Solaiappan Manimaran
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/PathoStat |
| Branch: RELEASE_3_6 |
| Last Commit: 3911148 |
| Last Changed Date: 2017-12-06 23:55:55 -0400 (Wed, 06 Dec 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:15:32 -0400 (Thu, 12 Apr 2018).
| Package 1005/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PathoStat 1.4.1 Solaiappan Manimaran
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: PathoStat |
| Version: 1.4.1 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PathoStat_1.4.1.tar.gz |
| StartedAt: 2018-04-12 01:40:53 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:45:18 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 265.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PathoStat.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PathoStat_1.4.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/PathoStat.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PathoStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PathoStat’ version ‘1.4.1’
* 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 ‘PathoStat’ 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
createPathoStat 1.988 0.04 18.911
* 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
PathoStat.Rcheck/00install.out
* installing *source* package ‘PathoStat’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (PathoStat)
PathoStat.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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.
> library(testthat)
> library(PathoStat)
>
> test_check("PathoStat")
inline R code fragments
label: unnamed-chunk-1 (with options)
List of 1
$ echo: logi FALSE
inline R code fragments
label: unnamed-chunk-2 (with options)
List of 5
$ eval : symbol eval_cell_1
$ echo : logi FALSE
$ message : logi FALSE
$ fig.width : num 12
$ fig.height: num 8
/usr/bin/pandoc +RTS -K512m -RTS pathostat_report.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output /home/biocbuild/bbs-3.6-bioc/meat/PathoStat.Rcheck/tests/testthat/PathoStat_report.html --email-obfuscation none --standalone --section-divs --table-of-contents --toc-depth 2 --template PathoStat.html --highlight-style pygments --css /home/biocbuild/bbs-3.6-bioc/R/library/rmarkdown/rmarkdown/templates/html_vignette/resources/vignette.css --mathjax
══ testthat results ═══════════════════════════════════════════════════════════
OK: 19 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
14.616 0.468 34.401
PathoStat.Rcheck/PathoStat-Ex.timings
| name | user | system | elapsed | |
| coreOTU | 0.040 | 0.000 | 0.039 | |
| coreOTUModule | 0.000 | 0.000 | 0.001 | |
| coreOTUModuleUI | 0.196 | 0.000 | 0.206 | |
| coreOTUNormalize | 0.088 | 0.000 | 0.089 | |
| coreOTUQuantile | 0.036 | 0.000 | 0.033 | |
| createPathoStat | 1.988 | 0.040 | 18.911 | |
| findRAfromCount | 0.140 | 0.000 | 0.142 | |
| findTaxonLevel | 0.064 | 0.004 | 0.549 | |
| findTaxonMat | 0.276 | 0.000 | 2.784 | |
| findTaxonomy | 0.232 | 0.004 | 2.563 | |
| getShinyInput | 0 | 0 | 0 | |
| getShinyInputCombat | 0 | 0 | 0 | |
| getShinyInputOrig | 0.000 | 0.000 | 0.001 | |
| grepTid | 0.000 | 0.000 | 0.001 | |
| loadPathoscopeReports | 2.540 | 0.420 | 2.964 | |
| loadPstat | 0.000 | 0.000 | 0.001 | |
| log2CPM | 0.024 | 0.000 | 0.022 | |
| pathostat | 0.220 | 0.012 | 0.257 | |
| plotConfRegion | 0.772 | 0.008 | 0.779 | |
| readPathoscopeData | 0.028 | 0.004 | 0.030 | |
| runPathoStat | 2.468 | 0.104 | 2.591 | |
| savePstat | 0.008 | 0.000 | 0.008 | |
| setShinyInput | 0 | 0 | 0 | |
| setShinyInputCombat | 0.000 | 0.000 | 0.001 | |
| setShinyInputOrig | 0 | 0 | 0 | |
| sizeNormalize | 0.032 | 0.004 | 0.036 | |