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This page was generated on 2017-08-16 13:18:20 -0400 (Wed, 16 Aug 2017).
| Package 538/1382 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| GenomicDataCommons 1.0.0 Davis Sean
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: GenomicDataCommons |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenomicDataCommons_1.0.0.tar.gz |
| StartedAt: 2017-08-15 23:21:08 -0400 (Tue, 15 Aug 2017) |
| EndedAt: 2017-08-15 23:22:43 -0400 (Tue, 15 Aug 2017) |
| EllapsedTime: 94.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomicDataCommons.Rcheck |
| Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenomicDataCommons_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GenomicDataCommons.Rcheck’ * using R version 3.4.1 (2017-06-30) * 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 ‘1.0.0’ * 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 loading without being on the library search path ... 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’ Undefined global functions or variables: defaults * 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 ... NOTE S3 methods shown with full name in documentation object 'as.data.frame.GDCResults': ‘as.data.frame.GDCResults’ The \usage entries for S3 methods should use the \method markup and not their full name. 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 6. Failure: legacy cases file manifest contains supplied file_ids (@test_legacy.R#89) all(files_legacy_ids %in% cres$id) isn't true. testthat results ================================================================ OK: 37 SKIPPED: 0 FAILED: 6 1. Error: manifest cases (@test_data.R#7) 2. Failure: legacy file ids found (@test_legacy.R#42) 3. Failure: legacy manifest matches legacy ids (@test_legacy.R#53) 4. Failure: legacy case ids found (@test_legacy.R#70) 5. Failure: legacy case ids in default archive, also (@test_legacy.R#78) 6. Failure: legacy cases file manifest contains supplied file_ids (@test_legacy.R#89) Error: testthat unit tests failed Execution halted * 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 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.5-bioc/meat/GenomicDataCommons.Rcheck/00check.log’ for details.
testthat.Rout.fail:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 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")
1. Error: manifest cases (@test_data.R#7) --------------------------------------
subscript out of bounds
1: manifest(q) at testthat/test_data.R:7
2: manifest.gdc_cases(q)
3: rbindlist2((x %>% select("files.file_id") %>% results(from = from, size = size))$files)[[1]]
4: `[[.data.frame`(rbindlist2((x %>% select("files.file_id") %>% results(from = from,
size = size))$files), 1)
5: (function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, i, exact = exact))(x,
..., exact = exact)
2. Failure: legacy file ids found (@test_legacy.R#42) --------------------------
`fres` has length 9, not length 10.
3. Failure: legacy manifest matches legacy ids (@test_legacy.R#53) -------------
nrow(fres) not equal to length(files_legacy_ids).
1/1 mismatches
[1] 9 - 10 == -1
4. Failure: legacy case ids found (@test_legacy.R#70) --------------------------
length(cres) not equal to length(cases_legacy_ids).
1/1 mismatches
[1] 9 - 10 == -1
5. Failure: legacy case ids in default archive, also (@test_legacy.R#78) -------
length(cres) not equal to 10.
1/1 mismatches
[1] 9 - 10 == -1
6. Failure: legacy cases file manifest contains supplied file_ids (@test_legacy.R#89)
all(files_legacy_ids %in% cres$id) isn't true.
testthat results ================================================================
OK: 37 SKIPPED: 0 FAILED: 6
1. Error: manifest cases (@test_data.R#7)
2. Failure: legacy file ids found (@test_legacy.R#42)
3. Failure: legacy manifest matches legacy ids (@test_legacy.R#53)
4. Failure: legacy case ids found (@test_legacy.R#70)
5. Failure: legacy case ids in default archive, also (@test_legacy.R#78)
6. Failure: legacy cases file manifest contains supplied file_ids (@test_legacy.R#89)
Error: testthat unit tests failed
Execution halted
GenomicDataCommons.Rcheck/00install.out:
* installing *source* package ‘GenomicDataCommons’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GenomicDataCommons)
GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings:
| name | user | system | elapsed | |
| aggregations | 0.552 | 0.012 | 0.868 | |
| as.data.frame.GDCResults | 0.240 | 0.004 | 0.544 | |
| available_expand | 0.020 | 0.000 | 0.046 | |
| available_fields | 0.056 | 0.000 | 0.110 | |
| available_values | 0.052 | 0.000 | 0.136 | |
| constants | 0.000 | 0.000 | 0.001 | |
| count | 0.264 | 0.004 | 0.383 | |
| default_fields | 0.052 | 0.000 | 0.109 | |
| entity_name | 0.044 | 0.000 | 0.092 | |
| expand | 0.116 | 0.004 | 0.241 | |
| faceting | 0.072 | 0.008 | 0.152 | |
| field_picker | 0.000 | 0.000 | 0.001 | |
| filtering | 0.192 | 0.000 | 0.349 | |
| gdc_client | 0.004 | 0.012 | 0.019 | |
| gdc_token | 0.000 | 0.000 | 0.002 | |
| gdcdata | 0.016 | 0.004 | 0.407 | |
| grep_fields | 0.028 | 0.004 | 0.057 | |
| id_field | 0.032 | 0.004 | 0.063 | |
| ids | 0.252 | 0.004 | 0.737 | |
| manifest | 0.760 | 0.004 | 2.078 | |
| mapping | 0.020 | 0.000 | 0.041 | |
| query | 0.056 | 0.000 | 0.112 | |
| rbindlist2 | 0.004 | 0.000 | 0.004 | |
| readDNAcopy | 0.136 | 0.000 | 0.133 | |
| readHTSeqFile | 0.052 | 0.000 | 0.054 | |
| response | 0.048 | 0.000 | 0.274 | |
| results | 0.056 | 0.000 | 0.299 | |
| results_all | 0.084 | 0.004 | 0.203 | |
| select | 0.136 | 0.000 | 0.255 | |
| slicing | 0 | 0 | 0 | |
| status | 0.008 | 0.000 | 0.029 | |
| transfer | 0 | 0 | 0 | |
| write_manifest | 0.092 | 0.000 | 0.169 | |