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This page was generated on 2023-02-04 11:04:53 -0500 (Sat, 04 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GenomicDataCommons on nebbiolo1


To the developers/maintainers of the GenomicDataCommons package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDataCommons.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 772/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDataCommons 1.23.2  (landing page)
Sean Davis
Snapshot Date: 2023-02-03 14:00:22 -0500 (Fri, 03 Feb 2023)
git_url: https://git.bioconductor.org/packages/GenomicDataCommons
git_branch: master
git_last_commit: e0e9824
git_last_commit_date: 2023-01-30 12:51:38 -0500 (Mon, 30 Jan 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    NA  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GenomicDataCommons
Version: 1.23.2
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomicDataCommons_1.23.2.tar.gz
StartedAt: 2023-02-03 20:55:19 -0500 (Fri, 03 Feb 2023)
EndedAt: 2023-02-03 20:57:54 -0500 (Fri, 03 Feb 2023)
EllapsedTime: 155.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDataCommons.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomicDataCommons_1.23.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicDataCommons.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicDataCommons’ version ‘1.23.2’
* package encoding: UTF-8
* 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 ... OK
* 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 ... OK
* 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 ...
  ‘overview.Rmd’ using ‘UTF-8’... OK
  ‘questions-and-answers.Rmd’ using ‘UTF-8’... OK
  ‘somatic_mutations.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

GenomicDataCommons.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomicDataCommons
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
  6.086   0.377  15.991 

Example timings

GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings

nameusersystemelapsed
aggregations0.1450.0040.767
available_expand0.0250.0040.085
available_fields0.0600.0000.149
available_values0.0510.0040.560
constants0.0010.0000.001
count0.0620.0000.264
default_fields0.0350.0000.123
entity_name0.0420.0000.128
expand0.1060.0360.321
faceting0.0640.0080.212
field_description0.1490.0120.431
filtering0.5260.1011.626
gdc_cache0.0000.0010.001
gdc_client0.0020.0020.004
gdc_clinical0.6090.1491.123
gdc_token0.0010.0000.001
gdcdata0.2640.0361.020
grep_fields0.0200.0040.059
id_field0.0280.0000.068
ids0.1790.0050.661
legacy0.0270.0000.061
manifest0.0660.0030.213
mapping0.0160.0000.044
query0.0650.0000.137
readDNAcopy0.2700.0280.312
readHTSeqFile0.1240.0120.135
response0.0420.0000.127
results0.0360.0030.123
results_all0.0670.0000.260
select0.0900.0000.267
slicing0.0000.0000.001
status0.0110.0000.045
transfer0.0000.0000.001
write_manifest0.0630.0020.201