Sebastian Gibb
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/topdownr |
| Branch: master |
| Last Commit: e40bde1 |
| Last Changed Date: 2019-03-27 15:59:00 -0400 (Wed, 27 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:36:01 -0400 (Tue, 09 Apr 2019).
| Package 1624/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| topdownr 1.5.6 Sebastian Gibb
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: topdownr |
| Version: 1.5.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:topdownr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings topdownr_1.5.6.tar.gz |
| StartedAt: 2019-04-09 04:09:49 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:15:01 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 311.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: topdownr.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:topdownr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings topdownr_1.5.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/topdownr.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘topdownr/DESCRIPTION’ ... OK
* this is package ‘topdownr’ version ‘1.5.6’
* package encoding: UTF-8
* 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 ‘topdownr’ 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 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 R/sysdata.rda ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
writeMethodXmls 79.781 0.277 90.481
* 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:
── 3. Failure: .resample (@test_method-xml.R#77) ──────────────────────────────
.resample(x) not equal to x[c(5:4, 10, 8, 2, 6, 1, 9, 3, 7), ].
Attributes: < Component "row.names": Mean relative difference: 0.7659574 >
Component "A": 8 string mismatches
Component "B": Mean relative difference: 0.7659574
══ testthat results ═══════════════════════════════════════════════════════════
OK: 646 SKIPPED: 0 FAILED: 3
1. Failure: .reorderSequence (@test_fragments.R#96)
2. Failure: .ms2Experiments (@test_method-xml.R#18)
3. Failure: .resample (@test_method-xml.R#77)
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
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/topdownr.Rcheck/00check.log’
for details.
topdownr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL topdownr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘topdownr’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (topdownr)
topdownr.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("topdownr")
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: ProtGenerics
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
This is topdownr version 1.5.6
Visit https://sgibb.github.io/topdownr/ to get started.
>
> test_check("topdownr")
── 1. Failure: .reorderSequence (@test_fragments.R#96) ────────────────────────
.reorderSequence("ABCDE", "random") not equal to "DABCE".
1/1 mismatches
x[1]: "ECBAD"
y[1]: "DABCE"
── 2. Failure: .ms2Experiments (@test_method-xml.R#18) ────────────────────────
.ms2Experiments(...) not equal to list(...).
Component 1: Component 1: Mean relative difference: 0.6666667
── 3. Failure: .resample (@test_method-xml.R#77) ──────────────────────────────
.resample(x) not equal to x[c(5:4, 10, 8, 2, 6, 1, 9, 3, 7), ].
Attributes: < Component "row.names": Mean relative difference: 0.7659574 >
Component "A": 8 string mismatches
Component "B": Mean relative difference: 0.7659574
══ testthat results ═══════════════════════════════════════════════════════════
OK: 646 SKIPPED: 0 FAILED: 3
1. Failure: .reorderSequence (@test_fragments.R#96)
2. Failure: .ms2Experiments (@test_method-xml.R#18)
3. Failure: .resample (@test_method-xml.R#77)
Error: testthat unit tests failed
Execution halted
topdownr.Rcheck/topdownr-Ex.timings
| name | user | system | elapsed | |
| AbstractTopDownSet-class | 0.813 | 0.054 | 0.875 | |
| FragmentViews-class | 0.132 | 0.012 | 0.145 | |
| NCBSet-class | 3.383 | 0.109 | 3.526 | |
| TopDownSet-class | 1.288 | 0.047 | 1.345 | |
| createExperimentsFragmentOptimisation | 0.229 | 0.002 | 0.233 | |
| expandMsConditions | 0.007 | 0.000 | 0.007 | |
| readTopDownFiles | 1.989 | 0.039 | 2.054 | |
| validMsSettings | 0.004 | 0.001 | 0.005 | |
| windows-specific-functions | 0.000 | 0.000 | 0.001 | |
| writeMethodXmls | 79.781 | 0.277 | 90.481 | |