Maren Sitte
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/pwOmics |
| Branch: RELEASE_3_10 |
| Last Commit: cdbf5ed |
| Last Changed Date: 2019-10-29 13:09:18 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:10:06 -0400 (Wed, 15 Apr 2020).
| Package 1335/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pwOmics 1.18.0 Maren Sitte
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: pwOmics |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pwOmics.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pwOmics_1.18.0.tar.gz |
| StartedAt: 2020-04-15 03:02:07 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:08:00 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 353.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: pwOmics.Rcheck |
| Warnings: 1 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pwOmics.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pwOmics_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/pwOmics.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pwOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pwOmics’ version ‘1.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pwOmics’ can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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 ... NOTE
identifyPWTFTGs: no visible binding for global variable ‘upreg’
identifyPWTFTGs: no visible binding for global variable ‘phosphoeffect’
infoConsensusGraph: no visible global function definition for ‘from’
Undefined global functions or variables:
from phosphoeffect upreg
* 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 'plotTimeProfileClusters':
‘...’
Documented arguments not in \usage in documentation object 'temp_correlations':
‘...’
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 examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
temp_correlations 212.576 0.404 216.862
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.10-bioc/meat/pwOmics.Rcheck/00check.log’
for details.
pwOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL pwOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘pwOmics’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (pwOmics)
pwOmics.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
> BiocGenerics:::testPackage("pwOmics")
RUNIT TEST PROTOCOL -- Wed Apr 15 03:07:56 2020
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
pwOmics RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
5.336 0.156 5.508
pwOmics.Rcheck/pwOmics-Ex.timings
| name | user | system | elapsed | |
| clusterTimeProfiles | 0 | 0 | 0 | |
| consDynamicNet | 0.000 | 0.000 | 0.001 | |
| findSignalingAxes | 0 | 0 | 0 | |
| generate_DSSignalingBase | 0.004 | 0.000 | 0.000 | |
| getBiopaxModel | 0 | 0 | 0 | |
| getDS_PWs | 0 | 0 | 0 | |
| getDS_TFs | 0 | 0 | 0 | |
| getDS_TGs | 0.004 | 0.000 | 0.000 | |
| getGenesIntersection | 0.000 | 0.000 | 0.001 | |
| getOmicsDataset | 0.000 | 0.000 | 0.001 | |
| getOmicsTimepoints | 0 | 0 | 0 | |
| getOmicsallGeneIDs | 0 | 0 | 0 | |
| getOmicsallProteinIDs | 0 | 0 | 0 | |
| getProteinIntersection | 0.000 | 0.000 | 0.001 | |
| getTFIntersection | 0.000 | 0.000 | 0.001 | |
| getUS_PWs | 0.000 | 0.000 | 0.001 | |
| getUS_TFs | 0.000 | 0.000 | 0.001 | |
| getUS_regulators | 0.000 | 0.000 | 0.001 | |
| get_matching_transcripts | 0.000 | 0.000 | 0.001 | |
| gettpIntersection | 0.000 | 0.000 | 0.001 | |
| identifyPR | 0.000 | 0.000 | 0.001 | |
| identifyPWTFTGs | 0.000 | 0.000 | 0.001 | |
| identifyPWs | 0 | 0 | 0 | |
| identifyRsofTFs | 0 | 0 | 0 | |
| identifyTFs | 0 | 0 | 0 | |
| infoConsensusGraph | 0.000 | 0.000 | 0.001 | |
| plotConsDynNet | 0.000 | 0.000 | 0.001 | |
| plotConsensusGraph | 0.000 | 0.000 | 0.001 | |
| plotConsensusProfiles | 0.000 | 0.000 | 0.001 | |
| plotTimeProfileClusters | 0.000 | 0.000 | 0.001 | |
| readOmics | 0.000 | 0.000 | 0.001 | |
| readPWdata | 0 | 0 | 0 | |
| readPhosphodata | 0 | 0 | 0 | |
| readTFdata | 0 | 0 | 0 | |
| staticConsensusNet | 0 | 0 | 0 | |
| temp_correlations | 212.576 | 0.404 | 216.862 | |