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This page was generated on 2026-04-14 11:36 -0400 (Tue, 14 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 alpha (2026-04-05 r89794) 4924
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-04-08 r89818) 4655
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

Package 1322/2394HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miloR 2.7.1  (landing page)
Mike Morgan
Snapshot Date: 2026-04-13 13:40 -0400 (Mon, 13 Apr 2026)
git_url: https://git.bioconductor.org/packages/miloR
git_branch: devel
git_last_commit: 936edb8
git_last_commit_date: 2026-04-13 04:51:39 -0400 (Mon, 13 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    WARNINGS  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  YES
See other builds for miloR in R Universe.

INSTALL results for miloR on kjohnson3

To the developers/maintainers of the miloR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miloR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: miloR
Version: 2.7.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miloR
StartedAt: 2026-04-13 15:31:53 -0400 (Mon, 13 Apr 2026)
EndedAt: 2026-04-13 15:32:30 -0400 (Mon, 13 Apr 2026)
EllapsedTime: 36.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### 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)