Package: netReg

Version: 1.6.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:netReg.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings netReg_1.6.0.tar.gz

StartedAt: 2019-04-16 01:45:47 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:46:10 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 23.2 seconds

RetCode: 0

Status:  OK

CheckDir: netReg.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:netReg.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings netReg_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/netReg.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netReg’ version ‘1.6.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘netReg’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 21.0Mb
  sub-directories of 1Mb or more:
    include  15.3Mb
    libs      4.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  BSL-1.0 + file LICENSE
* 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 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/netReg.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL netReg
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘netReg’ ...
configure: R home found in /home/biocbuild/bbs-3.8-bioc/R
configure: setting CXX to g++ -std=gnu++11
checking whether configure should try to set CXXFLAGS... no
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 g++ -std=gnu++11 accepts -g... yes
checking for a sed that does not truncate output... /bin/sed
checking for ranlib... ranlib
checking for library containing cblas_dgemm... no
configure: using rblas
checking whether g++ -std=gnu++11 supports C++11 features by default... yes
checking for g++ -std=gnu++11 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h

	Have fun with: netReg

	CXX:        g++ -std=gnu++11
	CXXFLAGS:   -g -O2
	CPPFLAGS:   -I/usr/local/include

** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c cv_set.cpp -o cv_set.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c data_factory.cpp -o data_factory.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c edgenet.cpp -o edgenet.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c edgenet_model_selection.cpp -o edgenet_model_selection.o
In file included from ../inst/include/dlib/matrix/../serialize.h:157:0,
                 from ../inst/include/dlib/matrix/matrix.h:9,
                 from ../inst/include/dlib/matrix.h:6,
                 from cross_validation.hpp:43,
                 from edgenet_model_selection.hpp:32,
                 from edgenet_model_selection.cpp:25:
../inst/include/dlib/matrix/../smart_pointers/shared_ptr.h:299:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<Y>& r
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from model_data.hpp:34,
                 from graph_model_data.hpp:28,
                 from graph_model_cv_data.hpp:28,
                 from edgenet_model_selection.hpp:31,
                 from edgenet_model_selection.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ../inst/include/dlib/matrix/../serialize.h:157:0,
                 from ../inst/include/dlib/matrix/matrix.h:9,
                 from ../inst/include/dlib/matrix.h:6,
                 from cross_validation.hpp:43,
                 from edgenet_model_selection.hpp:32,
                 from edgenet_model_selection.cpp:25:
../inst/include/dlib/matrix/../smart_pointers/shared_ptr.h:331:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<Y>& r
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from model_data.hpp:34,
                 from graph_model_data.hpp:28,
                 from graph_model_cv_data.hpp:28,
                 from edgenet_model_selection.hpp:31,
                 from edgenet_model_selection.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c edgenet_wrapper.cpp -o edgenet_wrapper.o
In file included from ../inst/include/dlib/matrix/../serialize.h:157:0,
                 from ../inst/include/dlib/matrix/matrix.h:9,
                 from ../inst/include/dlib/matrix.h:6,
                 from cross_validation.hpp:43,
                 from edgenet_model_selection.hpp:32,
                 from edgenet_wrapper.cpp:33:
../inst/include/dlib/matrix/../smart_pointers/shared_ptr.h:299:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<Y>& r
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from model_data.hpp:34,
                 from graph_model_data.hpp:28,
                 from edgenet_wrapper.hpp:29,
                 from edgenet_wrapper.cpp:31:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ../inst/include/dlib/matrix/../serialize.h:157:0,
                 from ../inst/include/dlib/matrix/matrix.h:9,
                 from ../inst/include/dlib/matrix.h:6,
                 from cross_validation.hpp:43,
                 from edgenet_model_selection.hpp:32,
                 from edgenet_wrapper.cpp:33:
../inst/include/dlib/matrix/../smart_pointers/shared_ptr.h:331:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<Y>& r
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from model_data.hpp:34,
                 from graph_model_data.hpp:28,
                 from edgenet_wrapper.hpp:29,
                 from edgenet_wrapper.cpp:31:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c graph_functions.cpp -o graph_functions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c graph_model_cv_data.cpp -o graph_model_cv_data.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c netReg_wrapper.cpp -o netReg_wrapper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c stat_functions.cpp -o stat_functions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -g -O2 -fopenmp -fpic  -g -O2 -Wall -c vector_functions.cpp -o vector_functions.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o netReg.so cv_set.o data_factory.o edgenet.o edgenet_model_selection.o edgenet_wrapper.o graph_functions.o graph_model_cv_data.o netReg_wrapper.o stat_functions.o vector_functions.o -fopenmp -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/netReg/libs
** R
** data
** 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
* DONE (netReg)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(netReg)
> 
> test_check("netReg")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 52 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  8.844   0.088   2.307 

name	user	system	elapsed
cv.edgenet	1.204	0.000	0.233
edgenet	0.328	0.000	0.061
predict.gaussian.edgenet	0	0	0