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This page was generated on 2019-04-16 11:58:42 -0400 (Tue, 16 Apr 2019).
| Package 1525/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SummarizedExperiment 1.12.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK |  | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: SummarizedExperiment |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SummarizedExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SummarizedExperiment_1.12.0.tar.gz |
| StartedAt: 2019-04-16 03:02:07 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:05:21 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 194.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SummarizedExperiment.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SummarizedExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SummarizedExperiment_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SummarizedExperiment.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SummarizedExperiment/DESCRIPTION’ ... OK
* this is package ‘SummarizedExperiment’ version ‘1.12.0’
* package encoding: UTF-8
* 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 ‘SummarizedExperiment’ 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
makeSummarizedExperimentFromExpressionSet 7.522 0.196 7.765
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.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
SummarizedExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SummarizedExperiment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘SummarizedExperiment’ ... ** 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 (SummarizedExperiment)
SummarizedExperiment.Rcheck/tests/run_unitTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.
> require("SummarizedExperiment") || stop("unable to load SummarizedExperiment package")
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: 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: 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
[1] TRUE
> SummarizedExperiment:::.test()
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
RUNIT TEST PROTOCOL -- Tue Apr 16 03:05:15 2019
***********************************************
Number of test functions: 35
Number of errors: 0
Number of failures: 0
1 Test Suite :
SummarizedExperiment RUnit Tests - 35 test functions, 0 errors, 0 failures
Number of test functions: 35
Number of errors: 0
Number of failures: 0
Warning messages:
1: In V_recycle(value, x, x_what = "value", skeleton_what = "x") :
'length(x)' is not a multiple of 'NROW(value)'
2: In V_recycle(value, x, x_what = "value", skeleton_what = "x") :
'length(x)' is not a multiple of 'NROW(value)'
3: In S4Vectors:::V_recycle(arg, x, argname, "x") :
'length(x)' is not a multiple of 'NROW(weight)'
4: In S4Vectors:::V_recycle(arg, x, argname, "x") :
'length(x)' is not a multiple of 'NROW(weight)'
5: In .deprecatedColsMessage() :
Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
deprecated. Please use a range based accessor like genes(), or select()
with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb
object instead.
6: 145 probes could not be mapped.
7: 169 probes could not be mapped.
>
> proc.time()
user system elapsed
22.976 0.755 23.874
SummarizedExperiment.Rcheck/SummarizedExperiment-Ex.timings
| name | user | system | elapsed | |
| Assays-class | 0.127 | 0.005 | 0.133 | |
| RangedSummarizedExperiment-class | 0.519 | 0.057 | 0.580 | |
| SummarizedExperiment-class | 0.741 | 0.064 | 0.821 | |
| coverage-methods | 0.089 | 0.000 | 0.092 | |
| findOverlaps-methods | 0.132 | 0.001 | 0.133 | |
| inter-range-methods | 0.151 | 0.001 | 0.154 | |
| intra-range-methods | 0.299 | 0.029 | 0.333 | |
| makeSummarizedExperimentFromDataFrame | 0.101 | 0.011 | 0.113 | |
| makeSummarizedExperimentFromExpressionSet | 7.522 | 0.196 | 7.765 | |
| makeSummarizedExperimentFromLoom | 0.219 | 0.026 | 0.248 | |
| nearest-methods | 0.449 | 0.061 | 0.513 | |
| readKallisto | 0.807 | 0.046 | 0.872 | |