Astrid Deschenes
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/methylInheritance |
| Branch: RELEASE_3_6 |
| Last Commit: afeb6cc |
| Last Changed Date: 2017-10-30 12:41:27 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:44:52 -0400 (Thu, 12 Apr 2018).
| Package 838/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methylInheritance 1.2.0 Astrid Deschenes
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: methylInheritance |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylInheritance_1.2.0.tar.gz |
| StartedAt: 2018-04-12 06:16:21 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 06:25:46 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 565.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylInheritance.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylInheritance_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/methylInheritance.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylInheritance/DESCRIPTION’ ... OK
* this is package ‘methylInheritance’ version ‘1.2.0’
* 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 ‘methylInheritance’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runPermutation 149.451 3.758 141.333
runObservation 73.090 0.393 74.710
samplesForTransgenerationalAnalysis 61.396 4.750 43.935
runOnePermutationOnAllGenerations 19.278 1.466 16.301
demoForTransgenerationalAnalysis 10.529 0.951 7.763
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* 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: OK
methylInheritance.Rcheck/00install.out
* installing *source* package ‘methylInheritance’ ... ** 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 (methylInheritance)
methylInheritance.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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.
> ## Run all tests presnt in the package
> BiocGenerics:::testPackage("methylInheritance")
Loading required package: stats4
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, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Permutation Analysis
Number of Generations: 3
Number of Permutations: 20
Observation Results:
SOURCE ELEMENT ANALYSIS TYPE RESULT
1 OBSERVATION SITES i2 HYPER1 4
2 OBSERVATION SITES i2 HYPER2 1
3 OBSERVATION SITES i2 HYPO1 2
4 OBSERVATION SITES i2 HYPO2 2
5 OBSERVATION SITES iAll HYPER 0
6 OBSERVATION SITES iAll HYPO 0
7 OBSERVATION TILES i2 HYPER1 1000
8 OBSERVATION TILES i2 HYPER2 0
9 OBSERVATION TILES i2 HYPO1 0
10 OBSERVATION TILES i2 HYPO2 0
11 OBSERVATION TILES iAll HYPER 0
12 OBSERVATION TILES iAll HYPO 0
RUNIT TEST PROTOCOL -- Thu Apr 12 06:25:41 2018
***********************************************
Number of test functions: 72
Number of errors: 0
Number of failures: 0
1 Test Suite :
methylInheritance RUnit Tests - 72 test functions, 0 errors, 0 failures
Number of test functions: 72
Number of errors: 0
Number of failures: 0
Warning messages:
1: In max(i) : no non-missing arguments to max; returning -Inf
2: In max(i) : no non-missing arguments to max; returning -Inf
>
> proc.time()
user system elapsed
69.791 2.400 63.038
methylInheritance.Rcheck/methylInheritance-Ex.timings
| name | user | system | elapsed | |
| calculateSignificantLevel | 0.226 | 0.015 | 0.247 | |
| createDataStructure | 0.103 | 0.002 | 0.104 | |
| createOutputDir | 0.001 | 0.000 | 0.002 | |
| demoForTransgenerationalAnalysis | 10.529 | 0.951 | 7.763 | |
| extractInfo | 0.362 | 0.001 | 0.369 | |
| formatInputMethylData | 0.657 | 0.045 | 0.711 | |
| getGRangesFromMethylDiff | 0.489 | 0.003 | 0.507 | |
| interGeneration | 0.850 | 0.018 | 0.881 | |
| isInterGenerationResults | 0.002 | 0.001 | 0.003 | |
| loadAllRDSResults | 0.255 | 0.002 | 0.258 | |
| loadConvergenceData | 0.425 | 0.002 | 0.435 | |
| mergePermutationAndObservation | 0.047 | 0.001 | 0.048 | |
| methylInheritanceAllResults | 0.007 | 0.011 | 0.018 | |
| methylInheritanceResults | 0.025 | 0.011 | 0.038 | |
| plotConvergenceGraph | 1.981 | 0.012 | 2.050 | |
| plotGraph | 1.370 | 0.016 | 1.415 | |
| readInterGenerationResults | 0.143 | 0.002 | 0.147 | |
| runObservation | 73.090 | 0.393 | 74.710 | |
| runOnePermutationOnAllGenerations | 19.278 | 1.466 | 16.301 | |
| runPermutation | 149.451 | 3.758 | 141.333 | |
| samplesForTransgenerationalAnalysis | 61.396 | 4.750 | 43.935 | |
| saveInterGenerationResults | 0.727 | 0.006 | 0.735 | |
| validateExtractInfo | 0.002 | 0.001 | 0.004 | |
| validateLoadConvergenceData | 0.002 | 0.000 | 0.002 | |
| validateMergePermutationAndObservation | 0.003 | 0.000 | 0.004 | |
| validateRunObservation | 0.118 | 0.013 | 0.132 | |
| validateRunPermutation | 0.112 | 0.007 | 0.124 | |