Surajit Bhattacharya
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/nanotatoR |
| Branch: RELEASE_3_9 |
| Last Commit: 7d7934f |
| Last Changed Date: 2019-05-02 11:54:15 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:05:00 -0400 (Wed, 16 Oct 2019).
| Package 1084/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| nanotatoR 1.0.0 Surajit Bhattacharya
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: nanotatoR |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nanotatoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nanotatoR_1.0.0.tar.gz |
| StartedAt: 2019-10-16 05:01:14 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:07:05 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 350.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nanotatoR.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:nanotatoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nanotatoR_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/nanotatoR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nanotatoR/DESCRIPTION’ ... OK
* this is package ‘nanotatoR’ version ‘1.0.0’
* 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 ‘nanotatoR’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clinvar_gene 4.645 0.394 6.610
gene_list_generation 3.764 0.207 7.639
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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
nanotatoR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL nanotatoR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘nanotatoR’ ... ** 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 (nanotatoR)
nanotatoR.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> library(testthat)
> library(nanotatoR)
>
> test_check("nanotatoR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
15.021 1.290 16.887
nanotatoR.Rcheck/nanotatoR-Ex.timings
| name | user | system | elapsed | |
| DGV_extraction | 0.000 | 0.000 | 0.001 | |
| Decipher_extraction | 0.952 | 0.082 | 1.036 | |
| buildrunBNBedFiles | 0.231 | 0.031 | 0.265 | |
| clinvar_gene | 4.645 | 0.394 | 6.610 | |
| cohortFrequency | 0.889 | 0.029 | 0.918 | |
| compSmapbed | 0.920 | 0.076 | 0.997 | |
| gene_extraction | 0.325 | 0.020 | 0.846 | |
| gene_list_generation | 3.764 | 0.207 | 7.639 | |
| gtr_gene | 0.279 | 0.011 | 0.712 | |
| internalFrequency | 1.588 | 0.110 | 1.703 | |
| makeMergedSVData | 0.322 | 0.016 | 0.342 | |
| makeMergedSmapData | 0.002 | 0.000 | 0.003 | |
| nanotatoR | 0.001 | 0.000 | 0.002 | |
| nonOverlapGenes | 0.720 | 0.010 | 0.731 | |
| omim_gene | 0.377 | 0.008 | 1.219 | |
| overlapGenes | 0.929 | 0.026 | 0.956 | |
| readBNBedFiles | 0.008 | 0.000 | 0.009 | |
| readSMap | 0.117 | 0.049 | 0.166 | |
| run_bionano_filter | 0.000 | 0.000 | 0.001 | |