Jianhong Ou
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/NADfinder |
| Branch: RELEASE_3_7 |
| Last Commit: 00f816e |
| Last Changed Date: 2018-04-30 10:35:46 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:30:06 -0400 (Wed, 17 Oct 2018).
| Package 977/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NADfinder 1.4.0 Jianhong Ou
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: NADfinder |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NADfinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NADfinder_1.4.0.tar.gz |
| StartedAt: 2018-10-16 02:17:53 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 02:24:01 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 368.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NADfinder.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NADfinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NADfinder_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/NADfinder.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 ‘NADfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NADfinder’ version ‘1.4.0’
* 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 ‘NADfinder’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
data 1.3Mb
extdata 5.0Mb
* 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 ... NOTE
tileCount2: no visible global function definition for 'readParam'
Undefined global functions or variables:
readParam
* 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
callPeaks 27.572 0.116 27.708
plotSig 5.888 0.240 6.144
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/NADfinder.Rcheck/00check.log’
for details.
NADfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL NADfinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘NADfinder’ ... ** 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 (NADfinder)
NADfinder.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-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("NADfinder") || stop("unable to load Package:NADfinder")
Loading required package: NADfinder
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: IRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: GenomicRanges
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
> require("SummarizedExperiment") ||
+ stop("unable to load Package:SummarizedExperiment")
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
>
> #test_check("NADfinder")
>
> proc.time()
user system elapsed
14.908 0.416 16.002
NADfinder.Rcheck/NADfinder-Ex.timings
| name | user | system | elapsed | |
| backgroundCorrection | 0.004 | 0.004 | 0.008 | |
| butterFilter | 0.028 | 0.036 | 0.065 | |
| callPeaks | 27.572 | 0.116 | 27.708 | |
| cumulativePercentage | 3.456 | 0.028 | 3.487 | |
| exportSignals | 0.516 | 0.000 | 0.518 | |
| getCorrelations | 1.052 | 0.000 | 1.052 | |
| groupZscores | 0.004 | 0.004 | 0.008 | |
| log2se | 0.220 | 0.000 | 0.222 | |
| peakdet | 0.000 | 0.000 | 0.002 | |
| plotSig | 5.888 | 0.240 | 6.144 | |
| smoothRatiosByChromosome | 1.428 | 0.052 | 1.483 | |
| tileCount | 0.000 | 0.000 | 0.001 | |
| tileCount2 | 0.004 | 0.000 | 0.001 | |
| transformData | 0.004 | 0.000 | 0.007 | |
| trimPeaks | 0.964 | 0.000 | 0.965 | |
| zscoreOverBck | 0.000 | 0.000 | 0.001 | |