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CHECK report for FlowSorted.Blood.EPIC on malbec1

This page was generated on 2019-04-16 15:26:20 -0400 (Tue, 16 Apr 2019).

Package 117/360HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSorted.Blood.EPIC 1.0.0
Lucas A. Salas
Snapshot Date: 2019-04-16 11:00:05 -0400 (Tue, 16 Apr 2019)
URL: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC
Branch: RELEASE_3_8
Last Commit: f4f54f3
Last Changed Date: 2018-10-30 11:36:26 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: FlowSorted.Blood.EPIC
Version: 1.0.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:FlowSorted.Blood.EPIC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings FlowSorted.Blood.EPIC_1.0.0.tar.gz
StartedAt: 2019-04-16 13:41:46 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 13:51:43 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 596.7 seconds
RetCode: 0
Status:  OK 
CheckDir: FlowSorted.Blood.EPIC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:FlowSorted.Blood.EPIC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings FlowSorted.Blood.EPIC_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-data-experiment/meat/FlowSorted.Blood.EPIC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSorted.Blood.EPIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FlowSorted.Blood.EPIC’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘minfi’ ‘SummarizedExperiment’ ‘genefilter’ ‘quadprog’ ‘nlme’
  ‘S4Vectors’ ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
  ‘ExperimentHub’
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 ‘FlowSorted.Blood.EPIC’ 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
estimateCellCounts2   190.300 10.404 202.236
FlowSorted.Blood.EPIC  49.092  0.756  50.578
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.8-data-experiment/meat/FlowSorted.Blood.EPIC.Rcheck/00check.log’
for details.



Installation output

FlowSorted.Blood.EPIC.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL FlowSorted.Blood.EPIC
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘FlowSorted.Blood.EPIC’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (FlowSorted.Blood.EPIC)

Tests output

FlowSorted.Blood.EPIC.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(FlowSorted.Blood.EPIC)
Loading required package: minfi
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: GenomicRanges
Loading required package: stats4
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: SummarizedExperiment
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

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: genefilter

Attaching package: 'genefilter'

The following objects are masked from 'package:matrixStats':

    rowSds, rowVars

Loading required package: quadprog
Loading required package: nlme

Attaching package: 'nlme'

The following object is masked from 'package:Biostrings':

    collapse

The following object is masked from 'package:IRanges':

    collapse

Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Loading required package: ExperimentHub
Loading required package: AnnotationHub

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

> 
> test_check("FlowSorted.Blood.EPIC")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 4 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
149.800   2.324 153.078 

Example timings

FlowSorted.Blood.EPIC.Rcheck/FlowSorted.Blood.EPIC-Ex.timings

nameusersystemelapsed
FlowSorted.Blood.EPIC49.092 0.75650.578
IDOLOptimizedCpGs000
IDOLOptimizedCpGs450klegacy000
estimateCellCounts2190.300 10.404202.236