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CHECK report for GenomicDataCommons on malbec2

This page was generated on 2019-04-09 11:47:49 -0400 (Tue, 09 Apr 2019).

Package 646/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDataCommons 1.7.3
Sean Davis
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/GenomicDataCommons
Branch: master
Last Commit: 76d3f9a
Last Changed Date: 2018-11-08 21:46:12 -0400 (Thu, 08 Nov 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: GenomicDataCommons
Version: 1.7.3
Command: /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_1.7.3.tar.gz
StartedAt: 2019-04-09 00:45:38 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:48:28 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 170.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicDataCommons.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /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_1.7.3.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GenomicDataCommons.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.7.3’
* 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

GenomicDataCommons.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GenomicDataCommons
###
##############################################################################
##############################################################################


* 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

GenomicDataCommons.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  9.941   0.392  19.321 

Example timings

GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings

nameusersystemelapsed
aggregations0.2230.0210.973
available_expand0.0190.0000.062
available_fields0.0790.0000.188
available_values0.0500.0000.284
constants0.0020.0000.001
count0.0940.0030.271
default_fields0.0530.0040.164
entity_name0.0510.0000.134
expand0.1350.0040.362
faceting0.0830.0040.213
filtering0.6910.0001.757
gdc_cache0.0070.0000.007
gdc_client0.0030.0330.037
gdc_clinical0.5570.0400.967
gdc_rnaseq0.0740.0080.250
gdc_token0.0010.0000.001
gdcdata0.2360.0160.656
grep_fields0.0330.0040.079
id_field0.0370.0000.082
ids0.2430.0040.713
manifest0.1100.0040.248
mapping0.0230.0000.060
query0.0730.0000.162
readDNAcopy0.0640.0000.076
readHTSeqFile0.0280.0000.029
response0.0570.0000.160
results0.0550.0000.157
results_all0.0980.0040.308
select0.1320.0000.362
slicing000
status0.0390.0000.077
transfer000
write_manifest0.1180.0200.431