Farhad Shokoohi
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/DMCHMM |
| Branch: RELEASE_3_9 |
| Last Commit: e1b82fe |
| Last Changed Date: 2019-05-02 11:54:08 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:11:53 -0400 (Wed, 16 Oct 2019).
| Package 446/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DMCHMM 1.6.0 Farhad Shokoohi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: DMCHMM |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DMCHMM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DMCHMM_1.6.0.tar.gz |
| StartedAt: 2019-10-16 01:14:35 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:21:17 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 402.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DMCHMM.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DMCHMM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DMCHMM_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DMCHMM.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMCHMM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMCHMM’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'SummarizedExperiment', 'S4Vectors', 'BiocParallel', 'GenomicRanges',
'IRanges', 'fdrtool'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘DMCHMM’ 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 ... NOTE
.findDMCs : .mfun3: no visible binding for global variable ‘Weights’
findDMCs,BSDMCs : .mfun3: no visible binding for global variable
‘Weights’
Undefined global functions or variables:
Weights
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘methVars’ ‘methVars<-’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qqDMCs-method 79.371 2.042 43.012
findDMCs-method 79.197 1.902 44.957
manhattanDMCs-method 78.346 2.592 42.781
methHMMCMC-method 70.472 1.631 39.544
methHMEM-method 6.140 0.687 4.184
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/DMCHMM.Rcheck/00check.log’
for details.
DMCHMM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DMCHMM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘DMCHMM’ ... ** using staged installation ** R ** 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 (DMCHMM)
DMCHMM.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> library(testthat)
> library(DMCHMM)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: fdrtool
DMCHMM package, Version 1.6.0, Released 2018-09-02
A pipeline for identifying differentially methylated CpG sites
using Hidden Markov Model in bisulfite sequencing data.
BugReports: https://github.com/shokoohi/DMCHMM/issues
Attaching package: 'DMCHMM'
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
>
> test_check("DMCHMM")
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
18.049 0.923 16.543
DMCHMM.Rcheck/DMCHMM-Ex.timings
| name | user | system | elapsed | |
| BSDMCs-class | 0.094 | 0.012 | 0.106 | |
| BSData-class | 0.128 | 0.016 | 0.144 | |
| cBSDMCs-method | 0.039 | 0.020 | 0.059 | |
| cBSData-method | 0.055 | 0.000 | 0.055 | |
| combine-method | 0.226 | 0.016 | 0.242 | |
| findDMCs-method | 79.197 | 1.902 | 44.957 | |
| manhattanDMCs-method | 78.346 | 2.592 | 42.781 | |
| methHMEM-method | 6.140 | 0.687 | 4.184 | |
| methHMMCMC-method | 70.472 | 1.631 | 39.544 | |
| methLevels-method | 0.104 | 0.012 | 0.117 | |
| methReads-method | 0.083 | 0.004 | 0.087 | |
| methStates-method | 0.081 | 0.008 | 0.089 | |
| qqDMCs-method | 79.371 | 2.042 | 43.012 | |
| readBismark-method | 0.432 | 0.035 | 0.486 | |
| totalReads-method | 0.080 | 0.004 | 0.084 | |