Multiple platform build/check report for BioC 3.10 - CHECK report for PharmacoGx on tokay1

Package: PharmacoGx

Version: 1.17.1

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PharmacoGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings PharmacoGx_1.17.1.tar.gz

StartedAt: 2020-04-15 05:28:49 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:36:37 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 468.2 seconds

RetCode: 0

Status: OK

CheckDir: PharmacoGx.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PharmacoGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings PharmacoGx_1.17.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/PharmacoGx.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/PharmacoGx.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/PharmacoGx_1.17.1.tar.gz && rm -rf PharmacoGx.buildbin-libdir && mkdir PharmacoGx.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PharmacoGx.buildbin-libdir PharmacoGx_1.17.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL PharmacoGx_1.17.1.zip && rm PharmacoGx_1.17.1.tar.gz PharmacoGx_1.17.1.zip
###
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install for i386

* installing *source* package 'PharmacoGx' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PharmacoGx'
    finding HTML links ... done
    CCLEsmall                               html  
    CMAPsmall                               html  
    GDSCsmall                               html  
    HDAC_genes                              html  
    PharmacoSet-class                       html  
    PharmacoSet                             html  
    amcc                                    html  
    availablePSets                          html  
    cellInfo-set                            html  
    cellInfo                                html  
    cellNames-set                           html  
    cellNames                               html  
    checkPSetStructure                      html  
    computeABC                              html  
    computeAUC                              html  
    computeAmax                             html  
    computeICn                              html  
    computeSlope                            html  
    connectivityScore                       html  
    cosinePerm                              html  
    dateCreated                             html  
    dim-PharmacoSet-method                  html  
    downloadPSet                            html  
    downloadPertSig                         html  
    drugDoseResponseCurve                   html  
    drugInfo-set                            html  
    drugInfo                                html  
    drugNames-set                           html  
    drugNames                               html  
    drugPerturbationSig                     html  
    drugSensitivitySig                      html  
    fNames                                  html  
    featureInfo-set                         html  
    featureInfo                             html  
    filterNoisyCurves                       html  
    gwc                                     html  
    intersectList                           html  
    intersectPSet                           html  
    logLogisticRegression                   html  
    mDataNames                              html  
    mcc                                     html  
    molecularProfiles-set                   html  
    molecularProfiles                       html  
    pSetName                                html  
    pertNumber-set                          html  
    pertNumber                              html  
    phenoInfo-set                           html  
    phenoInfo                               html  
    sensNumber-set                          html  
    sensNumber                              html  
    sensitivityInfo-set                     html  
    sensitivityInfo                         html  
    sensitivityMeasures                     html  
    sensitivityProfiles-set                 html  
    sensitivityProfiles                     html  
    show-PharmacoSet-method                 html  
    show-PharmacoSig-method                 html  
    showSigAnnot                            html  
    sub-PharmacoSet-ANY-ANY-ANY-method      html  
    subsetTo                                html  
    summarizeMolecularProfiles              html  
    summarizeSensitivityProfiles            html  
    symSetDiffList                          html  
    unionList                               html  
** 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

install for x64

* installing *source* package 'PharmacoGx' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PharmacoGx' as PharmacoGx_1.17.1.zip
* DONE (PharmacoGx)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'PharmacoGx' successfully unpacked and MD5 sums checked


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
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 

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

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== testthat results  ===========================================================
[ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  45.70    1.12   98.17


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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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  |======================================================================| 100%

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[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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 

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

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  |======================================================================| 100%
== testthat results  ===========================================================
[ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  53.04    1.06  116.75

name	user	system	elapsed
PharmacoSet	0.02	0.00	0.01
amcc	1.42	0.04	1.47
availablePSets	0	0	0
cellInfo-set	1.41	0.03	1.43
cellInfo	1.36	0.04	1.40
cellNames-set	0.86	0.00	0.85
cellNames	0.91	0.01	0.93
checkPSetStructure	1.2	0.0	1.2
computeABC	1.30	0.08	1.37
computeAUC	0.55	0.01	0.56
computeAmax	0.48	0.04	0.52
computeICn	1.50	0.03	1.53
computeSlope	0	0	0
connectivityScore	0.05	0.00	0.05
cosinePerm	0.03	0.00	0.03
dateCreated	0.80	0.02	0.82
downloadPSet	0	0	0
downloadPertSig	0	0	0
drugDoseResponseCurve	0	0	0
drugInfo-set	0.9	0.0	0.9
drugInfo	0.83	0.00	0.83
drugNames-set	0.81	0.01	0.83
drugNames	1.05	0.00	1.05
drugPerturbationSig	3.81	0.05	3.85
drugSensitivitySig	0.97	0.02	0.98
fNames	0.83	0.00	0.83
featureInfo-set	0.84	0.00	0.85
featureInfo	0.81	0.01	0.82
filterNoisyCurves	0.82	0.03	0.85
gwc	1.25	0.02	1.26
intersectList	0	0	0
intersectPSet	1.45	0.03	1.49
logLogisticRegression	0.48	0.02	0.50
mDataNames	1.3	0.0	1.3
mcc	3.66	0.00	3.65
molecularProfiles-set	1.21	0.00	1.22
molecularProfiles	1.88	0.23	2.11
pSetName	1.05	0.00	1.05
pertNumber-set	1.15	0.00	1.15
pertNumber	0.94	0.00	0.94
phenoInfo-set	0.83	0.00	0.83
phenoInfo	1.20	0.06	1.26
sensNumber-set	0.92	0.00	0.92
sensNumber	1.17	0.08	1.25
sensitivityInfo-set	0.88	0.02	0.89
sensitivityInfo	1.26	0.20	1.47
sensitivityMeasures	0.85	0.00	0.84
sensitivityProfiles-set	0.82	0.02	0.85
sensitivityProfiles	1.35	0.06	1.40
show-PharmacoSet-method	0.87	0.00	0.88
show-PharmacoSig-method	0.89	0.00	0.89
showSigAnnot	0.97	0.00	0.97
subsetTo	0.89	0.00	0.90
summarizeMolecularProfiles	0.09	0.00	0.09
summarizeSensitivityProfiles	0.03	0.00	0.03
symSetDiffList	0	0	0
unionList	0	0	0

name	user	system	elapsed
PharmacoSet	0	0	0
amcc	2.14	0.01	2.16
availablePSets	0	0	0
cellInfo-set	1.22	0.05	1.27
cellInfo	0.82	0.03	0.86
cellNames-set	0.80	0.00	0.79
cellNames	1.14	0.02	1.16
checkPSetStructure	1.24	0.00	1.23
computeABC	0.96	0.00	0.97
computeAUC	0.80	0.01	0.81
computeAmax	0.63	0.04	0.66
computeICn	1.18	0.04	1.24
computeSlope	0	0	0
connectivityScore	0.05	0.00	0.04
cosinePerm	0.03	0.00	0.03
dateCreated	0.83	0.03	0.86
downloadPSet	0	0	0
downloadPertSig	0	0	0
drugDoseResponseCurve	0	0	0
drugInfo-set	0.67	0.00	0.67
drugInfo	0.70	0.02	0.72
drugNames-set	1.14	0.00	1.14
drugNames	0.64	0.01	0.66
drugPerturbationSig	2.30	0.02	2.31
drugSensitivitySig	1.16	0.00	1.16
fNames	0.69	0.01	0.70
featureInfo-set	0.65	0.03	0.69
featureInfo	0.72	0.02	0.73
filterNoisyCurves	0.82	0.01	0.83
gwc	0.70	0.02	0.72
intersectList	0	0	0
intersectPSet	0.83	0.02	0.84
logLogisticRegression	0.50	0.07	0.58
mDataNames	0.68	0.02	0.70
mcc	2.32	0.03	2.35
molecularProfiles-set	0.67	0.02	0.68
molecularProfiles	1.72	0.17	1.89
pSetName	1.29	0.01	1.32
pertNumber-set	0.77	0.00	0.76
pertNumber	0.73	0.02	0.75
phenoInfo-set	0.70	0.03	0.73
phenoInfo	1.57	0.20	1.77
sensNumber-set	0.67	0.03	0.70
sensNumber	0.75	0.05	0.79
sensitivityInfo-set	1.29	0.01	1.32
sensitivityInfo	1.58	0.27	1.84
sensitivityMeasures	1.28	0.00	1.28
sensitivityProfiles-set	1.13	0.00	1.13
sensitivityProfiles	1.69	0.23	1.92
show-PharmacoSet-method	1.79	0.00	1.80
show-PharmacoSig-method	1.66	0.03	1.69
showSigAnnot	1.62	0.00	1.62
subsetTo	1.39	0.02	1.41
summarizeMolecularProfiles	0.16	0.00	0.16
summarizeSensitivityProfiles	0.06	0.00	0.06
symSetDiffList	0	0	0
unionList	0	0	0

CHECK report for PharmacoGx on tokay1

Summary

Command output

Installation output

Tests output

Example timings