Pascal Belleau
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/methInheritSim |
| Branch: RELEASE_3_6 |
| Last Commit: f557093 |
| Last Changed Date: 2017-10-30 12:41:30 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:45:03 -0400 (Thu, 12 Apr 2018).
| Package 832/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methInheritSim 1.0.0 Pascal Belleau
| 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: methInheritSim |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methInheritSim_1.0.0.tar.gz |
| StartedAt: 2018-04-12 06:12:41 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 06:17:30 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 288.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methInheritSim.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 methInheritSim_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/methInheritSim.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 ‘methInheritSim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methInheritSim’ version ‘1.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘methInheritSim’ 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
samplesForChrSynthetic 7.951 0.052 8.439
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/methInheritSim.Rcheck/00check.log’
for details.
methInheritSim.Rcheck/00install.out
* installing *source* package ‘methInheritSim’ ... ** 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 (methInheritSim)
methInheritSim.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("methInheritSim")
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
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
RUNIT TEST PROTOCOL -- Thu Apr 12 06:17:25 2018
***********************************************
Number of test functions: 104
Number of errors: 0
Number of failures: 0
1 Test Suite :
methInheritSim RUnit Tests - 104 test functions, 0 errors, 0 failures
Number of test functions: 104
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
62.695 0.539 64.242
methInheritSim.Rcheck/methInheritSim-Ex.timings
| name | user | system | elapsed | |
| calculateNbDiffCase | 0.002 | 0.000 | 0.002 | |
| createSampleID | 0.002 | 0.000 | 0.008 | |
| dataSimExample | 0.018 | 0.005 | 0.023 | |
| estBetaAlpha | 0.001 | 0.000 | 0.001 | |
| estBetaBeta | 0.001 | 0.000 | 0.001 | |
| fixSeed | 0.001 | 0.000 | 0.001 | |
| getDiffCase | 0.032 | 0.005 | 0.038 | |
| getDiffMeth | 0.076 | 0.010 | 0.086 | |
| getSim | 1.501 | 0.016 | 1.534 | |
| getSyntheticChr | 0.389 | 0.023 | 0.420 | |
| runOnEachSynCHR | 2.682 | 0.042 | 2.759 | |
| runSim | 4.665 | 0.040 | 4.790 | |
| samplesForChrSynthetic | 7.951 | 0.052 | 8.439 | |
| saveData | 0.000 | 0.000 | 0.001 | |
| simEachGeneration | 0.434 | 0.011 | 0.449 | |
| simInheritance | 0.854 | 0.007 | 0.870 | |
| testIfAlreadyDone | 0.001 | 0.000 | 0.001 | |
| validateRunSimDoubleParameters | 0.001 | 0.001 | 0.002 | |
| validateRunSimIntegerParameters | 0.001 | 0.000 | 0.002 | |
| validateRunSimLogicalParameters | 0.033 | 0.004 | 0.038 | |
| validateRunSimOtherParameters | 0.031 | 0.007 | 0.038 | |
| validateRunSimParameters | 0.030 | 0.004 | 0.035 | |