Malcolm Perry
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/GenomicInteractions |
| Branch: RELEASE_3_6 |
| Last Commit: 9c6453c |
| Last Changed Date: 2017-10-30 12:40:38 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:39:26 -0400 (Thu, 12 Apr 2018).
| Package 566/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicInteractions 1.12.0 Malcolm Perry
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GenomicInteractions |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.12.0.tar.gz |
| StartedAt: 2018-04-12 04:18:53 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 04:25:28 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 395.4 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 --no-vignettes --timings GenomicInteractions_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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 11.3Mb
sub-directories of 1Mb or more:
doc 2.3Mb
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 installed files from ‘inst/doc’ ... 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
‘/Users/biocbuild/bbs-3.6-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.
GenomicInteractions.Rcheck/00install.out
* installing *source* package ‘GenomicInteractions’ ... ** R ** data ** inst ** preparing package for lazy loading Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions' Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions' Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions' * DONE (GenomicInteractions)
GenomicInteractions.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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: 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 object is masked from 'package:base':
apply
Warning messages:
1: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
2: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions'
>
> test_check("GenomicInteractions")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 48 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
27.207 0.646 29.006
GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings
| name | user | system | elapsed | |
| GInteractions-subsetByFeatures-methods | 0.578 | 0.017 | 0.605 | |
| GenomicInteractions-class | 0.247 | 0.001 | 0.256 | |
| GenomicInteractions-package | 0.000 | 0.000 | 0.001 | |
| GenomicInteractions | 0.276 | 0.001 | 0.278 | |
| InteractionHelpers | 0.052 | 0.003 | 0.055 | |
| InteractionTrack | 1.070 | 0.006 | 1.086 | |
| annotateInteractions | 0.150 | 0.003 | 0.154 | |
| annotateRegions | 0.035 | 0.002 | 0.037 | |
| asBED-GInteractions-method | 0.332 | 0.008 | 0.344 | |
| availableDisplayPars | 0.023 | 0.001 | 0.025 | |
| calculateDistances | 0.042 | 0.000 | 0.042 | |
| categoriseInteractions | 0.281 | 0.004 | 0.285 | |
| export.bed12 | 3.992 | 0.064 | 4.117 | |
| export.bedpe | 0.158 | 0.005 | 0.164 | |
| export.chiasig | 0.118 | 0.005 | 0.124 | |
| export.igraph | 0.087 | 0.002 | 0.091 | |
| getters | 0.077 | 0.001 | 0.078 | |
| makeGenomicInteractionsFromFile | 1.819 | 0.043 | 1.887 | |
| plotAvgViewpoint | 0.214 | 0.003 | 0.223 | |
| plotCisTrans | 1.232 | 0.010 | 1.266 | |
| plotCounts | 0.978 | 0.005 | 1.005 | |
| plotDists | 0.235 | 0.003 | 0.249 | |
| plotInteractionAnnotations | 0.405 | 0.003 | 0.412 | |
| plotSummaryStats | 0.891 | 0.006 | 0.904 | |
| plotViewpoint | 0.432 | 0.006 | 0.449 | |
| resetAnnotations | 0.039 | 0.002 | 0.040 | |
| setters | 0.043 | 0.001 | 0.042 | |
| summariseByFeaturePairs | 0.811 | 0.007 | 0.835 | |
| summariseByFeatures | 0.400 | 0.005 | 0.413 | |
| viewPoint | 0.188 | 0.003 | 0.196 | |