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CHECK report for netbiov on tokay2

This page was generated on 2020-10-17 11:57:16 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE netbiov PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1183/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netbiov 1.22.0
Shailesh tripathi
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/netbiov
Branch: RELEASE_3_11
Last Commit: 20320ea
Last Changed Date: 2020-04-27 14:41:45 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: netbiov
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netbiov.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings netbiov_1.22.0.tar.gz
StartedAt: 2020-10-17 06:27:37 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:34:55 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 438.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: netbiov.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netbiov.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings netbiov_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/netbiov.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.22.0'
* 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 ... OK
* 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
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.NetworkSperical plot.NetworkSperical.startSet
  plot.abstract.module plot.abstract.nodes plot.modules plot.netbiov
  plot.spiral.graph
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* 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'
.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.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 rnorm
Consider adding
  importFrom("grDevices", "colors", "dev.off", "heat.colors", "palette",
             "pdf")
  importFrom("graphics", "hist", "par")
  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 ... WARNING
Documented arguments not in \usage in documentation object 'level.plot':
  '...'

Documented arguments not in \usage in documentation object 'mst.plot':
  '...'

Documented arguments not in \usage in documentation object 'mst.plot.mod':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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 (user + system) or elapsed time > 5s
                      user system elapsed
level.plot           75.88   0.61   76.50
plot.abstract.module 48.93   0.17   49.11
plot.modules         39.42   0.09   39.51
mst.plot             17.54   0.14   17.69
mst.plot.mod          6.96   0.09    7.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
level.plot           66.17   0.53   66.71
plot.abstract.module 37.72   0.17   37.89
plot.modules         31.64   0.10   31.73
mst.plot             15.32   0.03   15.36
mst.plot.mod          5.39   0.03    5.46
* 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: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/netbiov.Rcheck/00check.log'
for details.



Installation output

netbiov.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/netbiov_1.22.0.tar.gz && rm -rf netbiov.buildbin-libdir && mkdir netbiov.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=netbiov.buildbin-libdir netbiov_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL netbiov_1.22.0.zip && rm netbiov_1.22.0.tar.gz netbiov_1.22.0.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  521k  100  521k    0     0  7216k      0 --:--:-- --:--:-- --:--:-- 8413k

install for i386

* installing *source* package 'netbiov' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'netbiov' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'netbiov' as netbiov_1.22.0.zip
* DONE (netbiov)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'netbiov' successfully unpacked and MD5 sums checked

Tests output

netbiov.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 -- Sat Oct 17 06:34:33 2020 
*********************************************** 
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 -- Sat Oct 17 06:34:33 2020 
*********************************************** 
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 
  11.75    0.56   12.29 

netbiov.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 -- Sat Oct 17 06:34:47 2020 
*********************************************** 
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 -- Sat Oct 17 06:34:47 2020 
*********************************************** 
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 
  12.76    0.37   13.12 

Example timings

netbiov.Rcheck/examples_i386/netbiov-Ex.timings

nameusersystemelapsed
PPI_Athalina0.010.020.03
level.plot75.88 0.6176.50
mst.plot17.54 0.1417.69
mst.plot.mod6.960.097.04
plot.NetworkSperical0.980.000.99
plot.NetworkSperical.startSet0.270.020.28
plot.abstract.module48.93 0.1749.11
plot.abstract.nodes0.380.020.39
plot.modules39.42 0.0939.51
plot.netbiov1.080.021.10
plot.spiral.graph0.420.000.42
split.mst1.220.011.28

netbiov.Rcheck/examples_x64/netbiov-Ex.timings

nameusersystemelapsed
PPI_Athalina0.020.020.03
level.plot66.17 0.5366.71
mst.plot15.32 0.0315.36
mst.plot.mod5.390.035.46
plot.NetworkSperical0.710.000.70
plot.NetworkSperical.startSet0.250.020.26
plot.abstract.module37.72 0.1737.89
plot.abstract.nodes0.260.010.29
plot.modules31.64 0.1031.73
plot.netbiov0.860.010.88
plot.spiral.graph0.440.020.45
split.mst1.060.001.06