Karim Mezhoud
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/bioCancer |
| Branch: RELEASE_3_10 |
| Last Commit: 601af5c |
| Last Changed Date: 2020-03-16 13:44:03 -0400 (Mon, 16 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:11:26 -0400 (Wed, 15 Apr 2020).
| Package 147/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bioCancer 1.14.02 Karim Mezhoud
| 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: bioCancer |
| Version: 1.14.02 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings bioCancer_1.14.02.tar.gz |
| StartedAt: 2020-04-15 03:52:17 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:55:23 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 186.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: bioCancer.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings bioCancer_1.14.02.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/bioCancer.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 ‘bioCancer/DESCRIPTION’ ... OK
* this is package ‘bioCancer’ version ‘1.14.02’
* 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 ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
app 3.4Mb
extdata 1.6Mb
* 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’ ‘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 ... WARNING
checkRd: (5) bioCancer.Rd:0-20: Must have a \description
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/bioCancer.Rcheck/00check.log’
for details.
bioCancer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL bioCancer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (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.
> 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 objects are masked from 'package:base':
date, intersect, setdiff, union
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
11.344 0.404 12.646
bioCancer.Rcheck/bioCancer-Ex.timings
| name | user | system | elapsed | |
| Edges_Diseases_obj | 0.004 | 0.000 | 0.003 | |
| Mutation_obj | 0.004 | 0.000 | 0.005 | |
| Node_Diseases_obj | 0.000 | 0.000 | 0.002 | |
| Node_df_FreqIn | 0.000 | 0.000 | 0.001 | |
| Node_obj_CNA_ProfData | 0.000 | 0.000 | 0.001 | |
| Node_obj_FreqIn | 0.000 | 0.000 | 0.001 | |
| Node_obj_Met_ProfData | 0.004 | 0.000 | 0.002 | |
| Node_obj_mRNA_Classifier | 0.000 | 0.000 | 0.001 | |
| Studies_obj | 0.008 | 0.000 | 0.007 | |
| UnifyRowNames | 0 | 0 | 0 | |
| attriColorGene | 0.000 | 0.000 | 0.001 | |
| attriColorValue | 0 | 0 | 0 | |
| attriColorVector | 0 | 0 | 0 | |
| attriShape2Gene | 0 | 0 | 0 | |
| attriShape2Node | 0.004 | 0.000 | 0.000 | |
| bioCancer | 0 | 0 | 0 | |
| checkDimensions | 0 | 0 | 0 | |
| coffeewheel | 0 | 0 | 0 | |
| coffeewheelOutput | 0 | 0 | 0 | |
| displayTable | 0.060 | 0.000 | 0.117 | |
| findPhantom | 0 | 0 | 0 | |
| getFreqMutData | 0.000 | 0.000 | 0.001 | |
| getGenesClassification | 0.020 | 0.000 | 0.043 | |
| getListProfData | 0.004 | 0.000 | 0.001 | |
| getList_Cases | 0.020 | 0.000 | 0.043 | |
| getList_GenProfs | 0.020 | 0.000 | 0.043 | |
| getMegaProfData | 0.000 | 0.000 | 0.001 | |
| getSequensed_SampleSize | 0 | 0 | 0 | |
| grepRef | 0 | 0 | 0 | |
| metabologram | 0 | 0 | 0 | |
| metabologramOutput | 0.000 | 0.000 | 0.001 | |
| reStrColorGene | 0.000 | 0.000 | 0.001 | |
| reStrDimension | 0.004 | 0.000 | 0.001 | |
| reStrDisease | 0.000 | 0.000 | 0.001 | |
| renderCoffeewheel | 0 | 0 | 0 | |
| renderMetabologram | 0 | 0 | 0 | |
| returnTextAreaInput | 0 | 0 | 0 | |
| whichGeneList | 0 | 0 | 0 | |
| widgetThumbnail | 0 | 0 | 0 | |