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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:netboost.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings netboost_2.7.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/netboost.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘netboost/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netboost’ version ‘2.7.3’
* 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 ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 dependencies in R code ... OK
* 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   14.649  0.208  14.860
nb_summary  14.452  0.052  14.504
nb_clust    14.239  0.008  14.247
nb_mcupgma  14.010  0.068  14.079
tree_search 13.762  0.060  13.823
nb_dist     13.692  0.048  13.741
nb_filter    9.700  0.004   9.704
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘netboost.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/netboost.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL netboost
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
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: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -c boosting.cpp -o boosting.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -c dist_tom.cpp -o dist_tom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -c tree_sort.cpp -o tree_sort.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
strip -S netboost.so
installing via 'install.libs.R' to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC:  /home/biocbuild/bbs-3.17-bioc/meat/netboost"
[1] "R_PACKAGE_DIR:  /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-netboost/00new/netboost"
[1] "R_ARCH:         "
[1] "SHLIB_EXT:      .so"
[1] "INSTALL PATH:  /home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma/scripts/install_path.mk"
make: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma'
Clean build.
make: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma'
make: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma'
==== compiling clustering_util sources using external Makefile (clustering_util/Makefile) recursively 
make -C clustering_util  -f Makefile mcupgma_install
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma/clustering_util'
mkdir -p bin
mkdir -p obj.aarch64_Linux
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/ClusteringUtil.o ClusteringUtil.cpp
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/Tree.o Tree.cpp
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG   -o bin/edges2valid_clusters HashingMergerMain.cpp obj.aarch64_Linux/HashingMergerMain.cmdline.o obj.aarch64_Linux/ClusteringUtil.o obj.aarch64_Linux/Tree.o 
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -o bin/edge_collator EdgeCollatorMain.cpp obj.aarch64_Linux/EdgeCollatorMain.cmdline.o obj.aarch64_Linux/ClusteringUtil.o obj.aarch64_Linux/Tree.o 
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma/clustering_util'
==== compiling  sources using external Makefile (clustering_round/Makefile) recursively 
make -C clustering_round  -f Makefile
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma/clustering_round'
mkdir -p dep.aarch64_Linux 
test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/test_heap.d  obj.aarch64_Linux/test_heap.o  obj.aarch64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.aarch64_Linux/test_heap.d
test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d  obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o  obj.aarch64_Linux.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d
test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/HierarchicalClustering_main.d  obj.aarch64_Linux/HierarchicalClustering_main.o  obj.aarch64_Linux.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.aarch64_Linux/HierarchicalClustering_main.d
test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/test_heap.d  obj.aarch64_Linux/test_heap.o  obj.aarch64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.aarch64_Linux/test_heap.d
mkdir -p obj.aarch64_Linux 
mkdir -p bin
g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.aarch64_Linux/HierarchicalClustering_main.o
cc -O3 -I./ -c HierarchicalClustering_main.cmdline.c -o obj.aarch64_Linux/HierarchicalClustering_main.cmdline.o
g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o
g++ obj.aarch64_Linux/HierarchicalClustering_main.o obj.aarch64_Linux/HierarchicalClustering_main.cmdline.o obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o  -o bin/hierarchical_clustering  -O3
g++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.aarch64_Linux/test_heap.o
cc -O3 -I./ -c test_heap.cmdline.c -o obj.aarch64_Linux/test_heap.cmdline.o
g++ obj.aarch64_Linux/test_heap.o obj.aarch64_Linux/test_heap.cmdline.o  -o bin/test_heap  -O3
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma/clustering_round'
make: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma'
[1] "SRC:  /home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma"
[1] "DEST: /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma/clustering_round/bin TO: /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma/clustering_util/bin TO: /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.17-bioc/meat/netboost/src/mcupgma/scripts TO: /home/biocbuild/bbs-3.17-bioc/R/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)