Back to the "Build/check report"

BioC experimental data: CHECK report for TCGAWorkflowData on malbec2

This page was generated on 2017-08-15 15:08:03 -0400 (Tue, 15 Aug 2017).

Package 298/316HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAWorkflowData 1.0.0
Tiago Chedraoui Silva
Snapshot Date: 2017-08-15 09:00:06 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_5/experiment/pkgs/TCGAWorkflowData
Last Changed Rev: 4155 / Revision: 4227
Last Changed Date: 2017-04-24 16:09:26 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: TCGAWorkflowData
Version: 1.0.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TCGAWorkflowData_1.0.0.tar.gz
StartedAt: 2017-08-15 11:12:51 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 11:17:16 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 265.2 seconds
RetCode: 0
Status:  OK 
CheckDir: TCGAWorkflowData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TCGAWorkflowData_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/TCGAWorkflowData.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.0.0’
* 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 81.0Mb
  sub-directories of 1Mb or more:
    data  80.7Mb
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
TCGAWorkflowData 31.364  0.220  31.598
tmp.biogrid      12.020  0.048  12.072
GBMmut            9.720  0.104   9.826
LGGmut            7.340  0.012   7.356
mut               6.500  0.008   6.513
* 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-3.5-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’
for details.


TCGAWorkflowData.Rcheck/00install.out:

* installing *source* package ‘TCGAWorkflowData’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCGAWorkflowData)

TCGAWorkflowData.Rcheck/TCGAWorkflowData-Ex.timings:

nameusersystemelapsed
GBMmut9.7200.1049.826
LGGmut7.3400.0127.356
TCGAWorkflowData31.364 0.22031.598
cnvMatrix0.0080.0000.007
exp.elmer0.1720.0080.182
gbm.exp0.3960.0040.400
gbm.samples0.1840.0040.188
genes0.1960.0000.197
genes_GR0.1880.0000.191
gistic.allbygene0.0040.0000.006
gistic.thresholedbygene0.0080.0000.006
histone.marks1.5280.0121.541
lgg.exp0.3920.0040.396
lgg.samples0.1760.0040.181
markersMatrix3.0040.0203.024
met0.0040.0000.002
met.elmer0.1840.0000.183
mut6.5000.0086.513
tmp.biogrid12.020 0.04812.072