Multiple platform build/check report for BioC 3.23 - INSTALL results for martini on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"	4866
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences"	4545
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*
INSTALL results for martini on kjohnson3

To the developers/maintainers of the martini package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/martini.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: martini
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL martini
StartedAt: 2026-03-20 17:53:35 -0400 (Fri, 20 Mar 2026)
EndedAt: 2026-03-20 17:53:42 -0400 (Fri, 20 Mar 2026)
EllapsedTime: 7.0 seconds
RetCode: 0
Status: OK
Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘martini’ ...
** this is package ‘martini’ version ‘1.31.0’
** 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/RcppEigen/include' -I/opt/R/arm64/include   -std=c++11  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS  -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
5 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/RcppEigen/include' -I/opt/R/arm64/include   -std=c++11  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS  -fPIC  -falign-functions=64 -Wall -g -O2   -c mincut.cpp -o mincut.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
In file included from mincut.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from mincut.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from mincut.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from mincut.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
5 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/RcppEigen/include' -I/opt/R/arm64/include   -std=c++11  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS  -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/maxflow/maxflow.cpp -o lib/maxflow/maxflow.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
lib/maxflow/maxflow.cpp:628:6: warning: variable 'num1' set but not used [-Wunused-but-set-variable]
  628 |         int num1 = 0, num2 = 0;
      |             ^
lib/maxflow/maxflow.cpp:628:16: warning: variable 'num2' set but not used [-Wunused-but-set-variable]
  628 |         int num1 = 0, num2 = 0;
      |                       ^
lib/maxflow/maxflow.cpp:555:19: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  555 |                                         j -> is_sink = 1;
      |                                                      ^ ~
lib/maxflow/instances.inc:15:16: note: in instantiation of member function 'Graph<int, int, int>::maxflow' requested here
   15 | template class Graph<int,int,int>;
      |                ^
In file included from lib/maxflow/maxflow.cpp:7:
lib/maxflow/maxflow.h:510:15: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  510 |         i->is_marked = 1;
      |                      ^ ~
lib/maxflow/instances.inc:15:16: note: in instantiation of member function 'Graph<int, int, int>::mark_node' requested here
   15 | template class Graph<int,int,int>;
      |                ^
lib/maxflow/maxflow.cpp:159:17: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  159 |                         i -> is_sink = 1;
      |                                      ^ ~
lib/maxflow/instances.inc:15:16: note: in instantiation of member function 'Graph<int, int, int>::maxflow_init' requested here
   15 | template class Graph<int,int,int>;
      |                ^
lib/maxflow/maxflow.cpp:221:16: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  221 |                                 i->is_sink = 1;
      |                                            ^ ~
lib/maxflow/instances.inc:15:16: note: in instantiation of member function 'Graph<int, int, int>::maxflow_reuse_trees_init' requested here
   15 | template class Graph<int,int,int>;
      |                ^
lib/maxflow/maxflow.cpp:555:19: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  555 |                                         j -> is_sink = 1;
      |                                                      ^ ~
lib/maxflow/instances.inc:16:16: note: in instantiation of member function 'Graph<short, int, int>::maxflow' requested here
   16 | template class Graph<short,int,int>;
      |                ^
In file included from lib/maxflow/maxflow.cpp:7:
lib/maxflow/maxflow.h:510:15: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  510 |         i->is_marked = 1;
      |                      ^ ~
lib/maxflow/instances.inc:16:16: note: in instantiation of member function 'Graph<short, int, int>::mark_node' requested here
   16 | template class Graph<short,int,int>;
      |                ^
lib/maxflow/maxflow.cpp:159:17: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  159 |                         i -> is_sink = 1;
      |                                      ^ ~
lib/maxflow/instances.inc:16:16: note: in instantiation of member function 'Graph<short, int, int>::maxflow_init' requested here
   16 | template class Graph<short,int,int>;
      |                ^
lib/maxflow/maxflow.cpp:221:16: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  221 |                                 i->is_sink = 1;
      |                                            ^ ~
lib/maxflow/instances.inc:16:16: note: in instantiation of member function 'Graph<short, int, int>::maxflow_reuse_trees_init' requested here
   16 | template class Graph<short,int,int>;
      |                ^
lib/maxflow/maxflow.cpp:555:19: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  555 |                                         j -> is_sink = 1;
      |                                                      ^ ~
lib/maxflow/instances.inc:17:16: note: in instantiation of member function 'Graph<float, float, float>::maxflow' requested here
   17 | template class Graph<float,float,float>;
      |                ^
In file included from lib/maxflow/maxflow.cpp:7:
lib/maxflow/maxflow.h:510:15: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  510 |         i->is_marked = 1;
      |                      ^ ~
lib/maxflow/instances.inc:17:16: note: in instantiation of member function 'Graph<float, float, float>::mark_node' requested here
   17 | template class Graph<float,float,float>;
      |                ^
lib/maxflow/maxflow.cpp:159:17: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  159 |                         i -> is_sink = 1;
      |                                      ^ ~
lib/maxflow/instances.inc:17:16: note: in instantiation of member function 'Graph<float, float, float>::maxflow_init' requested here
   17 | template class Graph<float,float,float>;
      |                ^
lib/maxflow/maxflow.cpp:221:16: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  221 |                                 i->is_sink = 1;
      |                                            ^ ~
lib/maxflow/instances.inc:17:16: note: in instantiation of member function 'Graph<float, float, float>::maxflow_reuse_trees_init' requested here
   17 | template class Graph<float,float,float>;
      |                ^
lib/maxflow/maxflow.cpp:555:19: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  555 |                                         j -> is_sink = 1;
      |                                                      ^ ~
lib/maxflow/instances.inc:18:16: note: in instantiation of member function 'Graph<double, double, double>::maxflow' requested here
   18 | template class Graph<double,double,double>;
      |                ^
In file included from lib/maxflow/maxflow.cpp:7:
lib/maxflow/maxflow.h:510:15: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  510 |         i->is_marked = 1;
      |                      ^ ~
lib/maxflow/instances.inc:18:16: note: in instantiation of member function 'Graph<double, double, double>::mark_node' requested here
   18 | template class Graph<double,double,double>;
      |                ^
lib/maxflow/maxflow.cpp:159:17: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  159 |                         i -> is_sink = 1;
      |                                      ^ ~
lib/maxflow/instances.inc:18:16: note: in instantiation of member function 'Graph<double, double, double>::maxflow_init' requested here
   18 | template class Graph<double,double,double>;
      |                ^
lib/maxflow/maxflow.cpp:221:16: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
  221 |                                 i->is_sink = 1;
      |                                            ^ ~
lib/maxflow/instances.inc:18:16: note: in instantiation of member function 'Graph<double, double, double>::maxflow_reuse_trees_init' requested here
   18 | template class Graph<double,double,double>;
      |                ^
18 warnings generated.
ar -crus libmaxflow.a lib/maxflow/maxflow.o
cp -r lib/maxflow "/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-martini/00new/martini/include"
mkdir -p "/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-martini/00new/martini/usrlib"
cp libmaxflow.a "/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-martini/00new/martini/usrlib"
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 martini.so RcppExports.o mincut.o -pthread /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-martini/00new/martini/usrlib/libmaxflow.a -pthread -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-martini/00new/martini/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (martini)