Jianhong Ou
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/InPAS |
| Branch: RELEASE_3_8 |
| Last Commit: cad7f1f |
| Last Changed Date: 2019-04-09 11:10:07 -0400 (Tue, 09 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:27 -0400 (Tue, 16 Apr 2019).
| Package 776/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| InPAS 1.14.2 Jianhong Ou
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: InPAS |
| Version: 1.14.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InPAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InPAS_1.14.2.tar.gz |
| StartedAt: 2019-04-16 00:42:19 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:48:29 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 369.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: InPAS.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:InPAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InPAS_1.14.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/InPAS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InPAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘InPAS’ version ‘1.14.2’
* 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 ‘InPAS’ 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 ... OK
* 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 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
getUTR3eSet 10.441 0.062 10.580
testUsage 9.953 0.050 10.043
filterRes 9.847 0.105 9.994
* 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: OK
InPAS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL InPAS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘InPAS’ ... ** 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 * DONE (InPAS)
InPAS.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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("BSgenome.Mmusculus.UCSC.mm10") || stop("can not load BSgenome.")
Loading required package: BSgenome.Mmusculus.UCSC.mm10
Loading required package: BSgenome
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: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") || stop("can not load BSgenome.")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("TxDb.Mmusculus.UCSC.mm10.knownGene") || stop("can not load TxDb")
Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
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")'.
[1] TRUE
> require("rtracklayer") || stop("can not load rtracklayer.")
[1] TRUE
> require("limma") || stop("can not load limma")
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
[1] TRUE
> BiocGenerics:::testPackage("InPAS")
seqlevelsStyle of genome is different from bedgraph file.
RUNIT TEST PROTOCOL -- Tue Apr 16 00:48:23 2019
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
InPAS RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
30.452 1.124 31.701
InPAS.Rcheck/InPAS-Ex.timings
| name | user | system | elapsed | |
| CPsites | 0.002 | 0.001 | 0.002 | |
| coverageFromBedGraph | 0.001 | 0.000 | 0.001 | |
| coverageRate | 0.002 | 0.000 | 0.002 | |
| filterRes | 9.847 | 0.105 | 9.994 | |
| fisher.exact.test | 0.058 | 0.006 | 0.063 | |
| getUTR3eSet | 10.441 | 0.062 | 10.580 | |
| inPAS | 0.003 | 0.000 | 0.004 | |
| limmaAnalyze | 0.042 | 0.002 | 0.044 | |
| prepare4GSEA | 0.158 | 0.002 | 0.161 | |
| singleGroupAnalyze | 0.017 | 0.002 | 0.019 | |
| singleSampleAnalyze | 0.005 | 0.001 | 0.006 | |
| testUsage | 9.953 | 0.050 | 10.043 | |
| usage4plot | 1.509 | 0.238 | 1.749 | |
| utr3.danRer10 | 0.329 | 0.013 | 0.342 | |
| utr3.hg19 | 0.498 | 0.014 | 0.512 | |
| utr3.mm10 | 0.496 | 0.015 | 0.511 | |
| utr3Annotation | 0.001 | 0.000 | 0.000 | |
| utr3UsageEstimation | 0.002 | 0.000 | 0.001 | |