Karim Mezhoud
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/bioCancer |
| Branch: RELEASE_3_6 |
| Last Commit: f109742 |
| Last Changed Date: 2017-10-30 12:26:17 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:15:03 -0400 (Thu, 12 Apr 2018).
| Package 119/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bioCancer 1.6.0 Karim Mezhoud
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: bioCancer |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings bioCancer_1.6.0.tar.gz |
| StartedAt: 2018-04-11 21:47:06 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 21:49:19 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 133.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bioCancer.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings bioCancer_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/bioCancer.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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 ‘bioCancer’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
app 3.1Mb
doc 2.8Mb
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/bioCancer.Rcheck/00check.log’
for details.
bioCancer.Rcheck/00install.out
* installing *source* package ‘bioCancer’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (bioCancer)
bioCancer.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 object is masked from 'package:base':
date
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:magrittr':
extract
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 object is masked from 'package:dplyr':
mutate_each
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 FAILED: 0
>
> proc.time()
user system elapsed
6.704 0.124 9.977
bioCancer.Rcheck/bioCancer-Ex.timings
| name | user | system | elapsed | |
| Edges_Diseases_obj | 0.004 | 0.000 | 0.002 | |
| Mutation_obj | 0.068 | 0.000 | 0.066 | |
| Node_Diseases_obj | 0.004 | 0.000 | 0.003 | |
| Node_df_FreqIn | 0.000 | 0.000 | 0.001 | |
| Node_obj_CNA_ProfData | 0.004 | 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 | 0.005 | |
| UnifyRowNames | 0.000 | 0.000 | 0.001 | |
| attriColorGene | 0.000 | 0.004 | 0.001 | |
| attriColorValue | 0.000 | 0.000 | 0.001 | |
| attriColorVector | 0.004 | 0.000 | 0.001 | |
| attriShape2Gene | 0.000 | 0.000 | 0.001 | |
| attriShape2Node | 0.000 | 0.000 | 0.001 | |
| bioCancer | 0.000 | 0.004 | 0.001 | |
| checkDimensions | 0.000 | 0.000 | 0.001 | |
| coffeewheel | 0.000 | 0.000 | 0.001 | |
| coffeewheelOutput | 0.004 | 0.000 | 0.000 | |
| displayTable | 0.084 | 0.000 | 0.285 | |
| getFreqMutData | 0.004 | 0.000 | 0.002 | |
| getGenesClassification | 0.008 | 0.000 | 0.210 | |
| getListProfData | 0.004 | 0.000 | 0.002 | |
| getList_Cases | 0.008 | 0.000 | 0.214 | |
| getList_GenProfs | 0.008 | 0.000 | 0.312 | |
| getMegaProfData | 0.000 | 0.000 | 0.001 | |
| getSequensed_SampleSize | 0.000 | 0.000 | 0.001 | |
| grepRef | 0.000 | 0.000 | 0.001 | |
| reStrColorGene | 0.000 | 0.000 | 0.002 | |
| reStrDimension | 0.000 | 0.000 | 0.002 | |
| reStrDisease | 0.004 | 0.000 | 0.002 | |
| renderCoffeewheel | 0.000 | 0.004 | 0.001 | |
| returnTextAreaInput | 0.000 | 0.000 | 0.001 | |
| whichGeneList | 0 | 0 | 0 | |