Solaiappan Manimaran
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/PathoStat |
| Branch: RELEASE_3_9 |
| Last Commit: e1532ac |
| Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:09:47 -0400 (Wed, 16 Oct 2019).
| Package 1175/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PathoStat 1.10.0 Solaiappan Manimaran
| 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: PathoStat |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PathoStat_1.10.0.tar.gz |
| StartedAt: 2019-10-16 03:47:48 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:52:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 262.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PathoStat.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PathoStat_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PathoStat.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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 ‘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 13.512 0.104 13.616
* 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-3.9-bioc/meat/PathoStat.Rcheck/00check.log’
for details.
PathoStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PathoStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘PathoStat’ ... ** using staged installation ** 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 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 (PathoStat)
PathoStat.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-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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
9.518 0.352 9.876
PathoStat.Rcheck/PathoStat-Ex.timings
| name | user | system | elapsed | |
| Bootstrap_LOOCV_LR_AUC | 13.512 | 0.104 | 13.616 | |
| Chisq_Test_Pam | 0.000 | 0.003 | 0.003 | |
| Fisher_Test_Pam | 0.004 | 0.000 | 0.004 | |
| GET_PAM | 0.002 | 0.000 | 0.002 | |
| LOOAUC_simple_multiple_noplot_one_df | 2.851 | 0.000 | 2.852 | |
| LOOAUC_simple_multiple_one_df | 2.704 | 0.004 | 2.708 | |
| PathoStat-class | 0.044 | 0.000 | 0.044 | |
| TranslateIdToTaxLevel | 0.001 | 0.000 | 0.002 | |
| Wilcox_Test_df | 0.009 | 0.000 | 0.009 | |
| findRAfromCount | 0.698 | 0.000 | 0.699 | |
| findTaxonMat | 0.100 | 0.000 | 0.197 | |
| findTaxonomy | 0.077 | 0.000 | 0.076 | |
| findTaxonomy300 | 0.079 | 0.000 | 0.079 | |
| getShinyInput | 0 | 0 | 0 | |
| getShinyInputCombat | 0 | 0 | 0 | |
| getShinyInputOrig | 0 | 0 | 0 | |
| getSignatureFromMultipleGlmnet | 0.943 | 0.000 | 0.943 | |
| grepTid | 0.001 | 0.000 | 0.000 | |
| loadPathoscopeReports | 0.001 | 0.000 | 0.001 | |
| loadPstat | 0.002 | 0.000 | 0.002 | |
| log2CPM | 0.001 | 0.000 | 0.001 | |
| percent | 0 | 0 | 0 | |
| phyloseq_to_edgeR | 0.048 | 0.000 | 0.048 | |
| plotPCAPlotly | 0.139 | 0.004 | 0.143 | |
| plotPCoAPlotly | 0.136 | 0.004 | 0.140 | |
| readPathoscopeData | 0.037 | 0.000 | 0.037 | |
| runPathoStat | 0.062 | 0.000 | 0.062 | |
| savePstat | 0.003 | 0.000 | 0.003 | |
| setShinyInput | 0 | 0 | 0 | |
| setShinyInputCombat | 0 | 0 | 0 | |
| setShinyInputOrig | 0 | 0 | 0 | |
| summarizeTable | 0.002 | 0.000 | 0.002 | |