Michael Lawrence
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/HelloRanges |
| Branch: master |
| Last Commit: 2e0da74 |
| Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:17:08 -0400 (Tue, 09 Apr 2019).
| Package 736/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HelloRanges 1.9.0 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | 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: HelloRanges |
| Version: 1.9.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HelloRanges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HelloRanges_1.9.0.tar.gz |
| StartedAt: 2019-04-09 02:39:25 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:47:05 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 460.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HelloRanges.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HelloRanges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HelloRanges_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/HelloRanges.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 ‘HelloRanges/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HelloRanges’ version ‘1.9.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomicRanges', 'Biostrings', 'BSgenome', 'GenomicFeatures', 'VariantAnnotation', 'Rsamtools', 'GenomicAlignments', 'rtracklayer', 'GenomeInfoDb', 'SummarizedExperiment' 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 ‘HelloRanges’ 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 ... NOTE Packages in Depends field not imported from: ‘BSgenome’ ‘GenomicAlignments’ ‘GenomicFeatures’ ‘VariantAnnotation’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: ‘BiocGenerics:::testPackage’ ‘IRanges:::subgrouping’ ‘S4Vectors:::make_zero_col_DataFrame’ See the note in ?`:::` about the use of this operator. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘HelloRanges_unit_tests.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/HelloRanges.Rcheck/00check.log’ for details.
HelloRanges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HelloRanges ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘HelloRanges’ ... ** using staged installation ** 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 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 (HelloRanges)
HelloRanges.Rcheck/tests/HelloRanges_unit_tests.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.
> require("HelloRanges") || stop("unable to load HelloRanges package")
Loading required package: HelloRanges
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
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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: VariantAnnotation
Loading required package: SummarizedExperiment
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 object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: Rsamtools
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Loading required package: GenomicAlignments
[1] TRUE
> HelloRanges:::.test()
RUNIT TEST PROTOCOL -- Tue Apr 9 02:46:57 2019
***********************************************
Number of test functions: 17
Number of errors: 0
Number of failures: 0
1 Test Suite :
HelloRanges RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
77.913 2.152 83.235
HelloRanges.Rcheck/HelloRanges-Ex.timings
| name | user | system | elapsed | |
| bedtools_closest | 0.635 | 0.017 | 0.654 | |
| bedtools_complement | 0.036 | 0.001 | 0.037 | |
| bedtools_coverage | 0.309 | 0.047 | 0.356 | |
| bedtools_flank | 0.224 | 0.032 | 0.258 | |
| bedtools_genomecov | 0.220 | 0.036 | 0.256 | |
| bedtools_getfasta | 0.091 | 0.014 | 0.105 | |
| bedtools_groupby | 0.141 | 0.022 | 0.163 | |
| bedtools_intersect | 1.808 | 0.099 | 1.908 | |
| bedtools_jaccard | 0.197 | 0.001 | 0.198 | |
| bedtools_makewindows | 0.200 | 0.001 | 0.201 | |
| bedtools_map | 0.352 | 0.001 | 0.353 | |
| bedtools_merge | 0.380 | 0.027 | 0.406 | |
| bedtools_multiinter | 0.175 | 0.021 | 0.196 | |
| bedtools_nuc | 0.120 | 0.010 | 0.131 | |
| bedtools_shift | 0.122 | 0.007 | 0.128 | |
| bedtools_slop | 0.150 | 0.018 | 0.168 | |
| bedtools_subtract | 0.273 | 0.043 | 0.317 | |
| bedtools_unionbedg | 0.120 | 0.001 | 0.121 | |
| distmode | 0.005 | 0.001 | 0.006 | |