Multiple platform build/check report for BioC 3.9 - CHECK report for GenomicDataCommons on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GenomicDataCommons_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GenomicDataCommons.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 ‘GenomicDataCommons/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicDataCommons’ 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 ‘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 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’
gdc_rnaseq: no visible binding for global variable ‘case_id’
gdc_rnaseq: no visible binding for global variable ‘file_id’
Undefined global functions or variables:
  case_id defaults file_id
* 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 ... WARNING
Undocumented arguments in documentation object '.htseq_importer'
  ‘fnames’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/GenomicDataCommons.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GenomicDataCommons
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GenomicDataCommons’ ...
** using staged installation
** R
** inst
** 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 (GenomicDataCommons)

Tests output


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(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: 48 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  9.553   0.467  19.124

Example timings

name	user	system	elapsed
aggregations	0.168	0.032	0.648
available_expand	0.023	0.000	0.066
available_fields	0.048	0.008	0.159
available_values	0.047	0.000	0.321
constants	0.001	0.000	0.001
count	0.103	0.000	0.287
default_fields	0.057	0.000	0.159
entity_name	0.057	0.000	0.140
expand	0.134	0.000	0.351
faceting	0.084	0.004	0.268
filtering	1.431	0.051	2.633
gdc_cache	0.007	0.000	0.023
gdc_client	0.001	0.039	0.041
gdc_clinical	0.497	0.056	1.227
gdc_rnaseq	0.085	0.000	1.023
gdc_token	0.001	0.000	0.001
gdcdata	0.218	0.028	0.842
grep_fields	0.041	0.000	0.083
id_field	0.039	0.000	0.092
ids	0.261	0.016	0.828
manifest	0.654	0.056	0.858
mapping	0.022	0.000	0.057
query	0.077	0.000	0.175
readDNAcopy	0.067	0.000	0.090
readHTSeqFile	0.013	0.008	0.020
response	0.057	0.000	0.180
results	0.057	0.000	0.176
results_all	0.076	0.005	0.290
select	0.093	0.008	0.315
slicing	0	0	0
status	0.022	0.004	0.063
transfer	0	0	0
write_manifest	0.140	0.000	0.388

CHECK report for GenomicDataCommons on malbec2

Summary

Command output

Installation output

Tests output

Example timings