Shailesh tripathi
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/netbiov |
| git_branch: master |
| git_last_commit: 0cda439 |
| git_last_commit_date: 2021-10-26 12:14:46 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:10 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the netbiov package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netbiov.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1287/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netbiov 1.29.0 (landing page) Shailesh tripathi
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: netbiov |
| Version: 1.29.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netbiov.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings netbiov_1.29.0.tar.gz |
| StartedAt: 2022-03-17 19:43:31 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:45:50 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 139.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: netbiov.Rcheck |
| Warnings: 1 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netbiov.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings netbiov_1.29.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/netbiov.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.29.0'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
level.plot 25.29 1.76 27.06
plot.abstract.module 20.86 0.47 21.33
plot.modules 17.28 0.37 17.65
mst.plot 9.39 0.22 9.61
* 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: 1 WARNING, 4 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/netbiov.Rcheck/00check.log'
for details.
netbiov.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL netbiov
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (netbiov)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'sparsenetgls' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'veloviz' is missing or broken
done
netbiov.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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$"
> runitDirs <- c(".")
> TEST_DATA_DIR <- "data"
> BiocGenerics:::testPackage("netbiov")
RUNIT TEST PROTOCOL -- Thu Mar 17 19:45:36 2022
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
netbiov RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
> suite <- defineTestSuite(name="NetBioV Suite",
+ dirs=runitDirs,
+ testFileRegexp=pattern,
+ rngKind="default",
+ rngNormalKind="default")
> result <- runTestSuite(suite)
> printTextProtocol(result)
RUNIT TEST PROTOCOL -- Thu Mar 17 19:45:36 2022
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
NetBioV Suite - 0 test functions, 0 errors, 0 failures
Details
***************************
Test Suite: NetBioV Suite
Test function regexp: ^test.+
Test file regexp: ^test_.*\.R$
Involved directory:
.
no test files
>
> proc.time()
user system elapsed
7.78 0.68 8.43
netbiov.Rcheck/netbiov-Ex.timings
| name | user | system | elapsed | |
| PPI_Athalina | 0.00 | 0.02 | 0.01 | |
| level.plot | 25.29 | 1.76 | 27.06 | |
| mst.plot | 9.39 | 0.22 | 9.61 | |
| mst.plot.mod | 2.89 | 0.08 | 2.97 | |
| plot.NetworkSperical | 0.44 | 0.00 | 0.44 | |
| plot.NetworkSperical.startSet | 0.11 | 0.03 | 0.14 | |
| plot.abstract.module | 20.86 | 0.47 | 21.33 | |
| plot.abstract.nodes | 0.12 | 0.02 | 0.14 | |
| plot.modules | 17.28 | 0.37 | 17.65 | |
| plot.netbiov | 0.69 | 0.02 | 0.71 | |
| plot.spiral.graph | 0.45 | 0.00 | 0.45 | |
| split.mst | 0.50 | 0.01 | 0.51 | |