Shailesh tripathi
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/netbiov |
| Branch: RELEASE_3_12 |
| Last Commit: cda7778 |
| Last Changed Date: 2020-10-27 10:57:43 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:27 -0400 (Thu, 06 May 2021).
|
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 1213/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netbiov 1.24.0 (landing page) Shailesh tripathi
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: netbiov |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netbiov.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings netbiov_1.24.0.tar.gz |
| StartedAt: 2021-05-06 05:04:04 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:10:14 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 369.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: netbiov.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netbiov.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings netbiov_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/netbiov.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.24.0'
* 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 51.17 0.28 51.45
plot.abstract.module 34.03 0.08 34.11
plot.modules 32.92 0.05 32.97
mst.plot 13.47 0.08 13.55
mst.plot.mod 5.21 0.05 5.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
level.plot 65.16 0.39 65.95
plot.abstract.module 33.36 0.15 33.52
plot.modules 30.80 0.13 30.92
mst.plot 16.48 0.09 16.58
mst.plot.mod 5.05 0.03 5.08
* 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-3.12-bioc/meat/netbiov.Rcheck/00check.log'
for details.
netbiov.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/netbiov_1.24.0.tar.gz && rm -rf netbiov.buildbin-libdir && mkdir netbiov.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=netbiov.buildbin-libdir netbiov_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL netbiov_1.24.0.zip && rm netbiov_1.24.0.tar.gz netbiov_1.24.0.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 22.4M 0 --:--:-- --:--:-- --:--:-- 23.1M
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_1.24.0.zip
* DONE (netbiov)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'netbiov' successfully unpacked and MD5 sums checked
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netbiov.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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$"
> runitDirs <- c(".")
> TEST_DATA_DIR <- "data"
> BiocGenerics:::testPackage("netbiov")
RUNIT TEST PROTOCOL -- Thu May 06 05:09:54 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
netbiov RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
> suite <- defineTestSuite(name="NetBioV Suite",
+ dirs=runitDirs,
+ testFileRegexp=pattern,
+ rngKind="default",
+ rngNormalKind="default")
> result <- runTestSuite(suite)
> printTextProtocol(result)
RUNIT TEST PROTOCOL -- Thu May 06 05:09:54 2021
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
NetBioV Suite - 0 test functions, 0 errors, 0 failures
Details
***************************
Test Suite: NetBioV Suite
Test function regexp: ^test.+
Test file regexp: ^test_.*\.R$
Involved directory:
.
no test files
>
> proc.time()
user system elapsed
10.21 0.42 10.62
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netbiov.Rcheck/tests_x64/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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$"
> runitDirs <- c(".")
> TEST_DATA_DIR <- "data"
> BiocGenerics:::testPackage("netbiov")
RUNIT TEST PROTOCOL -- Thu May 06 05:10:09 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
netbiov RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
> suite <- defineTestSuite(name="NetBioV Suite",
+ dirs=runitDirs,
+ testFileRegexp=pattern,
+ rngKind="default",
+ rngNormalKind="default")
> result <- runTestSuite(suite)
> printTextProtocol(result)
RUNIT TEST PROTOCOL -- Thu May 06 05:10:09 2021
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
NetBioV Suite - 0 test functions, 0 errors, 0 failures
Details
***************************
Test Suite: NetBioV Suite
Test function regexp: ^test.+
Test file regexp: ^test_.*\.R$
Involved directory:
.
no test files
>
> proc.time()
user system elapsed
14.10 0.32 14.42
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netbiov.Rcheck/examples_i386/netbiov-Ex.timings
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netbiov.Rcheck/examples_x64/netbiov-Ex.timings
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