netReg 1.0.1
Simon Dirmeier
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/netReg | | Last Changed Rev: 129423 / Revision: 131943 | | Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings netReg_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/netReg.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.0.1’
* 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 70.1Mb
sub-directories of 1Mb or more:
include 65.3Mb
libs 4.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... 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 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cv.edgenet 9.88 0.024 0.977
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.5-bioc/meat/netReg.Rcheck/00check.log’
for details.
* installing *source* package ‘netReg’ ...
configure: R home found in /home/biocbuild/bbs-3.5-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
config.status: src/config.h is unchanged
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-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c cv_set.cpp -o cv_set.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c edgenet_binomial.cpp -o edgenet_binomial.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c edgenet_gaussian.cpp -o edgenet_gaussian.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c edgenet_gaussian_model_selection.cpp -o edgenet_gaussian_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 edgenet_gaussian_loss_function.hpp:42,
from optim.hpp:44,
from edgenet_gaussian_model_selection.cpp:10:
../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-3.5-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from linear_model_data.hpp:34,
from penalized_linear_model_data.hpp:28,
from graph_penalized_linear_model_data.hpp:9,
from graph_penalized_linear_model_cv_data.hpp:29,
from edgenet_gaussian_model_selection.hpp:12,
from edgenet_gaussian_model_selection.cpp:7:
/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 edgenet_gaussian_loss_function.hpp:42,
from optim.hpp:44,
from edgenet_gaussian_model_selection.cpp:10:
../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-3.5-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from linear_model_data.hpp:34,
from penalized_linear_model_data.hpp:28,
from graph_penalized_linear_model_data.hpp:9,
from graph_penalized_linear_model_cv_data.hpp:29,
from edgenet_gaussian_model_selection.hpp:12,
from edgenet_gaussian_model_selection.cpp:7:
/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-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c edgenet_wrapper.cpp -o edgenet_wrapper.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c graph_functions.cpp -o graph_functions.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c graph_penalized_linear_model_cv_data.cpp -o graph_penalized_linear_model_cv_data.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c math_functions.cpp -o math_functions.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c netReg_wrapper.cpp -o netReg_wrapper.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c stat_functions.cpp -o stat_functions.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -g -O2 -fopenmp -I. -fpic -g -O2 -c vector_functions.cpp -o vector_functions.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o netReg.so cv_set.o edgenet_binomial.o edgenet_gaussian.o edgenet_gaussian_model_selection.o edgenet_wrapper.o graph_functions.o graph_penalized_linear_model_cv_data.o math_functions.o netReg_wrapper.o stat_functions.o vector_functions.o -fopenmp -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/netReg.Rcheck/netReg/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (netReg)