| Back to the "Multiple platform build/check report" | A B C D E F G H I J K [L] M N O P Q R S T U V W X Y Z |
This page was generated on 2015-10-27 12:16:12 -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: rm -rf LOLA.buildbin-libdir LOLA.Rcheck && mkdir LOLA.buildbin-libdir LOLA.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LOLA.buildbin-libdir LOLA_1.1.0.tar.gz >LOLA.Rcheck\00install.out 2>&1 && cp LOLA.Rcheck\00install.out LOLA-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=LOLA.buildbin-libdir --install="check:LOLA-install.out" --force-multiarch --no-vignettes --timings LOLA_1.1.0.tar.gz |
| StartedAt: 2015-10-27 03:38:00 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 03:40:51 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 170.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: LOLA.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf LOLA.buildbin-libdir LOLA.Rcheck && mkdir LOLA.buildbin-libdir LOLA.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LOLA.buildbin-libdir LOLA_1.1.0.tar.gz >LOLA.Rcheck\00install.out 2>&1 && cp LOLA.Rcheck\00install.out LOLA-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=LOLA.buildbin-libdir --install="check:LOLA-install.out" --force-multiarch --no-vignettes --timings LOLA_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/LOLA.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'LOLA' 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 ... 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 ...
** running examples for arch 'i386' ... [27s] OK
** running examples for arch 'x64' ... [27s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [17s]
Warning message:
running command '"c:/biocbld/BBS-3˜1.3-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:
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
** running tests for arch 'x64' ...
Running 'testthat.R' [18s]
Warning message:
running command '"c:/biocbld/BBS-3˜1.3-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:
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: 2 ERRORs, 1 NOTE
See
'c:/biocbld/bbs-3.3-bioc/meat/LOLA.Rcheck/00check.log'
for details.
LOLA.Rcheck/tests_i386/testthat.Rout.fail:
R Under development (unstable) (2015-09-22 r69418) -- "Unsuffered Consequences"
Copyright (C) 2015 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(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/tests_x64/testthat.Rout.fail:
R Under development (unstable) (2015-09-22 r69418) -- "Unsuffered Consequences"
Copyright (C) 2015 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(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:
install for i386 * 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 install for x64 * installing *source* package 'LOLA' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'LOLA' as LOLA_1.1.0.zip * DONE (LOLA)
LOLA.Rcheck/examples_i386/LOLA-Ex.timings:
| name | user | system | elapsed | |
| buildRestrictedUniverse | 0.28 | 0.01 | 0.30 | |
| checkUniverseAppropriateness | 0.11 | 0.00 | 0.11 | |
| extractEnrichmentOverlaps | 2.01 | 0.05 | 4.28 | |
| getRegionSet | 1.38 | 0.00 | 3.45 | |
| listRegionSets | 0.01 | 0.00 | 1.11 | |
| loadRegionDB | 0.22 | 0.02 | 1.33 | |
| mergeRegionDBs | 0.49 | 0.00 | 1.58 | |
| readBed | 0 | 0 | 0 | |
| readCollection | 0.12 | 0.00 | 0.12 | |
| readCollectionAnnotation | 0 | 0 | 0 | |
| readCollectionFiles | 0.02 | 0.00 | 0.02 | |
| readRegionGRL | 0.21 | 0.01 | 1.22 | |
| readRegionSetAnnotation | 0.02 | 0.00 | 1.11 | |
| redefineUserSets | 1.13 | 0.00 | 3.34 | |
| runLOLA | 1.18 | 0.02 | 3.41 | |
| setSharedDataDir | 0 | 0 | 0 | |
| splitFileIntoCollection | 0.02 | 0.00 | 0.01 | |
| userSets | 0 | 0 | 0 | |
| writeCombinedEnrichment | 1.33 | 0.00 | 3.32 | |
LOLA.Rcheck/examples_x64/LOLA-Ex.timings:
| name | user | system | elapsed | |
| buildRestrictedUniverse | 0.43 | 0.01 | 0.43 | |
| checkUniverseAppropriateness | 0.11 | 0.00 | 0.11 | |
| extractEnrichmentOverlaps | 2.06 | 0.03 | 3.86 | |
| getRegionSet | 1.27 | 0.02 | 3.47 | |
| listRegionSets | 0.02 | 0.00 | 1.12 | |
| loadRegionDB | 0.23 | 0.02 | 1.35 | |
| mergeRegionDBs | 0.27 | 0.00 | 1.37 | |
| readBed | 0 | 0 | 0 | |
| readCollection | 0.35 | 0.00 | 0.36 | |
| readCollectionAnnotation | 0.02 | 0.00 | 0.02 | |
| readCollectionFiles | 0 | 0 | 0 | |
| readRegionGRL | 0.20 | 0.03 | 1.34 | |
| readRegionSetAnnotation | 0.02 | 0.00 | 1.00 | |
| redefineUserSets | 1.30 | 0.00 | 3.08 | |
| runLOLA | 1.36 | 0.00 | 3.55 | |
| setSharedDataDir | 0 | 0 | 0 | |
| splitFileIntoCollection | 0 | 0 | 0 | |
| userSets | 0 | 0 | 0 | |
| writeCombinedEnrichment | 1.47 | 0.01 | 3.57 | |