Lucas A. Salas
| Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC |
| Branch: RELEASE_3_10 |
| Last Commit: 64be62a |
| Last Changed Date: 2019-11-06 11:42:50 -0400 (Wed, 06 Nov 2019) |
| Back to Build/check report for BioC 3.10 experimental data |
This page was generated on 2020-04-14 17:46:29 -0400 (Tue, 14 Apr 2020).
| Package 125/384 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| FlowSorted.Blood.EPIC 1.4.1 Lucas A. Salas
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| Package: FlowSorted.Blood.EPIC |
| Version: 1.4.1 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:FlowSorted.Blood.EPIC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings FlowSorted.Blood.EPIC_1.4.1.tar.gz |
| StartedAt: 2020-04-14 13:50:46 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 14:00:32 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 586.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowSorted.Blood.EPIC.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:FlowSorted.Blood.EPIC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings FlowSorted.Blood.EPIC_1.4.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/FlowSorted.Blood.EPIC.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.4.1’
* 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 180.948 7.820 192.056
FlowSorted.Blood.EPIC 46.280 0.684 47.563
* 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-3.10-data-experiment/meat/FlowSorted.Blood.EPIC.Rcheck/00check.log’
for details.
FlowSorted.Blood.EPIC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL FlowSorted.Blood.EPIC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘FlowSorted.Blood.EPIC’ ... ** using staged installation ** 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 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 (FlowSorted.Blood.EPIC)
FlowSorted.Blood.EPIC.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.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, 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
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: 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: 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
Loading required package: BiocFileCache
Loading required package: dbplyr
Attaching package: 'AnnotationHub'
The following object is masked from 'package:Biobase':
cache
>
> test_check("FlowSorted.Blood.EPIC")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
147.768 2.544 151.465
FlowSorted.Blood.EPIC.Rcheck/FlowSorted.Blood.EPIC-Ex.timings
| name | user | system | elapsed | |
| FlowSorted.Blood.EPIC | 46.280 | 0.684 | 47.563 | |
| IDOLOptimizedCpGs | 0 | 0 | 0 | |
| IDOLOptimizedCpGs450klegacy | 0 | 0 | 0 | |
| estimateCellCounts2 | 180.948 | 7.820 | 192.056 | |