Tiago Chedraoui Silva
| Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TCGAWorkflowData |
| Branch: RELEASE_3_10 |
| Last Commit: 41c09af |
| Last Changed Date: 2019-10-29 13:29:49 -0400 (Tue, 29 Oct 2019) |
| Back to Build/check report for BioC 3.10 experimental data |
This page was generated on 2020-04-14 17:46:26 -0400 (Tue, 14 Apr 2020).
| Package 360/384 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| TCGAWorkflowData 1.10.0 Tiago Chedraoui Silva
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |
| Package: TCGAWorkflowData |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.10.0.tar.gz |
| StartedAt: 2020-04-14 13:43:15 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 13:50:45 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 450.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TCGAWorkflowData.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/TCGAWorkflowData.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 ‘TCGAWorkflowData/DESCRIPTION’ ... OK
* this is package ‘TCGAWorkflowData’ version ‘1.10.0’
* 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 ‘TCGAWorkflowData’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 77.5Mb
sub-directories of 1Mb or more:
data 77.3Mb
* 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 ... OK
* 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 ... WARNING
Undocumented data sets:
‘commonCNV’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAWorkflowData 38.504 0.320 38.854
GBMmut 14.924 0.120 15.060
tmp.biogrid 13.088 0.076 13.171
LGGmut 12.364 0.048 12.420
mut 12.024 0.056 12.091
* 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, 1 NOTE
See
‘/home/biocbuild/bbs-3.10-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’
for details.
TCGAWorkflowData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL TCGAWorkflowData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘TCGAWorkflowData’ ... ** using staged installation ** R ** data ** 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 (TCGAWorkflowData)
TCGAWorkflowData.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(TCGAWorkflowData)
>
> test_check("TCGAWorkflowData")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
47.552 0.816 48.411
TCGAWorkflowData.Rcheck/TCGAWorkflowData-Ex.timings
| name | user | system | elapsed | |
| GBMmut | 14.924 | 0.120 | 15.060 | |
| LGGmut | 12.364 | 0.048 | 12.420 | |
| TCGAWorkflowData | 38.504 | 0.320 | 38.854 | |
| cnvMatrix | 0.004 | 0.000 | 0.007 | |
| exp | 0.556 | 0.004 | 0.561 | |
| exp.elmer | 0.560 | 0.012 | 0.576 | |
| gbm.exp | 0.416 | 0.004 | 0.417 | |
| gbm.samples | 0.568 | 0.004 | 0.572 | |
| genes | 0.192 | 0.004 | 0.195 | |
| genes_GR | 0.188 | 0.008 | 0.197 | |
| gistic.allbygene | 0.008 | 0.000 | 0.007 | |
| gistic.thresholedbygene | 0.008 | 0.000 | 0.007 | |
| histone.marks | 1.596 | 0.032 | 1.630 | |
| lgg.exp | 0.420 | 0.004 | 0.421 | |
| lgg.samples | 0.560 | 0.004 | 0.566 | |
| markersMatrix | 3.184 | 0.044 | 3.232 | |
| met | 0.556 | 0.012 | 0.570 | |
| met.elmer | 0.828 | 0.020 | 0.847 | |
| mut | 12.024 | 0.056 | 12.091 | |
| tmp.biogrid | 13.088 | 0.076 | 13.171 | |