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 13:12:23 -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 02:14:35 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:22:56 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 500.5 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) (2019-03-18 r76245)
* 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 ... NOTE
Error: package or namespace load failed for ‘GenomicInteractions’:
.onLoad failed in loadNamespace() for 'Rsamtools', details:
call: (function (classes, fdef, mtable)
error: unable to find an inherited method for function ‘strand’ for signature ‘"!="’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domai
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 6.032 0.392 6.429
* 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: 2 NOTEs
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’ ... ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicInteractions)
GenomicInteractions.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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.
> 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
41.189 3.075 44.569
GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings
| name | user | system | elapsed | |
| GInteractions-subsetByFeatures-methods | 0.637 | 0.026 | 0.667 | |
| GenomicInteractions-class | 0.162 | 0.009 | 0.172 | |
| GenomicInteractions-package | 0.000 | 0.000 | 0.001 | |
| GenomicInteractions | 0.139 | 0.005 | 0.143 | |
| InteractionHelpers | 0.082 | 0.010 | 0.095 | |
| InteractionTrack | 1.106 | 0.019 | 1.126 | |
| annotateInteractions | 0.252 | 0.046 | 0.297 | |
| annotateRegions | 0.039 | 0.006 | 0.044 | |
| asBED-GInteractions-method | 1.582 | 0.056 | 1.639 | |
| availableDisplayPars | 0.035 | 0.003 | 0.039 | |
| calculateDistances | 0.095 | 0.001 | 0.096 | |
| categoriseInteractions | 0.364 | 0.013 | 0.377 | |
| export.bed12 | 6.032 | 0.392 | 6.429 | |
| export.bedpe | 0.200 | 0.017 | 0.216 | |
| export.chiasig | 0.145 | 0.008 | 0.153 | |
| export.igraph | 0.179 | 0.010 | 0.190 | |
| getters | 0.105 | 0.001 | 0.105 | |
| makeGenomicInteractionsFromFile | 1.356 | 0.118 | 1.480 | |
| plotAvgViewpoint | 0.409 | 0.007 | 0.416 | |
| plotCisTrans | 0.481 | 0.013 | 0.499 | |
| plotCounts | 1.114 | 0.014 | 1.134 | |
| plotDists | 0.392 | 0.012 | 0.409 | |
| plotInteractionAnnotations | 0.682 | 0.016 | 0.706 | |
| plotSummaryStats | 1.286 | 0.014 | 1.312 | |
| plotViewpoint | 0.859 | 0.016 | 0.881 | |
| resetAnnotations | 0.056 | 0.005 | 0.061 | |
| setters | 0.134 | 0.002 | 0.134 | |
| summariseByFeaturePairs | 1.460 | 0.032 | 1.577 | |
| summariseByFeatures | 0.670 | 0.021 | 0.699 | |
| viewPoint | 0.363 | 0.006 | 0.369 | |