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CHECK report for Xeva on malbec2

This page was generated on 2020-10-17 11:56:01 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Xeva PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1894/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Xeva 1.4.0
Benjamin Haibe-Kains
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Xeva
Branch: RELEASE_3_11
Last Commit: 676ae9f
Last Changed Date: 2020-04-27 15:23:57 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Xeva
Version: 1.4.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Xeva.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Xeva_1.4.0.tar.gz
StartedAt: 2020-10-17 06:30:11 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:34:00 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 229.3 seconds
RetCode: 0
Status:  OK 
CheckDir: Xeva.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Xeva.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Xeva_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/Xeva.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Xeva/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Xeva’ version ‘1.4.0’
* 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 ‘Xeva’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 31 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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-3.11-bioc/meat/Xeva.Rcheck/00check.log’
for details.



Installation output

Xeva.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL Xeva
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘Xeva’ ...
** 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 (Xeva)

Tests output


Example timings

Xeva.Rcheck/Xeva-Ex.timings

nameusersystemelapsed
ABC0.0070.0000.007
AUC0.0380.0040.040
TGI0.0010.0000.001
addExperimentalDesign0.2230.0040.227
angle0.0140.0000.013
batchInfo0.2060.0000.205
createXevaSet0.1680.0120.193
dosePlot0.5820.0120.590
downloadXevaSet0.0860.0120.315
drugInform0.1930.0000.194
drugSensitivitySig1.1420.0491.184
getExperiment0.1520.0200.185
getMolecularProfiles0.1260.0040.130
lmm0.1460.0360.180
mRECIST0.0020.0000.002
modelInfo0.1160.0040.119
plotPDX1.3060.1931.473
plotmRECIST2.4670.2072.657
response0.2020.0080.207
selectModelIds0.2950.0290.316
sensitivity0.1850.0000.185
setResponse4.2780.5354.677
slope0.0080.0040.012
subsetXeva0.2230.0000.221
summarizeMolecularProfiles0.1700.0000.168
summarizeResponse0.2610.0080.267
waterfall0.9280.0370.947