Benjamin Haibe-Kains
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/PharmacoGx |
| Branch: RELEASE_3_11 |
| Last Commit: 528b270 |
| Last Changed Date: 2020-09-03 13:39:48 -0400 (Thu, 03 Sep 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:11 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE PharmacoGx PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1301/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PharmacoGx 2.0.9 Benjamin Haibe-Kains
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: PharmacoGx |
| Version: 2.0.9 |
| 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_2.0.9.tar.gz |
| StartedAt: 2020-10-17 03:53:03 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:04:37 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 694.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PharmacoGx.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_2.0.9.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PharmacoGx.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.0.9’
* 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
PharmacoSet-class 37.765 0.643 38.444
computeICn 4.925 4.800 9.119
computeABC 3.761 3.733 7.063
mcc 4.659 2.437 6.802
* 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.
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)
PharmacoGx.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
Loading required package: CoreGx
Attaching package: ‘PharmacoGx’
The following objects are masked from ‘package:CoreGx’:
amcc, connectivityScore, cosinePerm, gwc, mcc
>
> test_check("PharmacoGx")
[1] NA 3
[1] 1 2 Inf
[1] NA 3
[1] 1 2 Inf
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[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: 127 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
187.573 95.943 273.423
PharmacoGx.Rcheck/PharmacoGx-Ex.timings
| name | user | system | elapsed | |
| PharmacoSet-class | 37.765 | 0.643 | 38.444 | |
| PharmacoSet | 0.003 | 0.000 | 0.003 | |
| amcc | 3.231 | 1.405 | 4.485 | |
| availablePSets | 0 | 0 | 0 | |
| cellInfo-set-PharmacoSet-data.frame-method | 1.778 | 0.012 | 1.791 | |
| checkPsetStructure | 1.810 | 0.028 | 1.838 | |
| computeABC | 3.761 | 3.733 | 7.063 | |
| computeAUC | 2.346 | 2.297 | 4.476 | |
| computeAmax | 2.461 | 2.389 | 4.541 | |
| computeICn | 4.925 | 4.800 | 9.119 | |
| computeSlope | 0.010 | 0.001 | 0.011 | |
| connectivityScore | 0.096 | 0.009 | 0.104 | |
| cosinePerm | 0.105 | 0.013 | 0.116 | |
| downloadPSet | 0.001 | 0.001 | 0.001 | |
| downloadPertSig | 0.000 | 0.001 | 0.001 | |
| drugDoseResponseCurve | 0.001 | 0.001 | 0.002 | |
| drugInfo-set | 1.712 | 0.014 | 1.727 | |
| drugInfo | 1.772 | 0.017 | 1.790 | |
| drugNames-set | 1.781 | 0.014 | 1.796 | |
| drugNames | 1.650 | 0.013 | 1.667 | |
| drugPerturbationSig | 4.225 | 0.543 | 4.729 | |
| drugSensitivitySig | 2.576 | 0.360 | 2.895 | |
| fNames-set-PharmacoSet-character-character-method | 1.771 | 0.014 | 1.786 | |
| filterNoisyCurves | 1.551 | 0.377 | 1.890 | |
| gwc | 1.736 | 0.022 | 1.761 | |
| logLogisticRegression | 2.476 | 2.439 | 4.617 | |
| mDataNames-PharmacoSet-method | 1.793 | 0.013 | 1.808 | |
| mcc | 4.659 | 2.437 | 6.802 | |
| plot.PharmacoSig | 2.489 | 0.370 | 2.877 | |
| show-PharmacoSet-method | 1.839 | 0.014 | 1.855 | |
| show-PharmacoSig-method | 2.447 | 0.352 | 2.763 | |
| showSigAnnot | 2.474 | 0.374 | 2.839 | |
| subsetTo | 1.875 | 0.027 | 1.902 | |
| summarizeMolecularProfiles | 0.299 | 0.036 | 0.332 | |
| summarizeSensitivityProfiles | 0.097 | 0.009 | 0.106 | |