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CHECK report for GeneNetworkBuilder on tokay1

This page was generated on 2019-04-13 11:22:19 -0400 (Sat, 13 Apr 2019).

Package 600/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneNetworkBuilder 1.24.1
Jianhong Ou
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GeneNetworkBuilder
Branch: RELEASE_3_8
Last Commit: c100f80
Last Changed Date: 2019-04-08 18:41:34 -0400 (Mon, 08 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneNetworkBuilder
Version: 1.24.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneNetworkBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneNetworkBuilder_1.24.1.tar.gz
StartedAt: 2019-04-13 02:28:16 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:30:43 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 146.8 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneNetworkBuilder.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneNetworkBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneNetworkBuilder_1.24.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'GeneNetworkBuilder' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data          2.8Mb
    htmlwidgets   1.8Mb
    libs          1.5Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/GeneNetworkBuilder/libs/i386/GeneNetworkBuilder.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
browseNetwork  2.3   0.14    5.13
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.Rcheck/00check.log'
for details.



Installation output

GeneNetworkBuilder.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GeneNetworkBuilder_1.24.1.tar.gz && rm -rf GeneNetworkBuilder.buildbin-libdir && mkdir GeneNetworkBuilder.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneNetworkBuilder.buildbin-libdir GeneNetworkBuilder_1.24.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GeneNetworkBuilder_1.24.1.zip && rm GeneNetworkBuilder_1.24.1.tar.gz GeneNetworkBuilder_1.24.1.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4145k  100 4145k    0     0  47.4M      0 --:--:-- --:--:-- --:--:-- 49.9M

install for i386

* installing *source* package 'GeneNetworkBuilder' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c geneTree.cpp -o geneTree.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c nodefilter.cpp -o nodefilter.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GeneNetworkBuilder.dll tmp.def geneTree.o nodefilter.o registerDynamicSymbol.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneNetworkBuilder'
    finding HTML links ... done
    GeneNetworkBuilder-package              html  
    browseNetwork-shiny                     html  
    browseNetwork                           html  
    buildNetwork                            html  
    ce.IDsMap                               html  
    ce.interactionmap                       html  
    ce.mapIDs                               html  
    ce.miRNA.map                            html  
    convertID                               html  
    example.data                            html  
    exportNetwork                           html  
    filterNetwork                           html  
    hs.IDsMap                               html  
    hs.interactionmap                       html  
    hs.mapIDs                               html  
    hs.miRNA.map                            html  
    networkFromGenes                        html  
    polishNetwork                           html  
    saveXGMML                               html  
    uniqueExprsData                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GeneNetworkBuilder' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c geneTree.cpp -o geneTree.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c nodefilter.cpp -o nodefilter.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GeneNetworkBuilder.dll tmp.def geneTree.o nodefilter.o registerDynamicSymbol.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneNetworkBuilder' as GeneNetworkBuilder_1.24.1.zip
* DONE (GeneNetworkBuilder)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GeneNetworkBuilder' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

GeneNetworkBuilder.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Sat Apr 13 02:30:38 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 
   1.39    0.14    1.53 

GeneNetworkBuilder.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Sat Apr 13 02:30:39 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 
   1.00    0.07    1.07 

Example timings

GeneNetworkBuilder.Rcheck/examples_i386/GeneNetworkBuilder-Ex.timings

nameusersystemelapsed
browseNetwork2.300.145.13
buildNetwork0.280.020.30
ce.IDsMap0.450.020.47
ce.interactionmap0.030.010.04
ce.mapIDs0.490.020.64
ce.miRNA.map0.000.010.02
convertID0.440.000.44
example.data0.030.000.03
exportNetwork1.940.102.72
filterNetwork1.490.041.53
hs.IDsMap0.320.000.46
hs.interactionmap0.050.000.32
hs.mapIDs0.060.000.22
hs.miRNA.map0.00.00.1
networkFromGenes0.110.000.11
polishNetwork1.630.071.68
uniqueExprsData0.310.000.32

GeneNetworkBuilder.Rcheck/examples_x64/GeneNetworkBuilder-Ex.timings

nameusersystemelapsed
browseNetwork2.230.112.44
buildNetwork0.390.000.39
ce.IDsMap0.360.000.36
ce.interactionmap0.030.000.03
ce.mapIDs0.340.000.34
ce.miRNA.map000
convertID0.610.010.63
example.data0.050.000.04
exportNetwork1.800.052.36
filterNetwork1.530.041.58
hs.IDsMap0.250.020.27
hs.interactionmap0.030.000.03
hs.mapIDs0.050.020.06
hs.miRNA.map0.010.000.02
networkFromGenes0.280.000.28
polishNetwork1.610.031.64
uniqueExprsData0.390.000.39