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BioC 3.5: CHECK report for networkBMA on malbec2

This page was generated on 2017-08-16 13:14:35 -0400 (Wed, 16 Aug 2017).

Package 897/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
networkBMA 2.16.1
Ka Yee Yeung
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/networkBMA
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 [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: networkBMA
Version: 2.16.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings networkBMA_2.16.1.tar.gz
StartedAt: 2017-08-16 00:59:03 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:00:45 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 102.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: networkBMA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings networkBMA_2.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/networkBMA.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 ‘networkBMA/DESCRIPTION’ ... OK
* this is package ‘networkBMA’ version ‘2.16.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘src’ contains:
  bmaNoMPI.hpp config.h.in fastBMA.hpp my_sort.hpp
These are unlikely file names for src files.
* 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  8.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.4Mb
* 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 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 installed files from ‘inst/doc’ ... 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/networkBMA.Rcheck/00check.log’
for details.

networkBMA.Rcheck/00install.out:

* installing *source* package ‘networkBMA’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/library/RcppArmadillo/include/armadillo:457:0,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.5-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-3.5-bioc/R/library/RcppArmadillo/include/armadillo:457:0,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.5-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-3.5-bioc/R/library/RcppArmadillo/include/armadillo:457:0,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.5-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-3.5-bioc/R/library/RcppArmadillo/include/armadillo:457:0,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I./include -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -L/usr/local/lib -o networkBMA.so MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/networkBMA.Rcheck/networkBMA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (networkBMA)

networkBMA.Rcheck/networkBMA-Ex.timings:

nameusersystemelapsed
ScanBMA0.1520.0080.162
ScanBMAcontrol4.2320.0164.249
contabs1.3880.0001.390
contabs.netwBMA000
contabs.prelim0.0000.0000.001
fastBMAcontrol0.0640.0000.061
fastgControl0.1080.0000.108
gControl4.0080.0004.009
iBMAcontrolLM0.9160.0040.921
iterateBMAlm0.7600.0080.770
networkBMA0.2840.0000.282
roc0.8440.0000.846
scores0.6440.0000.642
summary.networkBMA0.2360.0080.247
varord0.1480.0040.154
vignette3.3640.0003.366
writeEdges0.5440.0040.548