Solaiappan Manimaran
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/PathoStat |
| Branch: RELEASE_3_8 |
| Last Commit: e2b4a5c |
| Last Changed Date: 2018-12-01 20:44:43 -0400 (Sat, 01 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:23 -0400 (Tue, 16 Apr 2019).
| Package 1123/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PathoStat 1.8.4 Solaiappan Manimaran
| 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: PathoStat |
| Version: 1.8.4 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PathoStat_1.8.4.tar.gz |
| StartedAt: 2019-04-16 01:58:38 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:03:31 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 293.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PathoStat.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PathoStat_1.8.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/PathoStat.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.4’
* 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 ‘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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘ComplexHeatmap’ ‘RColorBrewer’
All declared Imports should be used.
* 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
Bootstrap_LOOCV_LR_AUC 33.396 0.068 33.499
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.8-bioc/meat/PathoStat.Rcheck/00check.log’
for details.
PathoStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL PathoStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘PathoStat’ ... ** 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 (PathoStat)
PathoStat.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
11.440 0.352 11.813
PathoStat.Rcheck/PathoStat-Ex.timings
| name | user | system | elapsed | |
| Bootstrap_LOOCV_LR_AUC | 33.396 | 0.068 | 33.499 | |
| Chisq_Test_Pam | 0.008 | 0.000 | 0.007 | |
| Fisher_Test_Pam | 0.008 | 0.000 | 0.007 | |
| GET_PAM | 0.004 | 0.000 | 0.004 | |
| LOOAUC_simple_multiple_noplot_one_df | 3.600 | 0.000 | 3.604 | |
| LOOAUC_simple_multiple_one_df | 3.664 | 0.000 | 3.674 | |
| PathoStat-class | 0.052 | 0.000 | 0.052 | |
| TranslateIdToTaxLevel | 0.000 | 0.000 | 0.001 | |
| Wilcox_Test_df | 0.012 | 0.000 | 0.010 | |
| findRAfromCount | 0.180 | 0.000 | 0.179 | |
| findTaxonMat | 0.356 | 0.004 | 1.392 | |
| findTaxonomy | 0.272 | 0.012 | 1.042 | |
| findTaxonomy300 | 0.332 | 0.000 | 1.028 | |
| getShinyInput | 0.000 | 0.000 | 0.001 | |
| getShinyInputCombat | 0.000 | 0.000 | 0.001 | |
| getShinyInputOrig | 0.000 | 0.000 | 0.001 | |
| getSignatureFromMultipleGlmnet | 1.532 | 0.008 | 1.547 | |
| grepTid | 0.000 | 0.000 | 0.001 | |
| loadPathoscopeReports | 0.000 | 0.000 | 0.001 | |
| loadPstat | 0.000 | 0.000 | 0.002 | |
| log2CPM | 0.004 | 0.000 | 0.001 | |
| percent | 0 | 0 | 0 | |
| phyloseq_to_edgeR | 0.096 | 0.000 | 0.096 | |
| plotPCAPlotly | 0.292 | 0.008 | 0.299 | |
| plotPCoAPlotly | 0.212 | 0.008 | 0.220 | |
| readPathoscopeData | 0.04 | 0.00 | 0.04 | |
| runPathoStat | 0.068 | 0.000 | 0.069 | |
| savePstat | 0.000 | 0.004 | 0.004 | |
| setShinyInput | 0 | 0 | 0 | |
| setShinyInputCombat | 0 | 0 | 0 | |
| setShinyInputOrig | 0.000 | 0.000 | 0.001 | |
| summarizeTable | 0.000 | 0.000 | 0.002 | |