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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netboost.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netboost_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/netboost.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netboost/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netboost’ version ‘2.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘netboost’ can be installed ... WARNING
Found the following significant warnings:
  HierarchicalClustering_with_unknown_edges.cpp:85:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized]
  HierarchicalClustering_with_unknown_edges.cpp:86:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized]
See ‘/Users/biocbuild/bbs-3.18-bioc/meat/netboost.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives 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
cut_trees   21.706  0.666  23.592
nb_summary  20.955  0.391  22.589
nb_clust    20.941  0.310  22.485
tree_search 20.508  0.369  22.040
nb_mcupgma  19.743  0.411  21.195
nb_dist     19.742  0.238  20.573
nb_filter   13.542  0.367  14.341
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/netboost.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netboost
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘netboost’ ...
** using staged installation
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 x86_64
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 x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking whether clang -arch x86_64 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 x86_64... none
checking how to run the C preprocessor... clang -arch x86_64 -E
checking build system type... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
checking for x86 cpuid  output... unknown
checking for x86-AVX xgetbv  output... unknown
checking for x86 cpuid 0x00000000 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 0x80000000 output... 80000008:0:0:0
checking for x86 cpuid 0x00000001 output... 306e4:1200800:7fbee3ff:bfebfbff
checking for x86 cpuid 0x00000007 output... 0:281:0:9c000400
checking for x86 cpuid 0x80000001 output... 0:0:1:2c100800
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether RDRND is supported by the processor... yes
checking whether RDRND is supported by the processor and OS... yes
checking whether C compiler accepts -mrdrnd... yes
checking whether BMI1 is supported by the processor... no
checking whether BMI2 is supported by the processor... no
checking whether ADX is supported by the processor... no
checking whether MPX is supported by the processor... no
checking whether PREFETCHWT1 is supported by the processor... no
checking whether ABM is supported by the processor... no
checking whether MMX is supported by the processor... yes
checking whether MMX is supported by the processor and OS... yes
checking whether C compiler accepts -mmmx... yes
checking whether SSE is supported by the processor... yes
checking whether SSE is supported by the processor and OS... yes
checking whether C compiler accepts -msse... yes
checking whether SSE2 is supported by the processor... yes
checking whether SSE2 is supported by the processor and OS... yes
checking whether C compiler accepts -msse2... yes
checking whether SSE3 is supported by the processor... yes
checking whether SSE3 is supported by the processor and OS... yes
checking whether C compiler accepts -msse3... yes
checking whether SSSE3 is supported by the processor... yes
checking whether SSSE3 is supported by the processor and OS... yes
checking whether C compiler accepts -mssse3... yes
checking whether SSE4.1 is supported by the processor... yes
checking whether SSE4.1 is supported by the processor and OS... yes
checking whether C compiler accepts -msse4.1... yes
checking whether SSE4.2 is supported by the processor... yes
checking whether SSE4.2 is supported by the processor and OS... yes
checking whether C compiler accepts -msse4.2... yes
checking whether SSE4a is supported by the processor... no
checking whether SHA is supported by the processor... no
checking whether AES is supported by the processor... yes
checking whether AES is supported by the processor and OS... yes
checking whether C compiler accepts -maes... yes
checking whether AVX is supported by the processor... yes
checking whether AVX is supported by the processor and OS... yes
checking whether C compiler accepts -mavx... yes
checking whether FMA3 is supported by the processor... no
checking whether FMA4 is supported by the processor... no
checking whether XOP is supported by the processor... no
checking whether AVX2 is supported by the processor... no
checking whether AVX512-F is supported by the processor... no
checking whether AVX512-CD is supported by the processor... no
checking whether AVX512-PF is supported by the processor... no
checking whether AVX512-ER is supported by the processor... no
checking whether AVX512-VL is supported by the processor... no
checking whether AVX512-BW is supported by the processor... no
checking whether AVX512-DQ is supported by the processor... no
checking whether AVX512-IFMA is supported by the processor... no
checking whether AVX512-VBMI is supported by the processor... no
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 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -fPIC  -falign-functions=64 -Wall -g -O2  -c boosting.cpp -o boosting.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -fPIC  -falign-functions=64 -Wall -g -O2  -c dist_tom.cpp -o dist_tom.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -fPIC  -falign-functions=64 -Wall -g -O2  -c tree_sort.cpp -o tree_sort.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
strip -S netboost.so
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC:  /Users/biocbuild/bbs-3.18-bioc/meat/netboost"
[1] "R_PACKAGE_DIR:  /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-netboost/00new/netboost"
[1] "R_ARCH:         "
[1] "SHLIB_EXT:      .so"
[1] "INSTALL PATH:  /Users/biocbuild/bbs-3.18-bioc/meat/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.x86_64_Darwin
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Darwin/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Darwin/ClusteringUtil.o ClusteringUtil.cpp
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Darwin/Tree.o Tree.cpp
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG   -o bin/edges2valid_clusters HashingMergerMain.cpp obj.x86_64_Darwin/HashingMergerMain.cmdline.o obj.x86_64_Darwin/ClusteringUtil.o obj.x86_64_Darwin/Tree.o 
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Darwin/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -o bin/edge_collator EdgeCollatorMain.cpp obj.x86_64_Darwin/EdgeCollatorMain.cmdline.o obj.x86_64_Darwin/ClusteringUtil.o obj.x86_64_Darwin/Tree.o 
==== compiling  sources using external Makefile (clustering_round/Makefile) recursively 
make -C clustering_round  -f Makefile
mkdir -p dep.x86_64_Darwin 
test -d dep.x86_64_Darwin && c++ -MM -MT 'dep.x86_64_Darwin/test_heap.d  obj.x86_64_Darwin/test_heap.o  obj.x86_64_Darwin.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.x86_64_Darwin/test_heap.d
test -d dep.x86_64_Darwin && c++ -MM -MT 'dep.x86_64_Darwin/HierarchicalClustering_with_unknown_edges.d  obj.x86_64_Darwin/HierarchicalClustering_with_unknown_edges.o  obj.x86_64_Darwin.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.x86_64_Darwin/HierarchicalClustering_with_unknown_edges.d
test -d dep.x86_64_Darwin && c++ -MM -MT 'dep.x86_64_Darwin/HierarchicalClustering_main.d  obj.x86_64_Darwin/HierarchicalClustering_main.o  obj.x86_64_Darwin.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.x86_64_Darwin/HierarchicalClustering_main.d
mkdir -p obj.x86_64_Darwin 
mkdir -p bin
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.x86_64_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.x86_64_Darwin/HierarchicalClustering_main.cmdline.o
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.x86_64_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.x86_64_Darwin/HierarchicalClustering_main.o obj.x86_64_Darwin/HierarchicalClustering_main.cmdline.o obj.x86_64_Darwin/HierarchicalClustering_with_unknown_edges.o  -o bin/hierarchical_clustering  -O3
c++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.x86_64_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.x86_64_Darwin/test_heap.cmdline.o
c++ obj.x86_64_Darwin/test_heap.o obj.x86_64_Darwin/test_heap.cmdline.o  -o bin/test_heap  -O3
[1] "SRC:  /Users/biocbuild/bbs-3.18-bioc/meat/netboost/src/mcupgma"
[1] "DEST: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /Users/biocbuild/bbs-3.18-bioc/meat/netboost/src/mcupgma/clustering_round/bin TO: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /Users/biocbuild/bbs-3.18-bioc/meat/netboost/src/mcupgma/clustering_util/bin TO: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /Users/biocbuild/bbs-3.18-bioc/meat/netboost/src/mcupgma/scripts TO: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/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)