Michael Lawrence
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/HelloRanges |
| Branch: RELEASE_3_7 |
| Last Commit: 94962db |
| Last Changed Date: 2018-04-30 10:35:44 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:29:34 -0400 (Wed, 17 Oct 2018).
| Package 678/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HelloRanges 1.6.0 Michael Lawrence
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: HelloRanges |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:HelloRanges.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings HelloRanges_1.6.0.tar.gz |
| StartedAt: 2018-10-16 01:07:46 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:11:31 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 225.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HelloRanges.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:HelloRanges.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings HelloRanges_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/HelloRanges.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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 ... WARNING
Missing link or links in documentation object 'bedtools_shift.Rd':
‘[GenomicRanges]{shift}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
* 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: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/HelloRanges.Rcheck/00check.log’
for details.
HelloRanges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL HelloRanges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘HelloRanges’ ... ** 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 (HelloRanges)
HelloRanges.Rcheck/tests/HelloRanges_unit_tests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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
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
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 Oct 16 01:11:27 2018
***********************************************
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
39.608 0.388 40.379
HelloRanges.Rcheck/HelloRanges-Ex.timings
| name | user | system | elapsed | |
| bedtools_closest | 0.256 | 0.000 | 0.259 | |
| bedtools_complement | 0.016 | 0.000 | 0.016 | |
| bedtools_coverage | 0.096 | 0.016 | 0.114 | |
| bedtools_flank | 0.084 | 0.004 | 0.086 | |
| bedtools_genomecov | 0.132 | 0.008 | 0.139 | |
| bedtools_getfasta | 0.044 | 0.000 | 0.045 | |
| bedtools_groupby | 0.052 | 0.000 | 0.053 | |
| bedtools_intersect | 0.412 | 0.028 | 0.441 | |
| bedtools_jaccard | 0.112 | 0.000 | 0.115 | |
| bedtools_makewindows | 0.076 | 0.000 | 0.076 | |
| bedtools_map | 0.144 | 0.000 | 0.147 | |
| bedtools_merge | 0.160 | 0.000 | 0.161 | |
| bedtools_multiinter | 0.064 | 0.000 | 0.064 | |
| bedtools_nuc | 0.044 | 0.000 | 0.044 | |
| bedtools_shift | 0.052 | 0.000 | 0.054 | |
| bedtools_slop | 0.052 | 0.000 | 0.052 | |
| bedtools_subtract | 0.748 | 0.000 | 0.750 | |
| bedtools_unionbedg | 0.040 | 0.004 | 0.044 | |
| distmode | 0.004 | 0.000 | 0.002 | |