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CHECK report for PharmacoGx on celaya2

This page was generated on 2020-01-16 13:45:57 -0500 (Thu, 16 Jan 2020).

Package 1252/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PharmacoGx 1.17.0
Benjamin Haibe-Kains
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/PharmacoGx
Branch: master
Last Commit: 9e7c488
Last Changed Date: 2019-10-29 13:42:04 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PharmacoGx
Version: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2020-01-16 07:25:13 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 07:50:22 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 1509.7 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PharmacoGx.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.17.0’
* 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 (user + system) or elapsed time > 5s
                       user system elapsed
computeICn            8.407  9.936  17.833
computeABC            6.305  7.600  13.686
mcc                   7.681  5.550  13.010
LogLogisticRegression 4.280  5.150   9.322
computeAmax           4.199  5.079   9.022
computeAUC            4.198  5.078   9.142
amcc                  4.249  3.166   7.228
drugPerturbationSig   4.798  0.949   5.717
* 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-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "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

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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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  |======================================================================| 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: 132 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 0 ]
> 
> proc.time()
    user   system  elapsed 
 213.511  199.576 1128.919

Example timings

PharmacoGx.Rcheck/PharmacoGx-Ex.timings

nameusersystemelapsed
LogLogisticRegression4.2805.1509.322
PharmacoSet0.0040.0010.004
amcc4.2493.1667.228
availablePSets0.0000.0000.001
cellInfo-set1.2460.0291.274
cellInfo1.8790.3142.261
cellNames-set1.3630.0321.394
cellNames1.6180.0281.653
checkPSetStructure0.9820.0251.007
computeABC 6.305 7.60013.686
computeAUC4.1985.0789.142
computeAmax4.1995.0799.022
computeICn 8.407 9.93617.833
computeSlope0.0010.0010.001
connectivityScore0.1140.0150.128
cosinePerm0.1340.0240.158
dateCreated0.9760.0070.982
downloadPSet0.0010.0000.001
downloadPertSig0.0000.0000.001
drugDoseResponseCurve0.0010.0000.001
drugInfo-set1.1390.0101.149
drugInfo1.5670.0161.584
drugNames-set1.1440.0121.155
drugNames1.2420.0321.273
drugPerturbationSig4.7980.9495.717
drugSensitivitySig2.5000.6273.171
fNames1.1090.0091.117
featureInfo-set1.1720.0111.183
featureInfo1.1120.0121.124
filterNoisyCurves1.9880.7272.695
gwc0.9230.0130.936
intersectList0.0010.0000.001
intersectPSet1.3980.0651.461
mDataNames1.2780.0091.287
mcc 7.681 5.55013.010
molecularProfiles-set1.0000.0081.008
molecularProfiles2.4010.9853.388
pSetName1.0240.0101.034
pertNumber-set0.9000.0080.908
pertNumber1.0700.0141.085
phenoInfo-set1.0980.0111.109
phenoInfo2.7030.4783.180
sensNumber-set1.1500.0071.157
sensNumber1.4150.3031.717
sensitivityInfo-set1.0740.0071.081
sensitivityInfo3.1691.3594.519
sensitivityMeasures1.1240.0101.134
sensitivityProfiles-set0.9670.0070.974
sensitivityProfiles3.3700.9954.360
show-PharmacoSet-method1.5030.0131.515
show-PharmacoSig-method2.5810.7213.269
showSigAnnot2.3760.6242.970
subsetTo1.0800.0341.112
summarizeMolecularProfiles0.1740.0320.206
summarizeSensitivityProfiles0.0680.0080.076
symSetDiffList0.0010.0000.001
unionList0.0000.0000.001