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CHECK report for PharmacoGx on malbec1

This page was generated on 2020-04-15 12:11:45 -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: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PharmacoGx_1.17.1.tar.gz
StartedAt: 2020-04-15 04:06:40 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:14:45 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 484.9 seconds
RetCode: 0
Status:  OK 
CheckDir: PharmacoGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PharmacoGx_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/PharmacoGx.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/PharmacoGx.Rcheck/00check.log’
for details.

Installation output

PharmacoGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL PharmacoGx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-pc-linux-gnu (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 
8 1 
[1] "Model did not converge"

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

0 1 
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[1] "Model did not converge"

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

0 1 
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[1] "Model did not converge"

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

0 1 
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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

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

0 1 
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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"

0 1 
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[1] "Model did not converge"

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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

0 1 
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[1] "Model did not converge"

0 1 
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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"

0 1 
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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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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"

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 
 86.808  33.940 296.136

Example timings

PharmacoGx.Rcheck/PharmacoGx-Ex.timings

nameusersystemelapsed
PharmacoSet0.0000.0000.003
amcc1.6240.6282.196
availablePSets000
cellInfo-set1.0640.0081.079
cellInfo1.2240.0481.279
cellNames-set1.3320.0121.344
cellNames1.0800.0081.089
checkPSetStructure0.9240.0000.931
computeABC2.2081.4643.464
computeAUC1.2840.8642.077
computeAmax1.2920.8882.107
computeICn2.9721.7484.667
computeSlope0.0000.0000.001
connectivityScore0.0760.0000.076
cosinePerm0.0600.0000.061
dateCreated1.3480.0001.349
downloadPSet000
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drugDoseResponseCurve000
drugInfo-set0.7560.0000.756
drugInfo1.3000.0001.303
drugNames-set0.7560.0000.761
drugNames0.9080.0000.906
drugPerturbationSig3.1320.2723.431
drugSensitivitySig1.3760.1201.519
fNames1.3560.0041.361
featureInfo-set0.9680.0000.970
featureInfo0.9160.0080.922
filterNoisyCurves0.9760.1361.101
gwc0.7760.0000.781
intersectList000
intersectPSet0.8920.0000.890
logLogisticRegression1.4800.9002.265
mDataNames0.720.000.72
mcc3.4640.9484.339
molecularProfiles-set1.3680.0001.371
molecularProfiles1.5240.2121.741
pSetName0.980.000.98
pertNumber-set0.9960.0000.998
pertNumber0.9240.0000.927
phenoInfo-set1.2440.0001.245
phenoInfo1.9560.0802.032
sensNumber-set0.8840.0000.885
sensNumber1.2760.0321.308
sensitivityInfo-set0.7840.0000.786
sensitivityInfo1.5880.2401.838
sensitivityMeasures0.8920.0000.894
sensitivityProfiles-set0.9880.0401.027
sensitivityProfiles1.2400.1881.429
show-PharmacoSet-method0.7520.0000.751
show-PharmacoSig-method1.5520.1401.722
showSigAnnot1.5800.1481.738
subsetTo1.0080.0081.016
summarizeMolecularProfiles0.0800.0040.082
summarizeSensitivityProfiles0.0440.0000.044
symSetDiffList0.0000.0000.001
unionList000