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CHECK report for FlowSorted.CordBloodCombined.450k on malbec2

This page was generated on 2020-10-12 15:59:08 -0400 (Mon, 12 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE FlowSorted.CordBloodCombined.450k PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 126/391HostnameOS / ArchINSTALLBUILDCHECK
FlowSorted.CordBloodCombined.450k 1.4.1
Lucas A. Salas
Snapshot Date: 2020-10-12 07:30:10 -0400 (Mon, 12 Oct 2020)
URL: https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k
Branch: RELEASE_3_11
Last Commit: a7f0244
Last Changed Date: 2020-05-10 15:10:00 -0400 (Sun, 10 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: FlowSorted.CordBloodCombined.450k
Version: 1.4.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:FlowSorted.CordBloodCombined.450k.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings FlowSorted.CordBloodCombined.450k_1.4.1.tar.gz
StartedAt: 2020-10-12 12:23:46 -0400 (Mon, 12 Oct 2020)
EndedAt: 2020-10-12 12:40:30 -0400 (Mon, 12 Oct 2020)
EllapsedTime: 1003.9 seconds
RetCode: 0
Status:  OK 
CheckDir: FlowSorted.CordBloodCombined.450k.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:FlowSorted.CordBloodCombined.450k.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings FlowSorted.CordBloodCombined.450k_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/FlowSorted.CordBloodCombined.450k.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSorted.CordBloodCombined.450k/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FlowSorted.CordBloodCombined.450k’ version ‘1.4.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'minfi', 'SummarizedExperiment',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19',
  'IlluminaHumanMethylationEPICanno.ilm10b4.hg19', 'ExperimentHub',
  'FlowSorted.Blood.EPIC'
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.CordBloodCombined.450k’ 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
* 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-3.11-data-experiment/meat/FlowSorted.CordBloodCombined.450k.Rcheck/00check.log’
for details.



Installation output

FlowSorted.CordBloodCombined.450k.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL FlowSorted.CordBloodCombined.450k
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘FlowSorted.CordBloodCombined.450k’ ...
** using staged installation
** 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 from temporary location
snapshotDate(): 2020-04-27
** testing if installed package can be loaded from final location
snapshotDate(): 2020-04-27
** testing if installed package keeps a record of temporary installation path
* DONE (FlowSorted.CordBloodCombined.450k)

Tests output

FlowSorted.CordBloodCombined.450k.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.CordBloodCombined.450k)
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, 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: 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


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: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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 1.5-9.4 	 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19

Attaching package: 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19'

The following objects are masked from 'package:IlluminaHumanMethylation450kanno.ilmn12.hg19':

    Islands.UCSC, Locations, Manifest, Other, SNPs.132CommonSingle,
    SNPs.135CommonSingle, SNPs.137CommonSingle, SNPs.138CommonSingle,
    SNPs.141CommonSingle, SNPs.142CommonSingle, SNPs.144CommonSingle,
    SNPs.146CommonSingle, SNPs.147CommonSingle, SNPs.Illumina

Loading required package: ExperimentHub
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

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

    cache

Loading required package: FlowSorted.Blood.EPIC
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

snapshotDate(): 2020-04-27
> 
> test_check("FlowSorted.CordBloodCombined.450k")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 61.069   2.075  63.580 

Example timings

FlowSorted.CordBloodCombined.450k.Rcheck/FlowSorted.CordBloodCombined.450k-Ex.timings

nameusersystemelapsed
FlowSorted.CordBloodCombined.450K2.2020.0612.327
FlowSorted.CordBloodCombined.450k.compTable0.0000.0000.001
IDOLOptimizedCpGsCordBlood0.0000.0000.001