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CHECK report for Xeva on merida1

This page was generated on 2021-05-06 12:37:21 -0400 (Thu, 06 May 2021).

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 1962/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Xeva 1.6.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/Xeva
Branch: RELEASE_3_12
Last Commit: 87d94c1
Last Changed Date: 2020-10-27 11:43:19 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Xeva
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Xeva.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Xeva_1.6.0.tar.gz
StartedAt: 2021-05-06 07:21:43 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:26:00 -0400 (Thu, 06 May 2021)
EllapsedTime: 256.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Xeva.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Xeva.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Xeva_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/Xeva.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.6.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/Xeva.Rcheck/00check.log’
for details.



Installation output

Xeva.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Xeva
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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
ABC0.0050.0010.006
AUC0.0260.0070.032
TGI0.0010.0000.001
addExperimentalDesign0.1200.0030.123
angle0.0110.0020.012
batchInfo0.1260.0050.131
createXevaSet0.1340.0310.166
dosePlot0.3740.0220.396
downloadXevaSet0.0160.0040.543
drugInform0.1110.0020.113
drugSensitivitySig0.9780.0821.053
getExperiment0.1760.0220.196
getMolecularProfiles0.1200.0030.123
lmm0.1040.0200.122
mRECIST0.0020.0010.004
modelInfo0.1190.0030.121
plotPDX1.2550.2371.481
plotmRECIST2.3790.4232.766
response0.1740.0160.189
selectModelIds0.2070.0310.236
sensitivity0.1170.0050.122
setResponse3.7270.6874.340
slope0.0100.0020.012
subsetXeva0.2230.0160.238
summarizeMolecularProfiles0.1530.0080.160
summarizeResponse0.2360.0090.245
waterfall0.9070.1000.998