Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:05:10 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for PathoStat on nebbiolo1


To the developers/maintainers of the PathoStat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PathoStat.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1415/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PathoStat 1.22.0  (landing page)
Solaiappan Manimaran
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/PathoStat
git_branch: RELEASE_3_15
git_last_commit: e6a7bac
git_last_commit_date: 2022-04-26 11:36:30 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: PathoStat
Version: 1.22.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings PathoStat_1.22.0.tar.gz
StartedAt: 2022-06-23 21:14:56 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:20:51 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 354.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PathoStat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings PathoStat_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/PathoStat.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.22.0’
* 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 (user + system) or elapsed time > 5s
                                user system elapsed
Bootstrap_LOOCV_LR_AUC         9.183  0.416   9.599
getSignatureFromMultipleGlmnet 7.788  0.076   7.865
* 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-3.15-bioc/meat/PathoStat.Rcheck/00check.log’
for details.



Installation output

PathoStat.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL PathoStat
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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)

Tests output

PathoStat.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 12.433   1.161  13.578 

Example timings

PathoStat.Rcheck/PathoStat-Ex.timings

nameusersystemelapsed
Bootstrap_LOOCV_LR_AUC9.1830.4169.599
Chisq_Test_Pam0.0040.0000.003
Fisher_Test_Pam0.0040.0000.005
GET_PAM0.0030.0000.002
LOOAUC_simple_multiple_noplot_one_df2.1240.0522.175
LOOAUC_simple_multiple_one_df1.9710.0121.983
PathoStat-class0.0390.0080.048
TranslateIdToTaxLevel0.0020.0000.003
Wilcox_Test_df0.0120.0040.017
findRAfromCount0.1470.0200.168
findTaxonMat0.0690.0000.073
findTaxonomy0.060.000.06
findTaxonomy3000.0590.0000.059
getShinyInput0.0010.0000.000
getShinyInputCombat0.0010.0000.000
getShinyInputOrig000
getSignatureFromMultipleGlmnet7.7880.0767.865
grepTid0.0000.0000.001
loadPathoscopeReports0.0000.0020.001
loadPstat0.0000.0020.001
log2CPM0.0010.0000.001
percent000
phyloseq_to_edgeR0.0480.0120.060
plotPCAPlotly0.1680.0280.196
plotPCoAPlotly0.1160.0110.127
readPathoscopeData0.0330.0000.033
runPathoStat0.0630.0040.068
savePstat0.0040.0000.003
setShinyInput0.0010.0000.000
setShinyInputCombat000
setShinyInputOrig000
summarizeTable0.0020.0000.002