Astrid Deschenes
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/methylInheritance |
| Branch: RELEASE_3_10 |
| Last Commit: 6822d45 |
| Last Changed Date: 2019-10-29 13:10:24 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:12:39 -0400 (Wed, 15 Apr 2020).
| Package 1023/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methylInheritance 1.10.0 Astrid Deschenes
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: methylInheritance |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings methylInheritance_1.10.0.tar.gz |
| StartedAt: 2020-04-15 04:46:31 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:01:29 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 898.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylInheritance.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings methylInheritance_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/methylInheritance.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylInheritance/DESCRIPTION’ ... OK
* this is package ‘methylInheritance’ version ‘1.10.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runPermutation 403.316 1.040 247.947
samplesForTransgenerationalAnalysis 208.792 0.752 111.640
runObservation 111.012 0.308 85.250
runOnePermutationOnAllGenerations 61.748 0.300 26.232
demoForTransgenerationalAnalysis 59.952 0.340 23.389
* 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
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL methylInheritance ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘methylInheritance’ ... ** using staged installation ** R ** data ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (methylInheritance)
methylInheritance.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> ## 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, basename, cbind, 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, 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
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
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 -- Wed Apr 15 05:01:26 2020
***********************************************
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: Use of `formatForGraphDataFrame$RESULT` is discouraged. Use `RESULT` instead.
2: In max(i) : no non-missing arguments to max; returning -Inf
3: In max(i) : no non-missing arguments to max; returning -Inf
>
> proc.time()
user system elapsed
288.760 2.024 132.361
methylInheritance.Rcheck/methylInheritance-Ex.timings
| name | user | system | elapsed | |
| calculateSignificantLevel | 0.236 | 0.020 | 0.258 | |
| createDataStructure | 0.088 | 0.000 | 0.113 | |
| createOutputDir | 0.000 | 0.000 | 0.001 | |
| demoForTransgenerationalAnalysis | 59.952 | 0.340 | 23.389 | |
| extractInfo | 0.200 | 0.004 | 0.237 | |
| formatInputMethylData | 0.296 | 0.024 | 0.322 | |
| getGRangesFromMethylDiff | 0.112 | 0.000 | 0.220 | |
| interGeneration | 1.464 | 0.000 | 1.470 | |
| isInterGenerationResults | 0.000 | 0.000 | 0.001 | |
| loadAllRDSResults | 0.256 | 0.000 | 0.261 | |
| loadConvergenceData | 0.292 | 0.000 | 0.322 | |
| mergePermutationAndObservation | 0.000 | 0.004 | 0.004 | |
| methylInheritanceAllResults | 0.008 | 0.000 | 0.007 | |
| methylInheritanceResults | 0.028 | 0.004 | 0.030 | |
| plotConvergenceGraph | 0.760 | 0.004 | 0.782 | |
| plotGraph | 0.564 | 0.004 | 0.573 | |
| readInterGenerationResults | 0.052 | 0.000 | 0.052 | |
| runObservation | 111.012 | 0.308 | 85.250 | |
| runOnePermutationOnAllGenerations | 61.748 | 0.300 | 26.232 | |
| runPermutation | 403.316 | 1.040 | 247.947 | |
| samplesForTransgenerationalAnalysis | 208.792 | 0.752 | 111.640 | |
| saveInterGenerationResults | 1.452 | 0.000 | 1.508 | |
| validateExtractInfo | 0.004 | 0.000 | 0.003 | |
| validateLoadConvergenceData | 0.004 | 0.000 | 0.001 | |
| validateMergePermutationAndObservation | 0.000 | 0.000 | 0.001 | |
| validateRunObservation | 0.176 | 0.004 | 0.180 | |
| validateRunPermutation | 0.180 | 0.000 | 0.182 | |