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CHECK report for networkBMA on malbec2

This page was generated on 2018-10-17 08:24:29 -0400 (Wed, 17 Oct 2018).

Package 994/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
networkBMA 2.20.0
Ka Yee Yeung
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/networkBMA
Branch: RELEASE_3_7
Last Commit: b0c0668
Last Changed Date: 2018-04-30 10:35:26 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: networkBMA
Version: 2.20.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:networkBMA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings networkBMA_2.20.0.tar.gz
StartedAt: 2018-10-16 02:22:16 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:23:16 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 59.7 seconds
RetCode: 0
Status:  OK 
CheckDir: networkBMA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:networkBMA.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings networkBMA_2.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/networkBMA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘networkBMA/DESCRIPTION’ ... OK
* this is package ‘networkBMA’ version ‘2.20.0’
* 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 ‘networkBMA’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.5Mb
* 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 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/networkBMA.Rcheck/00check.log’
for details.

Installation output

networkBMA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL networkBMA
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘networkBMA’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -c MurmurHash3.cpp -o MurmurHash3.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -c ScanBMA_full.cpp -o ScanBMA_full.o
ScanBMA_full.cpp: In function ‘const List ScanBMA_BIC(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double)’:
ScanBMA_full.cpp:137:45: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
   arma::uvec pord = sort_index(priorProbs, 1);
                                             ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:449:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
ScanBMA_full.cpp: In function ‘const List BMA_Diff_BIC(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::IntegerVector, bool, bool, Rcpp::IntegerVector, Rcpp::IntegerVector, double, double)’:
ScanBMA_full.cpp:328:43: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
 arma::uvec pord = sort_index(priorProbs, 1);
                                           ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:449:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
ScanBMA_full.cpp: In function ‘const List ScanBMA_g(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double, double)’:
ScanBMA_full.cpp:421:45: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
   arma::uvec pord = sort_index(priorProbs, 1);
                                             ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:449:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
ScanBMA_full.cpp: In function ‘const List BMA_Diff_g(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double, Rcpp::IntegerVector, bool, bool, Rcpp::IntegerVector, Rcpp::IntegerVector, double, double)’:
ScanBMA_full.cpp:614:43: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
 arma::uvec pord = sort_index(priorProbs, 1);
                                           ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:449:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -c fastBMAR.cpp -o fastBMAR.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o networkBMA.so MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/networkBMA/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 (networkBMA)

Tests output

Example timings

networkBMA.Rcheck/networkBMA-Ex.timings

nameusersystemelapsed
ScanBMA0.0840.0080.115
ScanBMAcontrol4.0880.0044.096
contabs1.2080.0041.213
contabs.netwBMA0.0040.0000.000
contabs.prelim0.0000.0000.001
fastBMAcontrol0.0600.0040.063
fastgControl0.0640.0000.064
gControl4.2200.0164.239
iBMAcontrolLM0.4160.0000.417
iterateBMAlm0.6920.0040.697
networkBMA0.2360.0080.243
roc0.6280.0000.628
scores0.6440.0040.652
summary.networkBMA0.2440.0000.247
varord0.1440.0000.145
vignette3.6040.0083.626
writeEdges0.5400.0000.539