Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

CHECK report for PharmacoGx on celaya2

This page was generated on 2019-03-18 11:49:58 -0400 (Mon, 18 Mar 2019).

Package 1165/1676HostnameOS / ArchINSTALLBUILDCHECK
PharmacoGx 1.13.0
Benjamin Haibe-Kains
Snapshot Date: 2019-03-17 17:01:51 -0400 (Sun, 17 Mar 2019)
URL: https://git.bioconductor.org/packages/PharmacoGx
Branch: master
Last Commit: 24cb9de
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ TIMEOUT ]

Summary

Package: PharmacoGx
Version: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2019-03-18 03:54:06 -0400 (Mon, 18 Mar 2019)
EndedAt: 2019-03-18 04:34:06 -0400 (Mon, 18 Mar 2019)
EllapsedTime: 2400.0 seconds
RetCode: None
Status:  TIMEOUT 
CheckDir: PharmacoGx.Rcheck
Warnings: NA

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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PharmacoGx.Rcheck’
* using R Under development (unstable) (2019-01-22 r76000)
* 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 ‘1.13.0’
* 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 ‘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
intersectPSet         14.339 24.729 1892.277
computeICn             7.993  9.453   17.180
computeABC             6.050  7.068   12.912
mcc                    7.765  5.242   13.107
LogLogisticRegression  4.184  4.674    8.745
computeAmax            4.053  4.765    8.690
computeAUC             4.000  4.703    8.586
amcc                   4.043  3.067    7.031
drugPerturbationSig    5.011  1.231    6.205
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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’ ...
** 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
* DONE (PharmacoGx)

Tests output

PharmacoGx.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-01-22 r76000) -- "Unsuffered Consequences"
Copyright (C) 2019 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

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
2 7 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
1 8 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
7 2 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
6 3 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
3 6 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
4 5 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
5 4 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 
[1] "Model did not converge"

0 1 
8 1 

Example timings

PharmacoGx.Rcheck/PharmacoGx-Ex.timings

nameusersystemelapsed
LogLogisticRegression4.1844.6748.745
PharmacoSet0.0030.0010.003
amcc4.0433.0677.031
availablePSets0.0010.0000.000
cellInfo-set1.0380.0271.065
cellInfo1.8150.3142.127
cellNames-set1.1500.0401.191
cellNames1.2040.0241.228
checkPSetStructure1.0510.0141.065
computeABC 6.050 7.06812.912
computeAUC4.0004.7038.586
computeAmax4.0534.7658.690
computeICn 7.993 9.45317.180
computeSlope0.0010.0010.001
connectivityScore0.1030.0160.119
cosinePerm0.0970.0230.119
dateCreated1.1360.0071.143
downloadPSet0.0000.0000.001
downloadPertSig0.0000.0000.001
drugDoseResponseCurve0.0010.0000.001
drugInfo-set1.2120.0101.222
drugInfo1.1820.0081.189
drugNames-set1.2160.0071.224
drugNames0.8480.0180.866
drugPerturbationSig5.0111.2316.205
drugSensitivitySig2.2620.5942.838
fNames1.0930.0081.101
featureInfo-set1.0270.0111.038
featureInfo0.9880.0161.004
filterNoisyCurves2.1010.7202.802
gwc1.2780.0171.294
intersectList0.0010.0010.001
intersectPSet 14.339 24.7291892.277
mDataNames1.1250.0241.223
mcc 7.765 5.24213.107
molecularProfiles-set1.2220.0121.282
molecularProfiles2.4410.9413.383
pSetName1.0370.0161.052
pertNumber-set1.5140.0111.525
pertNumber1.1590.0061.166
phenoInfo-set1.2640.0251.293
phenoInfo2.7230.4173.138
sensNumber-set0.9420.0090.951
sensNumber1.2070.2951.499
sensitivityInfo-set1.2820.0091.291
sensitivityInfo3.4541.3784.963
sensitivityMeasures1.2030.0071.296
sensitivityProfiles-set1.5250.0161.821
sensitivityProfiles3.5441.0674.700
show-PharmacoSet-method1.2060.0261.333
show-PharmacoSig-method2.3540.6462.995
showSigAnnot2.3490.5763.055
subsetTo1.2660.0301.295
summarizeMolecularProfiles0.1600.0310.190
summarizeSensitivityProfiles0.0620.0060.069
symSetDiffList0.0010.0000.001
unionList0.0010.0000.001