Sean Davis
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/GenomicDataCommons |
| Branch: RELEASE_3_7 |
| Last Commit: 2436472 |
| Last Changed Date: 2018-09-06 18:20:06 -0400 (Thu, 06 Sep 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:30:07 -0400 (Wed, 17 Oct 2018).
| Package 593/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicDataCommons 1.4.3 Sean Davis
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: GenomicDataCommons |
| Version: 1.4.3 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GenomicDataCommons_1.4.3.tar.gz |
| StartedAt: 2018-10-16 00:44:15 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 00:46:22 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 126.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicDataCommons.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GenomicDataCommons_1.4.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/GenomicDataCommons.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘1.4.3’ * 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-3.7-bioc/meat/GenomicDataCommons.Rcheck/00check.log’ for details.
GenomicDataCommons.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL GenomicDataCommons ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘GenomicDataCommons’ ... ** 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 * DONE (GenomicDataCommons)
GenomicDataCommons.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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
6.960 0.224 17.518
GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings
| name | user | system | elapsed | |
| aggregations | 0.264 | 0.008 | 0.665 | |
| available_expand | 0.020 | 0.004 | 1.112 | |
| available_fields | 0.056 | 0.000 | 0.171 | |
| available_values | 0.048 | 0.000 | 0.194 | |
| constants | 0.000 | 0.004 | 0.002 | |
| count | 0.084 | 0.000 | 0.277 | |
| default_fields | 0.052 | 0.000 | 0.173 | |
| entity_name | 0.040 | 0.000 | 0.127 | |
| expand | 0.104 | 0.004 | 0.338 | |
| faceting | 0.064 | 0.000 | 0.192 | |
| filtering | 0.152 | 0.000 | 0.478 | |
| gdc_cache | 0.004 | 0.000 | 0.004 | |
| gdc_client | 0.004 | 0.020 | 0.028 | |
| gdc_clinical | 0.176 | 0.024 | 0.620 | |
| gdc_rnaseq | 0.072 | 0.000 | 0.222 | |
| gdc_token | 0.004 | 0.000 | 0.002 | |
| gdcdata | 0.204 | 0.004 | 0.625 | |
| grep_fields | 0.036 | 0.004 | 0.082 | |
| id_field | 0.024 | 0.004 | 0.083 | |
| ids | 0.196 | 0.004 | 1.757 | |
| manifest | 0.208 | 0.000 | 0.347 | |
| mapping | 0.024 | 0.000 | 0.067 | |
| query | 0.060 | 0.004 | 0.162 | |
| readDNAcopy | 0.068 | 0.000 | 0.082 | |
| readHTSeqFile | 0.032 | 0.000 | 0.035 | |
| response | 0.052 | 0.000 | 0.250 | |
| results | 0.06 | 0.00 | 0.19 | |
| results_all | 0.088 | 0.000 | 0.320 | |
| select | 0.136 | 0.000 | 0.388 | |
| slicing | 0.004 | 0.000 | 0.000 | |
| status | 0.020 | 0.000 | 0.056 | |
| transfer | 0.000 | 0.000 | 0.001 | |
| write_manifest | 0.092 | 0.000 | 0.221 | |