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CHECK report for ToxicoGx on malbec1

This page was generated on 2021-05-06 12:29:28 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ToxicoGx package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1880/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ToxicoGx 1.0.1  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ToxicoGx
Branch: RELEASE_3_12
Last Commit: e5d0924
Last Changed Date: 2020-11-16 15:06:43 -0400 (Mon, 16 Nov 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: ToxicoGx
Version: 1.0.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ToxicoGx.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ToxicoGx_1.0.1.tar.gz
StartedAt: 2021-05-06 06:44:38 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:48:32 -0400 (Thu, 06 May 2021)
EllapsedTime: 233.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ToxicoGx.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ToxicoGx.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ToxicoGx_1.0.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ToxicoGx.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ToxicoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ToxicoGx’ version ‘1.0.1’
* 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 ‘ToxicoGx’ 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 ... NOTE
computeLimmaDiffExpr,ToxicoSet: no visible binding for global variable
  ‘cell’
Undefined global functions or variables:
  cell
* 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 47 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/ToxicoGx.Rcheck/00check.log’
for details.



Installation output

ToxicoGx.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ToxicoGx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ToxicoGx’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (ToxicoGx)

Tests output


Example timings

ToxicoGx.Rcheck/ToxicoGx-Ex.timings

nameusersystemelapsed
ToxicoSet-class2.6760.1122.791
annotation-set0.0600.0000.062
annotation0.0640.0000.066
availableTSets0.0960.0041.201
checkTSetStructure0.1200.0000.121
computeAUC0.6640.0080.677
computeICn0.9040.0440.949
computeLimmaDiffExpr-ToxicoSet-method000
curation-set0.0560.0120.069
curation0.5960.0000.597
datasetType-set0.0560.0000.053
dim-ToxicoSet-method0.0560.0080.063
downloadTSet0.0000.0000.001
drugGeneResponseCurve000
drugInfo-set0.060.000.06
drugInfo0.0560.0000.053
drugNames-set0.0720.0080.082
drugNames0.0520.0000.052
drugPerturbationSig000
drugTimeResponseCurve0.140.000.14
geneDrugPerturbation2.5840.0802.672
logLogisticRegression0.7040.0080.720
mDataNames-ToxicoSet-method0.0000.0000.001
name-ToxicoSet-method000
sensitivityRaw-set0.0000.0000.002
sensitivityRaw0.1240.0160.137
show-ToxicoSet-method0.0040.0000.005
show-ToxicoSig-method0.2600.0560.319
showSigAnnot0.2480.0640.316
sub-ToxicoSet-ANY-ANY-ANY-method0.0440.0000.045
subsetTo0.040.000.04
summarizeMolecularProfiles0.8760.0240.901
summarizeSensitivityProfiles0.0680.0000.068
updateCellId0.0920.0000.093
updateDrugId0.0880.0000.086