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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-03-18 11:49:58 -0400 (Mon, 18 Mar 2019).
| Package 1165/1676 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| PharmacoGx 1.13.0 Benjamin Haibe-Kains
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | |||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | ERROR | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ TIMEOUT ] |
| 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 |
##############################################################################
##############################################################################
###
### 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’
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)
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
|
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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
[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
PharmacoGx.Rcheck/PharmacoGx-Ex.timings
| name | user | system | elapsed | |
| LogLogisticRegression | 4.184 | 4.674 | 8.745 | |
| PharmacoSet | 0.003 | 0.001 | 0.003 | |
| amcc | 4.043 | 3.067 | 7.031 | |
| availablePSets | 0.001 | 0.000 | 0.000 | |
| cellInfo-set | 1.038 | 0.027 | 1.065 | |
| cellInfo | 1.815 | 0.314 | 2.127 | |
| cellNames-set | 1.150 | 0.040 | 1.191 | |
| cellNames | 1.204 | 0.024 | 1.228 | |
| checkPSetStructure | 1.051 | 0.014 | 1.065 | |
| computeABC | 6.050 | 7.068 | 12.912 | |
| computeAUC | 4.000 | 4.703 | 8.586 | |
| computeAmax | 4.053 | 4.765 | 8.690 | |
| computeICn | 7.993 | 9.453 | 17.180 | |
| computeSlope | 0.001 | 0.001 | 0.001 | |
| connectivityScore | 0.103 | 0.016 | 0.119 | |
| cosinePerm | 0.097 | 0.023 | 0.119 | |
| dateCreated | 1.136 | 0.007 | 1.143 | |
| downloadPSet | 0.000 | 0.000 | 0.001 | |
| downloadPertSig | 0.000 | 0.000 | 0.001 | |
| drugDoseResponseCurve | 0.001 | 0.000 | 0.001 | |
| drugInfo-set | 1.212 | 0.010 | 1.222 | |
| drugInfo | 1.182 | 0.008 | 1.189 | |
| drugNames-set | 1.216 | 0.007 | 1.224 | |
| drugNames | 0.848 | 0.018 | 0.866 | |
| drugPerturbationSig | 5.011 | 1.231 | 6.205 | |
| drugSensitivitySig | 2.262 | 0.594 | 2.838 | |
| fNames | 1.093 | 0.008 | 1.101 | |
| featureInfo-set | 1.027 | 0.011 | 1.038 | |
| featureInfo | 0.988 | 0.016 | 1.004 | |
| filterNoisyCurves | 2.101 | 0.720 | 2.802 | |
| gwc | 1.278 | 0.017 | 1.294 | |
| intersectList | 0.001 | 0.001 | 0.001 | |
| intersectPSet | 14.339 | 24.729 | 1892.277 | |
| mDataNames | 1.125 | 0.024 | 1.223 | |
| mcc | 7.765 | 5.242 | 13.107 | |
| molecularProfiles-set | 1.222 | 0.012 | 1.282 | |
| molecularProfiles | 2.441 | 0.941 | 3.383 | |
| pSetName | 1.037 | 0.016 | 1.052 | |
| pertNumber-set | 1.514 | 0.011 | 1.525 | |
| pertNumber | 1.159 | 0.006 | 1.166 | |
| phenoInfo-set | 1.264 | 0.025 | 1.293 | |
| phenoInfo | 2.723 | 0.417 | 3.138 | |
| sensNumber-set | 0.942 | 0.009 | 0.951 | |
| sensNumber | 1.207 | 0.295 | 1.499 | |
| sensitivityInfo-set | 1.282 | 0.009 | 1.291 | |
| sensitivityInfo | 3.454 | 1.378 | 4.963 | |
| sensitivityMeasures | 1.203 | 0.007 | 1.296 | |
| sensitivityProfiles-set | 1.525 | 0.016 | 1.821 | |
| sensitivityProfiles | 3.544 | 1.067 | 4.700 | |
| show-PharmacoSet-method | 1.206 | 0.026 | 1.333 | |
| show-PharmacoSig-method | 2.354 | 0.646 | 2.995 | |
| showSigAnnot | 2.349 | 0.576 | 3.055 | |
| subsetTo | 1.266 | 0.030 | 1.295 | |
| summarizeMolecularProfiles | 0.160 | 0.031 | 0.190 | |
| summarizeSensitivityProfiles | 0.062 | 0.006 | 0.069 | |
| symSetDiffList | 0.001 | 0.000 | 0.001 | |
| unionList | 0.001 | 0.000 | 0.001 | |