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CHECK report for GenomicDataCommons on malbec2

This page was generated on 2020-10-17 11:54:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GenomicDataCommons PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 707/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDataCommons 1.12.0
Sean Davis
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GenomicDataCommons
Branch: RELEASE_3_11
Last Commit: 2e7abc9
Last Changed Date: 2020-04-27 15:06:48 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicDataCommons
Version: 1.12.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GenomicDataCommons_1.12.0.tar.gz
StartedAt: 2020-10-17 01:39:58 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:42:57 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 179.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicDataCommons.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GenomicDataCommons_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/GenomicDataCommons.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.12.0’
* 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 ... WARNING
Missing link or links in documentation object 'grep_fields.Rd':
  ‘.gdc_entities’

Missing link or links in documentation object 'query.Rd':
  ‘facets’ ‘available_expands’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'available_fields'
  ‘entity’ ‘field’

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 ... WARNING
'library' or 'require' calls not declared from:
  ‘BiocParallel’ ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
* 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: 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/GenomicDataCommons.Rcheck/00check.log’
for details.



Installation output

GenomicDataCommons.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GenomicDataCommons
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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

GenomicDataCommons.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 
  9.998   0.371  19.342 

Example timings

GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings

nameusersystemelapsed
aggregations0.2080.0160.685
available_expand0.0250.0000.063
available_fields0.0640.0000.177
available_values0.0590.0000.437
constants0.0010.0000.001
count0.0860.0080.270
default_fields0.0500.0040.150
entity_name0.0630.0000.135
expand0.1500.0040.359
faceting0.1040.0000.227
field_description0.8230.0681.099
filtering0.7140.0201.667
gdc_cache0.0050.0040.021
gdc_client0.0040.0340.038
gdc_clinical0.5550.0280.950
gdc_rnaseq0.0800.0080.255
gdc_token0.0010.0000.002
gdcdata0.2670.0120.800
grep_fields0.0350.0000.072
id_field0.0390.0000.078
ids0.2690.0000.766
manifest0.1000.0040.235
mapping0.0230.0000.056
query0.0740.0040.157
readDNAcopy0.1340.0000.164
readHTSeqFile0.0300.0000.029
response0.0520.0000.148
results0.0520.0000.155
results_all0.0870.0000.296
select0.1930.0000.612
slicing000
status0.0170.0000.053
transfer0.0010.0000.000
write_manifest0.0990.0041.009