Kasper Daniel Hansen
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/bsseq |
| Branch: RELEASE_3_7 |
| Last Commit: 8494740 |
| Last Changed Date: 2018-06-12 23:43:44 -0400 (Tue, 12 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:50:37 -0400 (Wed, 17 Oct 2018).
| Package 170/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bsseq 1.16.1 Kasper Daniel Hansen
| 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: bsseq |
| Version: 1.16.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bsseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bsseq_1.16.1.tar.gz |
| StartedAt: 2018-10-16 20:12:28 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:17:35 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 306.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: bsseq.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bsseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bsseq_1.16.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/bsseq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘1.16.1’
* package encoding: UTF-8
* 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 ‘bsseq’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.6Mb
sub-directories of 1Mb or more:
data 7.7Mb
* 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
Unexported objects imported by ':::' calls:
‘DelayedArray:::RealizationSink’
‘DelayedArray:::get_max_block_length’
‘DelayedArray:::get_spacings_for_linear_capped_length_blocks’
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 ... WARNING
Undocumented S4 methods:
generic 'dimnames' and siglist 'arrayRealizationSink'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
getMeth 13.734 2.715 16.548
getCoverage 12.163 0.829 13.096
BSmooth.tstat 7.439 1.227 8.742
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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
‘/Users/biocbuild/bbs-3.7-bioc/meat/bsseq.Rcheck/00check.log’
for details.
bsseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bsseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘bsseq’ ... ** R ** data *** moving datasets to lazyload DB ** 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 (bsseq)
bsseq.Rcheck/tests/runTests.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-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("bsseq") || stop("unable to load bsseq")
Loading required package: bsseq
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: GenomicRanges
Loading required package: stats4
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
[1] TRUE
> BiocGenerics:::testPackage("bsseq")
Loading required package: rhdf5
RUNIT TEST PROTOCOL -- Tue Oct 16 20:17:29 2018
***********************************************
Number of test functions: 17
Number of errors: 0
Number of failures: 0
1 Test Suite :
bsseq 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
54.895 1.577 56.913
bsseq.Rcheck/bsseq-Ex.timings
| name | user | system | elapsed | |
| BS.chr22 | 2.727 | 0.265 | 3.004 | |
| BSmooth | 0.002 | 0.000 | 0.002 | |
| BSmooth.fstat | 0.001 | 0.000 | 0.001 | |
| BSmooth.tstat | 7.439 | 1.227 | 8.742 | |
| BSseq-class | 1.444 | 0.055 | 1.510 | |
| BSseq | 1.148 | 0.081 | 1.241 | |
| computeStat | 0.002 | 0.001 | 0.001 | |
| data.frame2GRanges | 0.025 | 0.000 | 0.025 | |
| dmrFinder | 1.888 | 0.350 | 2.247 | |
| fisherTests | 0.898 | 0.037 | 0.941 | |
| getCoverage | 12.163 | 0.829 | 13.096 | |
| getMeth | 13.734 | 2.715 | 16.548 | |
| getStats | 0.484 | 0.156 | 0.644 | |
| goodnessOfFit | 3.379 | 0.735 | 4.156 | |
| hasGRanges-class | 0.004 | 0.001 | 0.004 | |
| read.bismark | 0.715 | 0.038 | 0.755 | |
| read.umtab | 0.002 | 0.000 | 0.002 | |
| smoothSds | 0.001 | 0.001 | 0.002 | |