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CHECK report for GenomicDataCommons on merida1

This page was generated on 2021-05-06 12:35:06 -0400 (Thu, 06 May 2021).

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 715/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDataCommons 1.14.0  (landing page)
Sean Davis
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GenomicDataCommons
Branch: RELEASE_3_12
Last Commit: c08477c
Last Changed Date: 2020-10-27 11:23:06 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GenomicDataCommons
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicDataCommons_1.14.0.tar.gz
StartedAt: 2021-05-06 02:05:31 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:08:48 -0400 (Thu, 06 May 2021)
EllapsedTime: 196.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GenomicDataCommons.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicDataCommons_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GenomicDataCommons.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/GenomicDataCommons.Rcheck/00check.log’
for details.



Installation output

GenomicDataCommons.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenomicDataCommons
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
 10.745   0.512  20.696 

Example timings

GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings

nameusersystemelapsed
aggregations0.0850.0150.622
available_expand0.0330.0010.074
available_fields0.0350.0010.145
available_values0.0380.0010.466
constants0.0010.0010.002
count0.0660.0020.247
default_fields0.0330.0020.141
entity_name0.0430.0030.128
expand0.1050.0050.331
faceting0.0750.0050.221
field_description0.1320.0040.364
filtering0.9840.0142.053
gdc_cache0.0010.0010.002
gdc_client0.0040.0040.008
gdc_clinical0.4620.0250.983
gdc_rnaseq0.0580.0050.256
gdc_token0.0010.0000.002
gdcdata0.2130.0210.603
grep_fields0.0290.0020.072
id_field0.0330.0010.077
ids0.1980.0050.771
manifest0.0970.0020.258
mapping0.0170.0020.054
query0.0680.0010.158
readDNAcopy0.1290.0030.133
readHTSeqFile0.0470.0020.049
response0.0450.0020.208
results0.0440.0020.199
results_all0.0560.0010.281
select0.1080.0050.453
slicing0.0000.0010.000
status0.0120.0010.052
transfer0.0000.0000.001
write_manifest0.0760.0020.239