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CHECK report for PharmacoGx on merida1

This page was generated on 2020-04-15 12:44:07 -0400 (Wed, 15 Apr 2020).

Package 1254/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PharmacoGx 1.17.1
Benjamin Haibe-Kains
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/PharmacoGx
Branch: RELEASE_3_10
Last Commit: e34f5b8
Last Changed Date: 2020-01-29 13:32:34 -0400 (Wed, 29 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PharmacoGx
Version: 1.17.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PharmacoGx_1.17.1.tar.gz
StartedAt: 2020-04-15 04:34:29 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:49:10 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 881.3 seconds
RetCode: 0
Status:  OK 
CheckDir: PharmacoGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PharmacoGx_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/PharmacoGx.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PharmacoGx’ version ‘1.17.1’
* 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 ‘PharmacoGx’ 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 2251 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
Examples with CPU or elapsed time > 5s
                       user system elapsed
computeICn            5.328  4.991   9.774
mcc                   5.286  2.526   7.579
computeABC            3.642  3.208   6.600
logLogisticRegression 2.705  2.507   4.930
computeAUC            2.597  2.448   4.774
* 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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/PharmacoGx.Rcheck/00check.log’
for details.

Installation output

PharmacoGx.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘PharmacoGx’ ...
** 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 (PharmacoGx)

Tests output

PharmacoGx.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> Sys.unsetenv("R_TESTS")
> 
> library(testthat)
> library(PharmacoGx)
> 
> test_check("PharmacoGx")
[1] NA  3
[1]   1   2 Inf
[1] NA  3
[1]   1   2 Inf

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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

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[1] "Model did not converge"

0 1 
7 2 

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  |======================================================================| 100%
[1]  1  1 -1
[1] 0
[1] 0
             [,1] [,2] [,3]
lower_bounds    0    0    0
upper_bounds    1    1   -1

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══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
140.113  92.849 612.108

Example timings

PharmacoGx.Rcheck/PharmacoGx-Ex.timings

nameusersystemelapsed
PharmacoSet0.0020.0010.003
amcc3.1701.6834.687
availablePSets000
cellInfo-set1.0660.0151.089
cellInfo1.7670.1761.956
cellNames-set1.1890.0211.215
cellNames1.2650.0171.291
checkPSetStructure1.1050.0091.129
computeABC3.6423.2086.600
computeAUC2.5972.4484.774
computeAmax2.3662.1654.352
computeICn5.3284.9919.774
computeSlope0.0010.0000.001
connectivityScore0.0880.0080.094
cosinePerm0.0740.0080.080
dateCreated1.0430.0061.058
downloadPSet0.0000.0000.001
downloadPertSig0.0000.0000.001
drugDoseResponseCurve0.0010.0000.001
drugInfo-set1.0420.0081.058
drugInfo1.2470.0101.270
drugNames-set1.0010.0051.011
drugNames1.0860.0121.106
drugPerturbationSig3.6550.6054.223
drugSensitivitySig1.7090.2961.978
fNames1.0730.0071.091
featureInfo-set1.0510.0081.073
featureInfo1.1320.0091.150
filterNoisyCurves1.5010.3641.833
gwc1.0710.0081.083
intersectList0.0000.0010.000
intersectPSet1.3300.0321.367
logLogisticRegression2.7052.5074.930
mDataNames1.0520.0041.067
mcc5.2862.5267.579
molecularProfiles-set0.8510.0050.861
molecularProfiles2.2690.4582.728
pSetName0.8200.0130.834
pertNumber-set1.1330.0081.186
pertNumber1.1050.0051.125
phenoInfo-set1.0620.0161.098
phenoInfo2.7910.2983.149
sensNumber-set1.0590.0051.071
sensNumber1.2690.1541.498
sensitivityInfo-set1.1590.0081.178
sensitivityInfo3.0320.6383.787
sensitivityMeasures0.9680.0110.990
sensitivityProfiles-set1.0800.0051.094
sensitivityProfiles3.2610.5503.820
show-PharmacoSet-method0.9820.0050.989
show-PharmacoSig-method1.9590.3452.270
showSigAnnot1.9090.3132.195
subsetTo1.1330.0191.155
summarizeMolecularProfiles0.1410.0170.155
summarizeSensitivityProfiles0.0520.0040.055
symSetDiffList0.0010.0000.001
unionList0.0000.0000.001