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This page was generated on 2017-08-16 13:26:50 -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: rm -rf GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && mkdir GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.0.0.tar.gz >GenomicDataCommons.Rcheck\00install.out 2>&1 && cp GenomicDataCommons.Rcheck\00install.out GenomicDataCommons-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicDataCommons.buildbin-libdir --install="check:GenomicDataCommons-install.out" --force-multiarch --no-vignettes --timings GenomicDataCommons_1.0.0.tar.gz |
| StartedAt: 2017-08-16 00:01:17 -0400 (Wed, 16 Aug 2017) |
| EndedAt: 2017-08-16 00:04:16 -0400 (Wed, 16 Aug 2017) |
| EllapsedTime: 178.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomicDataCommons.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && mkdir GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.0.0.tar.gz >GenomicDataCommons.Rcheck\00install.out 2>&1 && cp GenomicDataCommons.Rcheck\00install.out GenomicDataCommons-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicDataCommons.buildbin-libdir --install="check:GenomicDataCommons-install.out" --force-multiarch --no-vignettes --timings GenomicDataCommons_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicDataCommons.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
readDNAcopy 0.19 0 5.21
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
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$id) isn't true.
testthat results ================================================================
OK: 37 SKIPPED: 0 FAILED: 6
1. Error: manifest cases (@test_data.R#7)
2. Failure: legacy file ids found (@test_legacy.R#42)
3. Failure: legacy manifest matches legacy ids (@test_legacy.R#53)
4. Failure: legacy case ids found (@test_legacy.R#70)
5. Failure: legacy case ids in default archive, also (@test_legacy.R#78)
6. Failure: legacy cases file manifest contains supplied file_ids (@test_legacy.R#89)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
6. Failure: legacy cases file manifest contains supplied file_ids (@test_legacy.R#89)
all(files_legacy_ids %in% cres$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: 2 ERRORs, 2 NOTEs
See
'C:/Users/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: i386-w64-mingw32/i386 (32-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$id) isn't true.
testthat results ================================================================
OK: 37 SKIPPED: 0 FAILED: 6
1. Error: manifest cases (@test_data.R#7)
2. Failure: legacy file ids found (@test_legacy.R#42)
3. Failure: legacy manifest matches legacy ids (@test_legacy.R#53)
4. Failure: legacy case ids found (@test_legacy.R#70)
5. Failure: legacy case ids in default archive, also (@test_legacy.R#78)
6. Failure: legacy cases file manifest contains supplied file_ids (@test_legacy.R#89)
Error: testthat unit tests failed
Execution halted
testthat.Rout.fail:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(GenomicDataCommons)
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Attaching package: 'GenomicDataCommons'
The following object is masked from 'package:stats':
filter
>
> test_check("GenomicDataCommons")
1. Error: manifest cases (@test_data.R#7) --------------------------------------
subscript out of bounds
1: manifest(q) at testthat/test_data.R:7
2: manifest.gdc_cases(q)
3: rbindlist2((x %>% select("files.file_id") %>% results(from = from, size = size))$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:
install for i386 * 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 install for x64 * installing *source* package 'GenomicDataCommons' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GenomicDataCommons' as GenomicDataCommons_1.0.0.zip * DONE (GenomicDataCommons)
GenomicDataCommons.Rcheck/examples_i386/GenomicDataCommons-Ex.timings:
| name | user | system | elapsed | |
| aggregations | 0.64 | 0.11 | 1.01 | |
| as.data.frame.GDCResults | 0.41 | 0.00 | 0.66 | |
| available_expand | 0.05 | 0.00 | 0.07 | |
| available_fields | 0.06 | 0.00 | 0.10 | |
| available_values | 0.08 | 0.00 | 0.18 | |
| constants | 0 | 0 | 0 | |
| count | 0.14 | 0.00 | 0.26 | |
| default_fields | 0.03 | 0.01 | 0.10 | |
| entity_name | 0.09 | 0.00 | 0.16 | |
| expand | 0.11 | 0.00 | 0.25 | |
| faceting | 0.09 | 0.00 | 0.15 | |
| field_picker | 0 | 0 | 0 | |
| filtering | 0.29 | 0.00 | 0.44 | |
| gdc_client | 0 | 0 | 0 | |
| gdc_token | 0 | 0 | 0 | |
| gdcdata | 0.01 | 0.00 | 1.47 | |
| grep_fields | 0.03 | 0.00 | 0.06 | |
| id_field | 0.06 | 0.00 | 0.09 | |
| ids | 0.36 | 0.02 | 0.81 | |
| manifest | 1.17 | 0.06 | 3.77 | |
| mapping | 0.01 | 0.00 | 0.03 | |
| query | 0.14 | 0.00 | 0.20 | |
| rbindlist2 | 0 | 0 | 0 | |
| readDNAcopy | 0.19 | 0.00 | 5.21 | |
| readHTSeqFile | 0.08 | 0.00 | 0.08 | |
| response | 0.10 | 0.00 | 0.47 | |
| results | 0.11 | 0.00 | 0.35 | |
| results_all | 0.08 | 0.00 | 0.18 | |
| select | 0.11 | 0.01 | 0.25 | |
| slicing | 0 | 0 | 0 | |
| status | 0.00 | 0.00 | 0.03 | |
| transfer | 0 | 0 | 0 | |
| write_manifest | 0.12 | 0.00 | 0.19 | |
GenomicDataCommons.Rcheck/examples_x64/GenomicDataCommons-Ex.timings:
| name | user | system | elapsed | |
| aggregations | 0.74 | 0.06 | 1.02 | |
| as.data.frame.GDCResults | 0.41 | 0.00 | 0.72 | |
| available_expand | 0.03 | 0.02 | 0.06 | |
| available_fields | 0.07 | 0.00 | 0.11 | |
| available_values | 0.06 | 0.00 | 0.16 | |
| constants | 0 | 0 | 0 | |
| count | 0.12 | 0.00 | 0.43 | |
| default_fields | 0.07 | 0.00 | 0.11 | |
| entity_name | 0.04 | 0.00 | 0.10 | |
| expand | 0.13 | 0.00 | 0.25 | |
| faceting | 0.08 | 0.01 | 0.17 | |
| field_picker | 0 | 0 | 0 | |
| filtering | 0.25 | 0.00 | 0.44 | |
| gdc_client | 0.01 | 0.00 | 0.01 | |
| gdc_token | 0 | 0 | 0 | |
| gdcdata | 0.00 | 0.02 | 0.41 | |
| grep_fields | 0.05 | 0.00 | 0.08 | |
| id_field | 0.08 | 0.00 | 0.11 | |
| ids | 0.54 | 0.00 | 1.00 | |
| manifest | 1.60 | 0.06 | 2.90 | |
| mapping | 0.01 | 0.00 | 0.03 | |
| query | 0.13 | 0.01 | 0.21 | |
| rbindlist2 | 0.01 | 0.00 | 0.01 | |
| readDNAcopy | 0.24 | 0.00 | 0.36 | |
| readHTSeqFile | 0.09 | 0.00 | 0.10 | |
| response | 0.09 | 0.00 | 0.31 | |
| results | 0.13 | 0.00 | 0.35 | |
| results_all | 0.06 | 0.00 | 0.19 | |
| select | 0.14 | 0.02 | 0.29 | |
| slicing | 0 | 0 | 0 | |
| status | 0.00 | 0.02 | 0.03 | |
| transfer | 0 | 0 | 0 | |
| write_manifest | 0.13 | 0.00 | 0.25 | |