Multiple platform build/check report for BioC 3.23 - BUILD BIN results for netboost on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4872
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4580
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*
BUILD BIN results for netboost on kjohnson3

To the developers/maintainers of the netboost package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netboost.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: netboost
Version: 2.19.0
Command: rm -rf netboost.buildbin-libdir && mkdir netboost.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netboost_2.19.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R netboost.buildbin-libdir
StartedAt: 2025-12-11 00:10:12 -0500 (Thu, 11 Dec 2025)
EndedAt: 2025-12-11 00:10:37 -0500 (Thu, 11 Dec 2025)
EllapsedTime: 24.5 seconds
RetCode: 0
Status: OK
PackageFile: netboost_2.19.0.tgz
PackageFileSize: 1.116 MiB
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf netboost.buildbin-libdir && mkdir netboost.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netboost_2.19.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R netboost.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=netboost.buildbin-libdir netboost_2.19.0.tar.gz'
>>>>>>> 

* installing *source* package ‘netboost’ ...
** this is package ‘netboost’ version ‘2.19.0’
** using staged installation
CLEANUP cleanup
Clean build.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang -arch arm64 -std=gnu2x
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 -std=gnu2x accepts -g... yes
checking for clang -arch arm64 -std=gnu2x option to accept ISO C89... unsupported
checking whether clang -arch arm64 -std=gnu2x understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of clang -arch arm64 -std=gnu2x... none
checking how to run the C preprocessor... clang -arch arm64 -std=gnu2x -E
checking build system type... arm-apple-darwin22.6.0
checking host system type... arm-apple-darwin22.6.0
checking for x86 cpuid  output... unknown
checking for x86-AVX xgetbv  output... unknown
checking whether C compiler accepts -Wno-deprecated... yes
checking for strip... strip
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/mcupgma/clustering_util/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -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'.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -falign-functions=64 -Wall -g -O2   -c boosting.cpp -o boosting.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
boosting.cpp:418:18: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
                 (col+1) * nrow,
                 ^~~~~~~~~~~~~~
boosting.cpp:419:18: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
                 (col+1) * (nrow + 256/sizeof(double))
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
boosting.cpp:646:29: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
                 bstep + 1, actual_sel + 1, actual_update);
                            ^~~~~~~~~~~~~~
boosting.cpp:729:19: note: in instantiation of function template specialization 'Boosting::filter_column_gen<true, false, true>' requested here
    return boost->filter_column_gen<true,false,true>(col_y-1);
                  ^
boosting.cpp:646:29: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
                 bstep + 1, actual_sel + 1, actual_update);
                            ^~~~~~~~~~~~~~
boosting.cpp:732:19: note: in instantiation of function template specialization 'Boosting::filter_column_gen<false, false, true>' requested here
    return boost->filter_column_gen<false,false,true>(col_y-1);
                  ^
boosting.cpp:79:15: warning: unused variable 'AVX_UNROLL' [-Wunused-const-variable]
constexpr int AVX_UNROLL = 4;
              ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -falign-functions=64 -Wall -g -O2   -c dist_tom.cpp -o dist_tom.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
In file included from dist_tom.cpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/Rcpp/r/check_r_headers.h:27:13: warning: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410 [-W#pragma-messages]
    #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -falign-functions=64 -Wall -g -O2   -c tree_sort.cpp -o tree_sort.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
In file included from tree_sort.cpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/Rcpp/r/check_r_headers.h:27:13: warning: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410 [-W#pragma-messages]
    #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
            ^
1 warning generated.
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -F/Library/Frameworks/R.framework/.. -framework R
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
strip -S netboost.so
installing via 'install.libs.R' to /Users/biocbuild/bbs-3.23-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC:  /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKyJwrX/R.INSTALLda8521e4713f/netboost"
[1] "R_PACKAGE_DIR:  /Users/biocbuild/bbs-3.23-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost"
[1] "R_ARCH:         "
[1] "SHLIB_EXT:      .so"
[1] "INSTALL PATH:  /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKyJwrX/R.INSTALLda8521e4713f/netboost/src/mcupgma/scripts/install_path.mk"
Clean build.
==== compiling clustering_util sources using external Makefile (clustering_util/Makefile) recursively 
make -C clustering_util  -f Makefile mcupgma_install
mkdir -p bin
mkdir -p obj.arm64_Darwin
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/ClusteringUtil.o ClusteringUtil.cpp
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/Tree.o Tree.cpp
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG   -o bin/edges2valid_clusters HashingMergerMain.cpp obj.arm64_Darwin/HashingMergerMain.cmdline.o obj.arm64_Darwin/ClusteringUtil.o obj.arm64_Darwin/Tree.o 
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -o bin/edge_collator EdgeCollatorMain.cpp obj.arm64_Darwin/EdgeCollatorMain.cmdline.o obj.arm64_Darwin/ClusteringUtil.o obj.arm64_Darwin/Tree.o 
==== compiling  sources using external Makefile (clustering_round/Makefile) recursively 
make -C clustering_round  -f Makefile
mkdir -p dep.arm64_Darwin 
test -d dep.arm64_Darwin && c++ -MM -MT 'dep.arm64_Darwin/test_heap.d  obj.arm64_Darwin/test_heap.o  obj.arm64_Darwin.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.arm64_Darwin/test_heap.d
test -d dep.arm64_Darwin && c++ -MM -MT 'dep.arm64_Darwin/HierarchicalClustering_with_unknown_edges.d  obj.arm64_Darwin/HierarchicalClustering_with_unknown_edges.o  obj.arm64_Darwin.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.arm64_Darwin/HierarchicalClustering_with_unknown_edges.d
test -d dep.arm64_Darwin && c++ -MM -MT 'dep.arm64_Darwin/HierarchicalClustering_main.d  obj.arm64_Darwin/HierarchicalClustering_main.o  obj.arm64_Darwin.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.arm64_Darwin/HierarchicalClustering_main.d
mkdir -p obj.arm64_Darwin 
mkdir -p bin
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.arm64_Darwin/HierarchicalClustering_main.o
HierarchicalClustering_main.cpp:79:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
cc -O3 -I./ -c HierarchicalClustering_main.cmdline.c -o obj.arm64_Darwin/HierarchicalClustering_main.cmdline.o
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.arm64_Darwin/HierarchicalClustering_with_unknown_edges.o
HierarchicalClustering_with_unknown_edges.cpp:26:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
HierarchicalClustering_with_unknown_edges.cpp:85:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized]
  ubEdgeHeap(edges.begin(), edges.size(), CompareEdgesByUpperBound(isLeftGreater)),
                                                                   ^
HierarchicalClustering_with_unknown_edges.cpp:86:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized]
  lbEdgeHeap(edges.begin(), edges.size(), CompareEdgesByLowerBound(isLeftGreater)),
                                                                   ^
3 warnings generated.
c++ obj.arm64_Darwin/HierarchicalClustering_main.o obj.arm64_Darwin/HierarchicalClustering_main.cmdline.o obj.arm64_Darwin/HierarchicalClustering_with_unknown_edges.o  -o bin/hierarchical_clustering  -O3
c++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.arm64_Darwin/test_heap.o
test_heap.cpp:20:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
cc -O3 -I./ -c test_heap.cmdline.c -o obj.arm64_Darwin/test_heap.cmdline.o
c++ obj.arm64_Darwin/test_heap.o obj.arm64_Darwin/test_heap.cmdline.o  -o bin/test_heap  -O3
[1] "SRC:  /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKyJwrX/R.INSTALLda8521e4713f/netboost/src/mcupgma"
[1] "DEST: /Users/biocbuild/bbs-3.23-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKyJwrX/R.INSTALLda8521e4713f/netboost/src/mcupgma/clustering_round/bin TO: /Users/biocbuild/bbs-3.23-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKyJwrX/R.INSTALLda8521e4713f/netboost/src/mcupgma/clustering_util/bin TO: /Users/biocbuild/bbs-3.23-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKyJwrX/R.INSTALLda8521e4713f/netboost/src/mcupgma/scripts TO: /Users/biocbuild/bbs-3.23-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "netboost.so"
** 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 (netboost)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR netboost.buildbin-libdir/netboost/libs/netboost.so
>>>>>>> 

>>>>>>> Paths before fix:
netboost.buildbin-libdir/netboost/libs/netboost.so:
	netboost.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libgcc_s.1.1.dylib" "netboost.buildbin-libdir/netboost/libs/netboost.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libgfortran.5.dylib" "netboost.buildbin-libdir/netboost/libs/netboost.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libquadmath.0.dylib" "netboost.buildbin-libdir/netboost/libs/netboost.so"

>>>>>>> Paths after fix:
netboost.buildbin-libdir/netboost/libs/netboost.so:
	netboost.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)