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CHECK report for netbiov on tokay1

This page was generated on 2018-04-12 13:24:35 -0400 (Thu, 12 Apr 2018).

Package 935/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netbiov 1.12.0
Shailesh tripathi
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/netbiov
Branch: RELEASE_3_6
Last Commit: 0e4040c
Last Changed Date: 2017-10-30 12:40:19 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: netbiov
Version: 1.12.0
Command: rm -rf netbiov.buildbin-libdir netbiov.Rcheck && mkdir netbiov.buildbin-libdir netbiov.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=netbiov.buildbin-libdir netbiov_1.12.0.tar.gz >netbiov.Rcheck\00install.out 2>&1 && cp netbiov.Rcheck\00install.out netbiov-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=netbiov.buildbin-libdir --install="check:netbiov-install.out" --force-multiarch --no-vignettes --timings netbiov_1.12.0.tar.gz
StartedAt: 2018-04-12 01:48:11 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:54:49 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 398.4 seconds
RetCode: 0
Status:  OK  
CheckDir: netbiov.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf netbiov.buildbin-libdir netbiov.Rcheck && mkdir netbiov.buildbin-libdir netbiov.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=netbiov.buildbin-libdir netbiov_1.12.0.tar.gz >netbiov.Rcheck\00install.out 2>&1 && cp netbiov.Rcheck\00install.out netbiov-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=netbiov.buildbin-libdir --install="check:netbiov-install.out" --force-multiarch --no-vignettes --timings netbiov_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/netbiov.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'netbiov/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'netbiov' version '1.12.0'
* 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 whether package 'netbiov' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
** checking loading without being on the library search path ... 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 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 ... NOTE
.edgeCol: no visible global function definition for 'colors'
.get.coord.abstract : dst: no visible global function definition for
  'dist'
.get.coord.mod : dst: no visible global function definition for 'dist'
.get.coord.mod_abs : dst: no visible global function definition for
  'dist'
.getalllevels: no visible global function definition for 'pdf'
.getalllevels: no visible global function definition for 'dev.off'
.getcrd.mod : dst: no visible global function definition for 'dist'
.getcrd.mod: no visible global function definition for 'rnorm'
.getcrd.mod.nodes : dst: no visible global function definition for
  'dist'
.getcrd.mod_abs : dst: no visible global function definition for 'dist'
.getcrd.mod_abs: no visible global function definition for 'rnorm'
.getcrd.mod_mst : dst: no visible global function definition for 'dist'
.getcrd.mod_mst: no visible global function definition for 'rnorm'
.ploteachstep: no visible global function definition for 'plot'
.set.mst.node.col: no visible global function definition for
  'heat.colors'
.set.mst.node.col_mod: no visible global function definition for
  'heat.colors'
.set.rank.abstract: no visible global function definition for 'colors'
.set.rank.abstract: no visible global function definition for 'hist'
.set.rank.abstract: no visible global function definition for
  'heat.colors'
.set.rank.mod: no visible global function definition for 'hist'
.set.rank.mod: no visible global function definition for 'colors'
.set.rank.mod: no visible global function definition for 'heat.colors'
.set.rank.mod_abs: no visible global function definition for 'hist'
.set.rank.mod_abs: no visible global function definition for 'colors'
.set.rank.mod_abs: no visible global function definition for
  'heat.colors'
.set.rank.nodes: no visible global function definition for 'hist'
.set.rank.nodes: no visible global function definition for 'colors'
.set.rank.nodes: no visible global function definition for
  'heat.colors'
.set.rank.spiral: no visible global function definition for 'hist'
.set.rank.spiral: no visible global function definition for 'colors'
.set.rank.spiral: no visible global function definition for
  'heat.colors'
.set.split.vertex.color: no visible global function definition for
  'colors'
level.plot: no visible global function definition for 'colors'
plot.NetworkSperical: no visible global function definition for
  'colors'
plot.NetworkSperical: no visible global function definition for
  'palette'
plot.NetworkSperical.startSet: no visible global function definition
  for 'colors'
plot.NetworkSperical.startSet: no visible global function definition
  for 'palette'
plot.netbiov: no visible global function definition for 'par'
plot.netbiov: no visible global function definition for 'plot'
plot.spiral.graph : dst: no visible global function definition for
  'dist'
tkplot.netbiov: no visible global function definition for 'par'
Undefined global functions or variables:
  colors dev.off dist heat.colors hist palette par pdf plot rnorm
Consider adding
  importFrom("grDevices", "colors", "dev.off", "heat.colors", "palette",
             "pdf")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("stats", "dist", "rnorm")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files are already in R: 'Sweave.sty'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
level.plot           58.94   0.53   59.47
plot.abstract.module 35.78   0.17   35.96
plot.modules         29.79   0.00   29.80
mst.plot             13.50   0.03   13.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
level.plot           75.47   0.59   76.09
plot.abstract.module 41.96   0.19   42.14
plot.modules         32.50   0.05   32.61
mst.plot             14.89   0.05   14.98
mst.plot.mod          5.81   0.00    5.86
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/netbiov.Rcheck/00check.log'
for details.

Installation output

netbiov.Rcheck/00install.out


install for i386

* installing *source* package 'netbiov' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'netbiov'
    finding HTML links ... done
    PPI_Athalina                            html  
    color_list                              html  
    gnet_bcell                              html  
    level.plot                              html  
    modules_PPI_Athalina                    html  
    modules_bcell                           html  
    mst.plot                                html  
    mst.plot.mod                            html  
    plot.NetworkSperical                    html  
    plot.NetworkSperical.startSet           html  
    plot.abstract.module                    html  
    plot.abstract.nodes                     html  
    plot.modules                            html  
    plot.netbiov                            html  
    plot.spiral.graph                       html  
    split.mst                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'netbiov' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'netbiov' as netbiov_1.12.0.zip
* DONE (netbiov)
In R CMD INSTALL
In R CMD INSTALL

Tests output

netbiov.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("RUnit")
Loading required package: RUnit
> require("netbiov")
Loading required package: netbiov
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> pattern="^test_.*\\.R$"
> runitDirs <- c(".")
> TEST_DATA_DIR <- "data"
> BiocGenerics:::testPackage("netbiov")


RUNIT TEST PROTOCOL -- Thu Apr 12 01:54:32 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
netbiov RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> suite <- defineTestSuite(name="NetBioV Suite",
+                          dirs=runitDirs,
+                          testFileRegexp=pattern,
+                          rngKind="default",
+                          rngNormalKind="default")
> result <- runTestSuite(suite)
> printTextProtocol(result)
RUNIT TEST PROTOCOL -- Thu Apr 12 01:54:32 2018 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
NetBioV Suite - 0 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: NetBioV Suite 
Test function regexp: ^test.+ 
Test file regexp: ^test_.*\.R$ 
Involved directory: 
. 
no test files 
> 
> proc.time()
   user  system elapsed 
  11.04    0.26   11.29

netbiov.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("RUnit")
Loading required package: RUnit
> require("netbiov")
Loading required package: netbiov
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> pattern="^test_.*\\.R$"
> runitDirs <- c(".")
> TEST_DATA_DIR <- "data"
> BiocGenerics:::testPackage("netbiov")


RUNIT TEST PROTOCOL -- Thu Apr 12 01:54:45 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
netbiov RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> suite <- defineTestSuite(name="NetBioV Suite",
+                          dirs=runitDirs,
+                          testFileRegexp=pattern,
+                          rngKind="default",
+                          rngNormalKind="default")
> result <- runTestSuite(suite)
> printTextProtocol(result)
RUNIT TEST PROTOCOL -- Thu Apr 12 01:54:45 2018 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
NetBioV Suite - 0 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: NetBioV Suite 
Test function regexp: ^test.+ 
Test file regexp: ^test_.*\.R$ 
Involved directory: 
. 
no test files 
> 
> proc.time()
   user  system elapsed 
  12.84    0.25   13.07

Example timings

netbiov.Rcheck/examples_i386/netbiov-Ex.timings

nameusersystemelapsed
PPI_Athalina0.010.000.01
level.plot58.94 0.5359.47
mst.plot13.50 0.0313.53
mst.plot.mod4.700.034.73
plot.NetworkSperical0.920.000.92
plot.NetworkSperical.startSet0.480.020.50
plot.abstract.module35.78 0.1735.96
plot.abstract.nodes0.540.020.54
plot.modules29.79 0.0029.80
plot.netbiov0.710.010.72
plot.spiral.graph0.480.000.48
split.mst0.830.000.83

netbiov.Rcheck/examples_x64/netbiov-Ex.timings

nameusersystemelapsed
PPI_Athalina0.020.000.02
level.plot75.47 0.5976.09
mst.plot14.89 0.0514.98
mst.plot.mod5.810.005.86
plot.NetworkSperical1.080.021.10
plot.NetworkSperical.startSet0.590.010.61
plot.abstract.module41.96 0.1942.14
plot.abstract.nodes0.410.000.42
plot.modules32.50 0.0532.61
plot.netbiov0.660.000.66
plot.spiral.graph0.680.000.69
split.mst0.940.010.96