Back to Build/check report for BioC 3.14 experimental data
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-19 15:52:17 -0400 (Tue, 19 Oct 2021).

CHECK results for FlowSorted.CordBloodCombined.450k on nebbiolo2

To the developers/maintainers of the FlowSorted.CordBloodCombined.450k package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 129/404HostnameOS / ArchINSTALLBUILDCHECK
FlowSorted.CordBloodCombined.450k 1.9.0  (landing page)
Lucas A. Salas
Snapshot Date: 2021-10-19 09:30:02 -0400 (Tue, 19 Oct 2021)
git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k
git_branch: master
git_last_commit: ac99dd4
git_last_commit_date: 2021-05-19 12:07:45 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FlowSorted.CordBloodCombined.450k
Version: 1.9.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:FlowSorted.CordBloodCombined.450k.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings FlowSorted.CordBloodCombined.450k_1.9.0.tar.gz
StartedAt: 2021-10-19 12:16:57 -0400 (Tue, 19 Oct 2021)
EndedAt: 2021-10-19 12:33:35 -0400 (Tue, 19 Oct 2021)
EllapsedTime: 998.3 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSorted.CordBloodCombined.450k.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:FlowSorted.CordBloodCombined.450k.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings FlowSorted.CordBloodCombined.450k_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/FlowSorted.CordBloodCombined.450k.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.9.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
FlowSorted.CordBloodCombined.450K 5.326   2.18   7.781
* 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-3.14-data-experiment/meat/FlowSorted.CordBloodCombined.450k.Rcheck/00check.log’
for details.



Installation output

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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL FlowSorted.CordBloodCombined.450k
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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(): 2021-10-18
** testing if installed package can be loaded from final location
snapshotDate(): 2021-10-18
** 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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

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: parallel
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:MatrixGenerics':

    rowSds, rowVars

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(): 2021-10-18
> 
> test_check("FlowSorted.CordBloodCombined.450k")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 58.585   3.889  63.401 

Example timings

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

nameusersystemelapsed
FlowSorted.CordBloodCombined.450K5.3262.1807.781
FlowSorted.CordBloodCombined.450k.compTable000
IDOLOptimizedCpGsCordBlood0.0000.0000.001