Karim Mezhoud
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/bioCancer |
| Branch: RELEASE_3_9 |
| Last Commit: 252f51e |
| Last Changed Date: 2019-05-02 11:54:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:58:04 -0400 (Wed, 16 Oct 2019).
| Package 141/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bioCancer 1.12.0 Karim Mezhoud
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: bioCancer |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bioCancer_1.12.0.tar.gz |
| StartedAt: 2019-10-16 00:52:54 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:57:40 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 285.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bioCancer.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bioCancer_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/bioCancer.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bioCancer/DESCRIPTION’ ... OK * this is package ‘bioCancer’ version ‘1.12.0’ * package encoding: UTF-8 * 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 ‘bioCancer’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 ... NOTE Namespaces in Imports field not imported from: ‘AlgDesign’ ‘dplyr’ ‘import’ ‘methods’ ‘shinythemes’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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 NOTE See ‘/Users/biocbuild/bbs-3.9-bioc/meat/bioCancer.Rcheck/00check.log’ for details.
bioCancer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bioCancer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘bioCancer’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (bioCancer)
bioCancer.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.
> library(testthat)
> library(bioCancer)
Loading required package: radiant.data
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Loading required package: ggplot2
Loading required package: lubridate
Attaching package: 'lubridate'
The following object is masked from 'package:base':
date
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:magrittr':
extract
The following object is masked from 'package:testthat':
matches
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:lubridate':
intersect, setdiff, union
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'radiant.data'
The following objects are masked from 'package:lubridate':
month, wday
The following object is masked from 'package:ggplot2':
diamonds
The following object is masked from 'package:testthat':
describe
Loading required package: cgdsr
Please send questions to cbioportal@googlegroups.com
Loading required package: XML
>
> test_check("bioCancer")
getCancerStudies... OK
getCaseLists (1/2) ... OK
getCaseLists (2/2) ... OK
getGeneticProfiles (1/2) ... OK
getGeneticProfiles (2/2) ... OK
getClinicalData (1/1) ... OK
getProfileData (1/6) ... OK
getProfileData (2/6) ... OK
getProfileData (3/6) ... OK
getProfileData (4/6) ... OK
getProfileData (5/6) ... OK
getProfileData (6/6) ... OK
ReactomeFI connection... OK
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.291 1.251 16.530
bioCancer.Rcheck/bioCancer-Ex.timings
| name | user | system | elapsed | |
| Edges_Diseases_obj | 0.005 | 0.001 | 0.006 | |
| Mutation_obj | 0.005 | 0.001 | 0.006 | |
| Node_Diseases_obj | 0.005 | 0.001 | 0.006 | |
| Node_df_FreqIn | 0.001 | 0.001 | 0.002 | |
| Node_obj_CNA_ProfData | 0.001 | 0.001 | 0.002 | |
| Node_obj_FreqIn | 0.000 | 0.000 | 0.001 | |
| Node_obj_Met_ProfData | 0.001 | 0.000 | 0.002 | |
| Node_obj_mRNA_Classifier | 0.003 | 0.000 | 0.003 | |
| Studies_obj | 0.014 | 0.001 | 0.015 | |
| UnifyRowNames | 0.002 | 0.001 | 0.002 | |
| attriColorGene | 0.002 | 0.000 | 0.002 | |
| attriColorValue | 0.002 | 0.000 | 0.002 | |
| attriColorVector | 0.002 | 0.000 | 0.002 | |
| attriShape2Gene | 0.000 | 0.000 | 0.001 | |
| attriShape2Node | 0.001 | 0.001 | 0.001 | |
| bioCancer | 0.000 | 0.000 | 0.001 | |
| checkDimensions | 0.001 | 0.000 | 0.002 | |
| coffeewheel | 0.000 | 0.001 | 0.001 | |
| coffeewheelOutput | 0.001 | 0.001 | 0.000 | |
| displayTable | 0.530 | 0.007 | 0.588 | |
| findPhantom | 0.000 | 0.000 | 0.001 | |
| getFreqMutData | 0.001 | 0.001 | 0.002 | |
| getGenesClassification | 0.020 | 0.001 | 0.050 | |
| getListProfData | 0.002 | 0.000 | 0.002 | |
| getList_Cases | 0.020 | 0.001 | 0.043 | |
| getList_GenProfs | 0.019 | 0.001 | 0.042 | |
| getMegaProfData | 0.001 | 0.000 | 0.001 | |
| getSequensed_SampleSize | 0.001 | 0.001 | 0.001 | |
| grepRef | 0.001 | 0.001 | 0.001 | |
| metabologram | 0.000 | 0.001 | 0.001 | |
| metabologramOutput | 0.000 | 0.000 | 0.001 | |
| reStrColorGene | 0.002 | 0.000 | 0.002 | |
| reStrDimension | 0.002 | 0.000 | 0.002 | |
| reStrDisease | 0.001 | 0.001 | 0.002 | |
| renderCoffeewheel | 0.000 | 0.000 | 0.001 | |
| renderMetabologram | 0.001 | 0.000 | 0.000 | |
| returnTextAreaInput | 0.000 | 0.000 | 0.001 | |
| whichGeneList | 0.001 | 0.000 | 0.001 | |
| widgetThumbnail | 0.000 | 0.000 | 0.001 | |