Package: GeneNetworkBuilder

Version: 1.24.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GeneNetworkBuilder.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GeneNetworkBuilder_1.24.1.tar.gz

StartedAt: 2019-04-16 00:08:27 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:09:19 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 52.8 seconds

RetCode: 0

Status:  OK

CheckDir: GeneNetworkBuilder.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:GeneNetworkBuilder.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GeneNetworkBuilder_1.24.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.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 ‘GeneNetworkBuilder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneNetworkBuilder’ version ‘1.24.1’
* 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 ‘GeneNetworkBuilder’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data          2.8Mb
    htmlwidgets   1.9Mb
* 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 ... 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 ‘runTests.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL GeneNetworkBuilder
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘GeneNetworkBuilder’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c geneTree.cpp -o geneTree.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c nodefilter.cpp -o nodefilter.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o GeneNetworkBuilder.so geneTree.o nodefilter.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/GeneNetworkBuilder/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 (GeneNetworkBuilder)

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.

> require("GeneNetworkBuilder") || stop("unable to load Package:GeneNetworkBuilder")
Loading required package: GeneNetworkBuilder
Loading required package: Rcpp
[1] TRUE
> BiocGenerics:::testPackage("GeneNetworkBuilder")


RUNIT TEST PROTOCOL -- Tue Apr 16 00:09:16 2019 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GeneNetworkBuilder RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.240   0.052   1.322 

name	user	system	elapsed
browseNetwork	3.176	0.096	3.492
buildNetwork	0.664	0.012	0.677
ce.IDsMap	0.504	0.008	0.513
ce.interactionmap	0.032	0.000	0.035
ce.mapIDs	0.348	0.004	0.356
ce.miRNA.map	0.004	0.000	0.003
convertID	0.736	0.008	0.748
example.data	0.048	0.000	0.047
exportNetwork	2.388	0.048	2.474
filterNetwork	1.876	0.052	1.934
hs.IDsMap	0.116	0.004	0.122
hs.interactionmap	0.040	0.000	0.062
hs.mapIDs	0.048	0.000	0.047
hs.miRNA.map	0.008	0.000	0.005
networkFromGenes	0.256	0.008	0.267
polishNetwork	1.972	0.012	1.991
uniqueExprsData	0.388	0.000	0.388