##############################################################################
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###
### 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_2.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/miloR.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-15 01:03:26 UTC
* using option ‘--no-vignettes’
* checking for file ‘miloR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miloR’ version ‘2.7.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Milo.Rd: SingleCellExperiment-class
  buildGraph.Rd: SingleCellExperiment-class
  testNhoods.Rd: BiocParallelParam-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
  -std=c++11
* 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 ... INFO
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 ... 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/miloR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miloR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘miloR’ ...
** this is package ‘miloR’ version ‘2.7.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c computeMatrices.cpp -o computeMatrices.o
In file included from computeMatrices.cpp:1:
In file included from ./computeMatrices.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
computeMatrices.cpp:246:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable]
  246 |     int stot = 0;
      |         ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
In file included from fitGeneticPLGlmm.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
fitGeneticPLGlmm.cpp:113:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
  113 |     double _intercept = constval; // intercept for HE regression
      |            ^
fitGeneticPLGlmm.cpp:200:10: warning: unused variable '_phi_est' [-Wunused-variable]
  200 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c fitPLGlmm.cpp -o fitPLGlmm.o
In file included from fitPLGlmm.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
fitPLGlmm.cpp:106:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
  106 |     double _intercept = constval; // intercept for HE regression?? need a better estimate.
      |            ^
fitPLGlmm.cpp:172:10: warning: unused variable '_phi_est' [-Wunused-variable]
  172 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c inference.cpp -o inference.o
In file included from inference.cpp:1:
In file included from ./inference.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c invertPseudoVar.cpp -o invertPseudoVar.o
In file included from invertPseudoVar.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c multiP.cpp -o multiP.o
In file included from multiP.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c paramEst.cpp -o paramEst.o
In file included from paramEst.cpp:2:
In file included from ./paramEst.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
paramEst.cpp:36:33: warning: left operand of comma operator has no effect [-Wunused-value]
   36 |         double rhs = 0.5 * mid1[0, 0];
      |                                 ^
paramEst.cpp:172:12: warning: unused variable 'lambda' [-Wunused-variable]
  172 |     double lambda = 1e-1;
      |            ^~~~~~
paramEst.cpp:173:12: warning: unused variable 'lambda_step' [-Wunused-variable]
  173 |     double lambda_step = 10;
      |            ^~~~~~~~~~~
paramEst.cpp:174:12: warning: unused variable '_illcond_eps' [-Wunused-variable]
  174 |     double _illcond_eps = 1e-6;
      |            ^~~~~~~~~~~~
paramEst.cpp:175:12: warning: unused variable '_lcond_target' [-Wunused-variable]
  175 |     double _lcond_target = 1e-5;
      |            ^~~~~~~~~~~~~
paramEst.cpp:241:19: warning: unused variable 'nsq' [-Wunused-variable]
  241 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix, no diag
      |                   ^~~
paramEst.cpp:242:18: warning: unused variable 'i' [-Wunused-variable]
  242 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:242:21: warning: unused variable 'j' [-Wunused-variable]
  242 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:243:12: warning: unused variable '_ycovij' [-Wunused-variable]
  243 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp:276:19: warning: unused variable 'nsq' [-Wunused-variable]
  276 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:277:18: warning: unused variable 'i' [-Wunused-variable]
  277 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:277:21: warning: unused variable 'j' [-Wunused-variable]
  277 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:278:12: warning: unused variable '_ycovij' [-Wunused-variable]
  278 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp:342:19: warning: unused variable 'nsq' [-Wunused-variable]
  342 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:407:19: warning: unused variable 'nsq' [-Wunused-variable]
  407 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:408:18: warning: unused variable 'i' [-Wunused-variable]
  408 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:408:21: warning: unused variable 'j' [-Wunused-variable]
  408 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:439:19: warning: unused variable 'nsq' [-Wunused-variable]
  439 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:440:18: warning: unused variable 'i' [-Wunused-variable]
  440 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:440:21: warning: unused variable 'j' [-Wunused-variable]
  440 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:780:12: warning: unused variable 'half_logli' [-Wunused-variable]
  780 |     double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
      |            ^~~~~~~~~~
paramEst.cpp:785:10: warning: unused variable 'comp_vals' [-Wunused-variable]
  785 |     bool comp_vals = false;
      |          ^~~~~~~~~
23 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c pseudovarPartial.cpp -o pseudovarPartial.o
In file included from pseudovarPartial.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2   -std=c++11 -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
In file included from utils.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                 ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/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 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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> 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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
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 objects are masked from 'package:edgeR':

    cpm, tpm

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 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 214 ]
> 
> proc.time()
   user  system elapsed 
 99.678   1.752 103.290