BioC experimental data: CHECK report for TCGAWorkflowData on malbec1

Package: TCGAWorkflowData

Version: 1.1.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCGAWorkflowData_1.1.0.tar.gz

StartedAt: 2017-08-15 11:14:37 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 11:19:01 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 264.2 seconds

RetCode: 0

Status:  OK

CheckDir: TCGAWorkflowData.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCGAWorkflowData_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.1.0’
* 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 32.548  0.164  32.730
tmp.biogrid      12.484  0.036  12.523
GBMmut            9.988  0.076  10.064
LGGmut            7.640  0.028   7.671
mut               6.776  0.012   6.792
* 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-3.6-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
GBMmut	9.988	0.076	10.064
LGGmut	7.640	0.028	7.671
TCGAWorkflowData	32.548	0.164	32.730
cnvMatrix	0.008	0.000	0.008
exp.elmer	0.196	0.008	0.200
gbm.exp	0.400	0.004	0.405
gbm.samples	0.188	0.004	0.190
genes	0.204	0.000	0.204
genes_GR	0.188	0.000	0.190
gistic.allbygene	0.004	0.000	0.007
gistic.thresholedbygene	0.008	0.000	0.008
histone.marks	1.548	0.020	1.572
lgg.exp	0.420	0.004	0.428
lgg.samples	0.188	0.000	0.192
markersMatrix	3.076	0.000	3.082
met	0.000	0.000	0.002
met.elmer	0.188	0.000	0.185
mut	6.776	0.012	6.792
tmp.biogrid	12.484	0.036	12.523