Tiago Chedraoui Silva
| Snapshot Date: 2019-10-17 09:00:12 -0400 (Thu, 17 Oct 2019) |
| URL: https://git.bioconductor.org/packages/TCGAWorkflowData |
| Branch: RELEASE_3_9 |
| Last Commit: c334e91 |
| Last Changed Date: 2019-05-02 11:56:48 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 experimental data |
This page was generated on 2019-10-17 16:51:35 -0400 (Thu, 17 Oct 2019).
| Package 348/371 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TCGAWorkflowData 1.8.0 Tiago Chedraoui Silva
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |
| Package: TCGAWorkflowData |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.8.0.tar.gz |
| StartedAt: 2019-10-17 13:52:49 -0400 (Thu, 17 Oct 2019) |
| EndedAt: 2019-10-17 13:59:15 -0400 (Thu, 17 Oct 2019) |
| EllapsedTime: 386.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TCGAWorkflowData.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/TCGAWorkflowData.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.0’
* 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 76.2Mb
sub-directories of 1Mb or more:
data 76.1Mb
* 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 ... 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
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAWorkflowData 34.270 0.240 34.510
GBMmut 13.626 0.115 13.742
LGGmut 10.800 0.060 10.860
tmp.biogrid 10.469 0.055 10.526
mut 10.111 0.039 10.151
* 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
‘/home/biocbuild/bbs-3.9-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’
for details.
TCGAWorkflowData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TCGAWorkflowData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
35.772 0.653 36.423
TCGAWorkflowData.Rcheck/TCGAWorkflowData-Ex.timings
| name | user | system | elapsed | |
| GBMmut | 13.626 | 0.115 | 13.742 | |
| LGGmut | 10.80 | 0.06 | 10.86 | |
| TCGAWorkflowData | 34.27 | 0.24 | 34.51 | |
| cnvMatrix | 0.008 | 0.000 | 0.008 | |
| exp | 0.613 | 0.008 | 0.621 | |
| gbm.exp | 0.381 | 0.003 | 0.384 | |
| gbm.samples | 0.509 | 0.005 | 0.513 | |
| genes | 0.182 | 0.000 | 0.181 | |
| genes_GR | 0.181 | 0.000 | 0.181 | |
| gistic.allbygene | 0.007 | 0.000 | 0.007 | |
| gistic.thresholedbygene | 0.007 | 0.000 | 0.006 | |
| histone.marks | 1.216 | 0.043 | 1.260 | |
| lgg.exp | 0.548 | 0.004 | 0.551 | |
| lgg.samples | 0.485 | 0.005 | 0.489 | |
| markersMatrix | 2.635 | 0.032 | 2.666 | |
| met | 0.492 | 0.004 | 0.495 | |
| mut | 10.111 | 0.039 | 10.151 | |
| tmp.biogrid | 10.469 | 0.055 | 10.526 | |