Tim Peters
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/DMRcate |
| Branch: RELEASE_3_7 |
| Last Commit: 60f320a |
| Last Changed Date: 2018-04-30 10:35:32 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:25:53 -0400 (Wed, 17 Oct 2018).
| Package 397/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DMRcate 1.16.0 Tim Peters
| 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 | TIMEOUT | OK |
| Package: DMRcate |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DMRcate_1.16.0.tar.gz |
| StartedAt: 2018-10-15 23:55:40 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-16 00:18:22 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 1362.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DMRcate.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:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DMRcate_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/DMRcate.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 ‘DMRcate/DESCRIPTION’ ... OK
* this is package ‘DMRcate’ version ‘1.16.0’
* 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 ‘DMRcate’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DMRcate-package 514.08 2.912 534.483
* 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
DMRcate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL DMRcate ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘DMRcate’ ... ** 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 * DONE (DMRcate)
DMRcate.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.
> BiocGenerics:::testPackage("DMRcate")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
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
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
locfit 1.5-9.1 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'bsseq'
The following object is masked from 'package:minfi':
getMeth
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Fitting chr20...
Consecutive mode specified, lambda is now set at -1 consecutive CpGs.
Fitting chr20...
Demarcating regions...
Done!
Fitting chr20...
Demarcating regions...
Done!
RUNIT TEST PROTOCOL -- Tue Oct 16 00:18:20 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
DMRcate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
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> proc.time()
user system elapsed
550.212 1.508 552.231
DMRcate.Rcheck/DMRcate-Ex.timings
| name | user | system | elapsed | |
| DMR.plot | 0.000 | 0.000 | 0.001 | |
| DMRcate-package | 514.080 | 2.912 | 534.483 | |
| cpg.annotate | 0.000 | 0.000 | 0.001 | |
| dmrcate | 0.004 | 0.000 | 0.001 | |
| extractRanges | 0.000 | 0.000 | 0.001 | |
| rmSNPandCH | 0.000 | 0.000 | 0.001 | |