Package: GenomicDataCommons

Version: 1.2.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GenomicDataCommons_1.2.0.tar.gz

StartedAt: 2018-04-11 23:48:51 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:50:22 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 91.3 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicDataCommons.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 GenomicDataCommons_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GenomicDataCommons.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicDataCommons’ version ‘1.2.0’
* 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 ‘GenomicDataCommons’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
default_fields.character: no visible binding for global variable
  ‘defaults’
Undefined global functions or variables:
  defaults
* 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 ... NOTE
S3 methods shown with full name in documentation object 'as.data.frame.GDCResults':
  ‘as.data.frame.GDCResults’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/GenomicDataCommons.Rcheck/00check.log’
for details.

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

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(GenomicDataCommons)
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not


Attaching package: 'GenomicDataCommons'

The following object is masked from 'package:stats':

    filter

> 
> test_check("GenomicDataCommons")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 40 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  5.612   0.132   8.487 

name	user	system	elapsed
aggregations	0.584	0.036	0.994
as.data.frame.GDCResults	0.348	0.000	0.607
available_expand	0.02	0.00	0.06
available_fields	0.060	0.000	0.153
available_values	0.040	0.000	0.208
constants	0.000	0.000	0.001
count	0.080	0.004	0.236
default_fields	0.052	0.004	0.151
entity_name	0.268	0.004	0.346
expand	0.124	0.000	0.324
faceting	0.084	0.000	0.204
filtering	0.164	0.024	0.440
gdc_client	0.000	0.012	0.017
gdc_token	0.000	0.000	0.001
gdcdata	0.012	0.008	0.629
grep_fields	0.028	0.008	0.082
id_field	0.036	0.000	0.099
ids	0.244	0.020	0.982
manifest	0.768	0.012	0.975
mapping	0.020	0.000	0.054
query	0.068	0.000	0.162
rbindlist2	0.000	0.004	0.003
readDNAcopy	0.28	0.00	0.28
readHTSeqFile	0.232	0.000	0.232
response	0.056	0.000	0.241
results	0.056	0.004	0.230
results_all	0.096	0.000	0.278
select	0.120	0.004	0.330
slicing	0	0	0
status	0.020	0.000	0.049
transfer	0	0	0
write_manifest	0.100	0.000	0.239