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This page was generated on 2016-04-23 10:29:43 -0700 (Sat, 23 Apr 2016).
| Package 608/1103 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| MEAL 1.0.4 Carlos Ruiz
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | ERROR | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ ERROR ] | OK |
| Package: MEAL |
| Version: 1.0.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.0.4.tar.gz |
| StartedAt: 2016-04-23 01:49:54 -0700 (Sat, 23 Apr 2016) |
| EndedAt: 2016-04-23 01:58:59 -0700 (Sat, 23 Apr 2016) |
| EllapsedTime: 544.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MEAL.Rcheck |
| Warnings: NA |
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.0.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MEAL.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.0.4’
* 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 ‘MEAL’ can be installed ... [36s/43s] WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/MEAL.Rcheck/00install.out’ for details.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotVolcano,AnalysisResults: no visible binding for global variable
‘adj.p’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [112s/120s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DAPipeline 16.303 0.981 20.609
plotRegion-methods 10.522 0.705 11.273
add.methy-methods 10.246 0.857 15.086
plotRDA-methods 10.052 0.693 10.818
DARegionAnalysis 7.110 0.173 7.314
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [60s/62s]
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[cpgCollapseAnnotation] Defining blocks.
[cpgCollapse] Collapsing data
coercing object of mode numeric to SnpMatrix
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Error in eval(expr, envir, enclos) : could not find function "add_methy"
Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval
In addition: Warning message:
In matrix(runif(6, max = 15), 4) :
data length [6] is not a sub-multiple or multiple of the number of rows [4]
testthat results ================================================================
OK: 216 SKIPPED: 0 FAILED: 0
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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/MEAL.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R version 3.2.4 (2016-03-10) -- "Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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(MEAL)
Loading required package: Biobase
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
>
> test_check("MEAL")
[cpgCollapse] Creating annotation.
[cpgCollapseAnnotation] Clustering islands and clusters of probes.
[cpgCollapseAnnotation] Computing new annotation.
[cpgCollapseAnnotation] Defining blocks.
[cpgCollapse] Collapsing data
coercing object of mode numeric to SnpMatrix
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Error in eval(expr, envir, enclos) : could not find function "add_methy"
Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval
In addition: Warning message:
In matrix(runif(6, max = 15), 4) :
data length [6] is not a sub-multiple or multiple of the number of rows [4]
testthat results ================================================================
OK: 216 SKIPPED: 0 FAILED: 0
Execution halted
MEAL.Rcheck/00install.out:
* installing *source* package ‘MEAL’ ... ** R ** inst ** preparing package for lazy loading Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE * DONE (MEAL)
MEAL.Rcheck/MEAL-Ex.timings:
| name | user | system | elapsed | |
| AnalysisRegionResults-class | 0.003 | 0.000 | 0.004 | |
| AnalysisResults-class | 0.002 | 0.000 | 0.003 | |
| DAPipeline | 16.303 | 0.981 | 20.609 | |
| DAProbe | 0.663 | 0.027 | 0.691 | |
| DARegion | 2.515 | 0.165 | 2.681 | |
| DARegionAnalysis | 7.110 | 0.173 | 7.314 | |
| MethylationSet-class | 0.002 | 0.001 | 0.002 | |
| RDAset | 1.931 | 0.096 | 2.045 | |
| add.genexp-methods | 0.093 | 0.001 | 0.095 | |
| add.methy-methods | 10.246 | 0.857 | 15.086 | |
| add.set-methods | 0.063 | 0.001 | 0.063 | |
| calculateRelevantSNPs | 0.001 | 0.000 | 0.001 | |
| checkProbes-methods | 1.848 | 0.035 | 1.884 | |
| checkSamples-methods | 1.820 | 0.045 | 1.866 | |
| chrNumToChar | 0.001 | 0.000 | 0.002 | |
| createRanges | 0.026 | 0.002 | 0.028 | |
| explainedVariance | 0.035 | 0.002 | 0.088 | |
| exportResults-methods | 2.394 | 0.172 | 2.617 | |
| filterSet-methods | 1.552 | 0.035 | 1.613 | |
| getGeneVals-methods | 3.437 | 0.196 | 3.639 | |
| getMs-methods | 1.538 | 0.037 | 1.577 | |
| normalSNP | 0.001 | 0.000 | 0.001 | |
| plotBestFeatures | 2.269 | 0.144 | 2.430 | |
| plotEWAS-methods | 3.879 | 0.275 | 4.158 | |
| plotFeature | 2.117 | 0.046 | 2.173 | |
| plotQQ-methods | 2.356 | 0.137 | 2.496 | |
| plotRDA-methods | 10.052 | 0.693 | 10.818 | |
| plotRegion-methods | 10.522 | 0.705 | 11.273 | |
| plotVolcano-methods | 2.684 | 0.110 | 2.798 | |
| prepareMethylationSet | 2.423 | 0.167 | 2.624 | |
| preparePhenotype | 0.006 | 0.000 | 0.006 | |