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This page was generated on 2015-10-27 12:13:48 -0400 (Tue, 27 Oct 2015).
| Package 572/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| LOLA 1.1.0 Nathan Sheffield
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | ||||||
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | OK |
| Package: LOLA |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings LOLA_1.1.0.tar.gz |
| StartedAt: 2015-10-27 05:18:20 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 05:19:49 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 89.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: LOLA.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings LOLA_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/LOLA.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LOLA/DESCRIPTION’ ... OK
* this is package ‘LOLA’ version ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘simpleCache’
* 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 ‘LOLA’ can be installed ... [6s/6s] 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/8s]
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
7: expectation(identical(as.vector(x), FALSE), "isn't false", "is false")
8: structure(list(passed = passed, error = FALSE, skipped = FALSE, failure_msg = failure_msg,
success_msg = success_msg, srcref = srcref), class = "expectation")
9: identical(as.vector(x), FALSE)
10: as.vector(x)
11: "*" %in% as.character(strand(rb))
testthat results ================================================================
OK: 29 SKIPPED: 0 FAILED: 1
1. Error: readBed
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, 1 NOTE
See
‘/home/biocbuild/bbs-3.3-bioc/meat/LOLA.Rcheck/00check.log’
for details.
LOLA.Rcheck/tests/testthat.Rout.fail:
R Under development (unstable) (2015-09-09 r69333) -- "Unsuffered Consequences"
Copyright (C) 2015 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(LOLA)
>
> test_check("LOLA")
There were 15 warnings (use warnings() to see them)
1. Error: readBed --------------------------------------------------------------
error in evaluating the argument 'table' in selecting a method for function '%in%': could not find function "strand"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_false("*" %in% as.character(strand(rb))) at test_all.R:143
5: expect_that(object, is_false(), info, label)
6: condition(object)
7: expectation(identical(as.vector(x), FALSE), "isn't false", "is false")
8: structure(list(passed = passed, error = FALSE, skipped = FALSE, failure_msg = failure_msg,
success_msg = success_msg, srcref = srcref), class = "expectation")
9: identical(as.vector(x), FALSE)
10: as.vector(x)
11: "*" %in% as.character(strand(rb))
testthat results ================================================================
OK: 29 SKIPPED: 0 FAILED: 1
1. Error: readBed
Error: testthat unit tests failed
Execution halted
LOLA.Rcheck/00install.out:
* installing *source* package ‘LOLA’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (LOLA)
LOLA.Rcheck/LOLA-Ex.timings:
| name | user | system | elapsed | |
| buildRestrictedUniverse | 0.522 | 0.004 | 0.526 | |
| checkUniverseAppropriateness | 0.162 | 0.000 | 0.162 | |
| extractEnrichmentOverlaps | 1.729 | 0.120 | 1.852 | |
| getRegionSet | 1.907 | 0.097 | 2.003 | |
| listRegionSets | 0.023 | 0.034 | 0.060 | |
| loadRegionDB | 0.355 | 0.038 | 0.392 | |
| mergeRegionDBs | 0.255 | 0.058 | 0.312 | |
| readBed | 0.008 | 0.000 | 0.008 | |
| readCollection | 0.144 | 0.008 | 0.151 | |
| readCollectionAnnotation | 0.004 | 0.000 | 0.004 | |
| readCollectionFiles | 0.010 | 0.000 | 0.009 | |
| readRegionGRL | 0.360 | 0.047 | 0.407 | |
| readRegionSetAnnotation | 0.016 | 0.027 | 0.043 | |
| redefineUserSets | 1.179 | 0.075 | 1.253 | |
| runLOLA | 1.477 | 0.093 | 1.571 | |
| setSharedDataDir | 0 | 0 | 0 | |
| splitFileIntoCollection | 0.003 | 0.004 | 0.007 | |
| userSets | 0.000 | 0.000 | 0.001 | |
| writeCombinedEnrichment | 1.147 | 0.069 | 1.215 | |