BioC experimental data: CHECK report for TCGAWorkflowData on malbec2

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: 2017-10-18 11:15:20 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 11:19:45 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 265.2 seconds

RetCode: 0

Status:  OK

CheckDir: TCGAWorkflowData.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TCGAWorkflowData_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/TCGAWorkflowData.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 32.584  0.220  32.822
tmp.biogrid      12.908  0.080  12.994
GBMmut           10.368  0.064  10.438
LGGmut            7.600  0.012   7.612
mut               5.856  0.008   5.866
* 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.

* 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	10.368	0.064	10.438
LGGmut	7.600	0.012	7.612
TCGAWorkflowData	32.584	0.220	32.822
cnvMatrix	0.008	0.000	0.008
exp.elmer	0.180	0.004	0.184
gbm.exp	0.392	0.000	0.393
gbm.samples	0.180	0.000	0.182
genes	0.184	0.004	0.186
genes_GR	0.200	0.000	0.201
gistic.allbygene	0.000	0.004	0.007
gistic.thresholedbygene	0.004	0.000	0.007
histone.marks	1.532	0.000	1.534
lgg.exp	0.416	0.000	0.417
lgg.samples	0.184	0.000	0.187
markersMatrix	3.540	0.008	3.553
met	0.004	0.000	0.002
met.elmer	0.184	0.000	0.183
mut	5.856	0.008	5.866
tmp.biogrid	12.908	0.080	12.994