible binding for global variable ‘Nhood’
plotDAbeeswarm: no visible binding for global variable ‘logFC_color’
plotNhoodCounts: no visible binding for global variable ‘cond’
plotNhoodCounts: no visible binding for global variable ‘values’
plotNhoodCounts: no visible binding for global variable ‘y’
plotNhoodExpressionDA: no visible binding for global variable ‘Nhood’
plotNhoodExpressionDA: no visible binding for global variable ‘logFC’
plotNhoodExpressionDA: no visible binding for global variable
  ‘SpatialFDR’
plotNhoodExpressionDA: no visible binding for global variable
  ‘logFC_rank’
plotNhoodExpressionDA: no visible binding for global variable ‘.’
plotNhoodExpressionDA: no visible binding for global variable
  ‘is_signif’
plotNhoodExpressionDA: no visible binding for global variable ‘feature’
plotNhoodExpressionDA: no visible binding for global variable
  ‘avg_expr’
plotNhoodExpressionDA: no visible binding for global variable ‘label’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘Nhood’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘NhoodGroup’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘logFC’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘feature’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘logFC_rank’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘avg_expr’
plotNhoodExpressionGroups: no visible binding for global variable ‘.’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘label’
plotNhoodGraph: no visible binding for global variable ‘weight’
plotNhoodGraph: no visible binding for global variable ‘size’
plotNhoodGraphDA: no visible binding for global variable ‘layout’
plotNhoodGroups: no visible binding for global variable ‘layout’
plotNhoodMA: no visible binding for global variable ‘logCPM’
plotNhoodMA: no visible binding for global variable ‘logFC’
plotNhoodMA: no visible binding for global variable ‘Sig’
plotNhoodSizeHist: no visible binding for global variable ‘nh_size’
testNhoods: no visible global function definition for ‘type’
Undefined global functions or variables:
  . Nhood NhoodGroup Sig SpatialFDR avg_expr cond feature is_signif
  label layout logCPM logFC logFC_color logFC_rank nh_size size type
  values weight y
Consider adding
  importFrom("graphics", "layout")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
findNhoodMarkers 9.755  0.182  11.886
testDiffExp      9.319  0.171  10.681
testNhoods       8.401  0.081   9.274
checkSeparation  8.325  0.106   9.898
plotNhoodCounts  7.167  0.075   7.829
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/miloR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miloR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp:237:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable]
    int stot = 0;
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp:197:10: warning: unused variable '_phi_est' [-Wunused-variable]
    bool _phi_est = true; // control if we re-estimate phi or not
         ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp:177:10: warning: unused variable '_phi_est' [-Wunused-variable]
    bool _phi_est = true; // control if we re-estimate phi or not
         ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c inference.cpp -o inference.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c invertPseudoVar.cpp -o invertPseudoVar.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c multiP.cpp -o multiP.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c paramEst.cpp -o paramEst.o
paramEst.cpp:29:33: warning: left operand of comma operator has no effect [-Wunused-value]
        double rhs = 0.5 * mid1[0, 0];
                                ^
paramEst.cpp:252:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:252:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:253:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:294:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:294:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:295:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:373:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:373:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:374:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:484:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:484:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:485:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:543:18: warning: variable 'inner_count' set but not used [-Wunused-but-set-variable]
    unsigned int inner_count = 0;
                 ^
paramEst.cpp:544:18: warning: unused variable 'outer_count' [-Wunused-variable]
    unsigned int outer_count = 0;
                 ^
paramEst.cpp:688:9: warning: unused variable 'j' [-Wunused-variable]
    int j, k, l, a;
        ^
paramEst.cpp:688:12: warning: unused variable 'k' [-Wunused-variable]
    int j, k, l, a;
           ^
paramEst.cpp:688:15: warning: unused variable 'l' [-Wunused-variable]
    int j, k, l, a;
              ^
paramEst.cpp:688:18: warning: unused variable 'a' [-Wunused-variable]
    int j, k, l, a;
                 ^
paramEst.cpp:866:12: warning: unused variable 'half_logli' [-Wunused-variable]
    double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
           ^
paramEst.cpp:871:10: warning: unused variable 'comp_vals' [-Wunused-variable]
    bool comp_vals = false;
         ^
21 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c pseudovarPartial.cpp -o pseudovarPartial.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-miloR/00new/miloR/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘graph’ in package ‘miloR’
** 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 (miloR)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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(miloR)
Loading required package: edgeR
Loading required package: limma
> require(mvtnorm)
Loading required package: mvtnorm
> require(scran)
Loading required package: scran
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 object is masked from 'package:limma':

    plotMA

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


Attaching package: 'SingleCellExperiment'

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

    cpm

Loading required package: scuttle
> require(scater)
Loading required package: scater
Loading required package: ggplot2

Attaching package: 'scater'

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

    plotMDS

> require(MASS)
Loading required package: MASS
> 
> test_check("miloR")
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected

Layout:
2 patch areas, spanning 2 columns and 1 rows

    t l b r
1:  1 1 1 1
2:  1 2 1 2
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected

Layout:
2 patch areas, spanning 2 columns and 1 rows

    t l b r
1:  1 1 1 1
2:  1 2 1 2
Coefficients not estimable: ConditionA 

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 213 ]
> 
> proc.time()
   user  system elapsed 
586.753  11.029 697.943