Pascal Belleau
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/methInheritSim |
| Branch: RELEASE_3_7 |
| Last Commit: bd76f21 |
| Last Changed Date: 2018-04-30 10:35:47 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:30:19 -0400 (Wed, 17 Oct 2018).
| Package 882/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methInheritSim 1.2.0 Pascal Belleau
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: methInheritSim |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:methInheritSim.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings methInheritSim_1.2.0.tar.gz |
| StartedAt: 2018-10-16 01:53:03 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:56:17 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 193.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methInheritSim.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:methInheritSim.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings methInheritSim_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/methInheritSim.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 ... 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 ... NOTE
Found the following non-portable file path:
methInheritSim/vignettes/methInheritSim_cache/html/syntheticChr_acdd0a3b4cd09c90fc362bf34d9555e5.RData
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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 ... NOTE
Error in .requirePackage(package) :
unable to find required package 'methylKit'
Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
Execution halted
* 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
samplesForChrSynthetic 9.16 0.016 9.182
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/methInheritSim.Rcheck/00check.log’
for details.
methInheritSim.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL methInheritSim ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘methInheritSim’ ... ** 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 * DONE (methInheritSim)
methInheritSim.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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("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, basename, cbind, colMeans, colSums, colnames,
dirname, 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 -- Tue Oct 16 01:56:15 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
21.396 0.416 21.844
methInheritSim.Rcheck/methInheritSim-Ex.timings
| name | user | system | elapsed | |
| calculateNbDiffCase | 0.004 | 0.000 | 0.001 | |
| createSampleID | 0.004 | 0.000 | 0.001 | |
| dataSimExample | 0.008 | 0.004 | 0.013 | |
| estBetaAlpha | 0.000 | 0.000 | 0.001 | |
| estBetaBeta | 0 | 0 | 0 | |
| fixSeed | 0.000 | 0.000 | 0.001 | |
| getDiffCase | 0.000 | 0.000 | 0.001 | |
| getDiffMeth | 0.568 | 0.000 | 0.568 | |
| getSim | 0.416 | 0.016 | 0.430 | |
| getSyntheticChr | 0.156 | 0.012 | 0.166 | |
| runOnEachSynCHR | 1.828 | 0.056 | 1.887 | |
| runSim | 4.732 | 0.016 | 4.754 | |
| samplesForChrSynthetic | 9.160 | 0.016 | 9.182 | |
| saveData | 0 | 0 | 0 | |
| simEachGeneration | 0.440 | 0.004 | 0.443 | |
| simInheritance | 0.732 | 0.000 | 0.733 | |
| testIfAlreadyDone | 0.000 | 0.000 | 0.001 | |
| validateRunSimDoubleParameters | 0.004 | 0.000 | 0.001 | |
| validateRunSimIntegerParameters | 0.000 | 0.000 | 0.001 | |
| validateRunSimLogicalParameters | 0.028 | 0.000 | 0.029 | |
| validateRunSimOtherParameters | 0.028 | 0.000 | 0.029 | |
| validateRunSimParameters | 0.032 | 0.000 | 0.030 | |