Liz Ing-Simmons
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GenomicInteractions |
| Branch: master |
| Last Commit: d8c4c15 |
| Last Changed Date: 2018-10-30 11:54:33 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:30:28 -0400 (Tue, 09 Apr 2019).
| Package 649/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicInteractions 1.17.0 Liz Ing-Simmons
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: GenomicInteractions |
| Version: 1.17.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicInteractions.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicInteractions_1.17.0.tar.gz |
| StartedAt: 2019-04-09 01:07:43 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:14:28 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 405.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomicInteractions.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:GenomicInteractions.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicInteractions_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GenomicInteractions.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicInteractions/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicInteractions’ version ‘1.17.0’
* 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 ‘GenomicInteractions’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
extdata 7.9Mb
* 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
export.bed12 5.073 0.307 5.521
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.
GenomicInteractions.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenomicInteractions ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘GenomicInteractions’ ... ** 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 * DONE (GenomicInteractions)
GenomicInteractions.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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.
> library(testthat)
> library(GenomicInteractions)
Loading required package: InteractionSet
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, 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: 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
>
> test_check("GenomicInteractions")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 48 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
28.143 1.326 29.648
GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings
| name | user | system | elapsed | |
| GInteractions-subsetByFeatures-methods | 0.534 | 0.023 | 0.595 | |
| GenomicInteractions-class | 0.195 | 0.013 | 0.223 | |
| GenomicInteractions-package | 0.000 | 0.001 | 0.001 | |
| GenomicInteractions | 0.124 | 0.012 | 0.138 | |
| InteractionHelpers | 0.074 | 0.007 | 0.083 | |
| InteractionTrack | 1.069 | 0.030 | 1.136 | |
| annotateInteractions | 0.227 | 0.025 | 0.255 | |
| annotateRegions | 0.054 | 0.005 | 0.060 | |
| asBED-GInteractions-method | 1.404 | 0.033 | 1.446 | |
| availableDisplayPars | 0.032 | 0.003 | 0.036 | |
| calculateDistances | 0.088 | 0.002 | 0.094 | |
| categoriseInteractions | 0.364 | 0.016 | 0.399 | |
| export.bed12 | 5.073 | 0.307 | 5.521 | |
| export.bedpe | 0.174 | 0.007 | 0.183 | |
| export.chiasig | 0.129 | 0.008 | 0.137 | |
| export.igraph | 0.145 | 0.006 | 0.151 | |
| getters | 0.090 | 0.001 | 0.092 | |
| makeGenomicInteractionsFromFile | 1.123 | 0.068 | 1.196 | |
| plotAvgViewpoint | 0.313 | 0.005 | 0.322 | |
| plotCisTrans | 0.373 | 0.005 | 0.379 | |
| plotCounts | 0.743 | 0.006 | 0.755 | |
| plotDists | 0.280 | 0.005 | 0.285 | |
| plotInteractionAnnotations | 0.494 | 0.008 | 0.506 | |
| plotSummaryStats | 1.055 | 0.013 | 1.099 | |
| plotViewpoint | 0.668 | 0.036 | 0.706 | |
| resetAnnotations | 0.051 | 0.001 | 0.053 | |
| setters | 0.101 | 0.001 | 0.101 | |
| summariseByFeaturePairs | 1.080 | 0.011 | 1.094 | |
| summariseByFeatures | 0.487 | 0.035 | 0.523 | |
| viewPoint | 0.274 | 0.022 | 0.298 | |