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BioC 3.5: CHECK report for GenomicDataCommons on malbec2

This page was generated on 2017-08-16 13:18:20 -0400 (Wed, 16 Aug 2017).

Package 538/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDataCommons 1.0.0
Davis Sean
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GenomicDataCommons
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
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 

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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:

nameusersystemelapsed
aggregations0.5520.0120.868
as.data.frame.GDCResults0.2400.0040.544
available_expand0.0200.0000.046
available_fields0.0560.0000.110
available_values0.0520.0000.136
constants0.0000.0000.001
count0.2640.0040.383
default_fields0.0520.0000.109
entity_name0.0440.0000.092
expand0.1160.0040.241
faceting0.0720.0080.152
field_picker0.0000.0000.001
filtering0.1920.0000.349
gdc_client0.0040.0120.019
gdc_token0.0000.0000.002
gdcdata0.0160.0040.407
grep_fields0.0280.0040.057
id_field0.0320.0040.063
ids0.2520.0040.737
manifest0.7600.0042.078
mapping0.0200.0000.041
query0.0560.0000.112
rbindlist20.0040.0000.004
readDNAcopy0.1360.0000.133
readHTSeqFile0.0520.0000.054
response0.0480.0000.274
results0.0560.0000.299
results_all0.0840.0040.203
select0.1360.0000.255
slicing000
status0.0080.0000.029
transfer000
write_manifest0.0920.0000.169