Olivier Gevaert
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/AMARETTO |
| Branch: master |
| Last Commit: a59a1b0 |
| Last Changed Date: 2019-03-29 17:00:52 -0400 (Fri, 29 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:39:31 -0400 (Tue, 09 Apr 2019).
| Package 46/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AMARETTO 0.99.20 Olivier Gevaert
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: AMARETTO |
| Version: 0.99.20 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AMARETTO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AMARETTO_0.99.20.tar.gz |
| StartedAt: 2019-04-08 23:11:38 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:16:13 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 275.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AMARETTO.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:AMARETTO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AMARETTO_0.99.20.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AMARETTO.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AMARETTO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AMARETTO’ version ‘0.99.20’
* 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 ‘AMARETTO’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
extdata 3.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Apache License (== 2.0) + file LICENSE
'LinkingTo' field is unused: package has no 'src' directory
* 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 ... OK
* 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
AMARETTO_Download 13.788 1.047 19.503
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/AMARETTO.Rcheck/00check.log’
for details.
AMARETTO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AMARETTO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘AMARETTO’ ... ** R ** data *** moving datasets to lazyload DB ** 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 (AMARETTO)
AMARETTO.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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.
> library(testthat)
> library(AMARETTO)
Loading required package: impute
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: ComplexHeatmap
Loading required package: grid
========================================
ComplexHeatmap version 1.99.7
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
========================================
>
> test_check("AMARETTO")
Found 1 CNV driver genes.
Found 24 MethylMix driver genes.
Found a total of 24 unique drivers with your selected method.
Running AMARETTO on 80 genes and 45 samples.
Stopping if less then 0.8 genes reassigned.
Autoregulation is turned ON.
Elapsed time is 1.990000 seconds
Average nr of regulators per module: 7.600000
Elapsed time is 0.091000 seconds
Nr of reassignments is: 7
Elapsed time is 1.457000 seconds
Average nr of regulators per module: 7.800000
Elapsed time is 0.064000 seconds
Nr of reassignments is: 4
Elapsed time is 1.301000 seconds
Average nr of regulators per module: 7.400000
Elapsed time is 0.066000 seconds
Nr of reassignments is: 4
Elapsed time is 1.200000 seconds
Average nr of regulators per module: 7.800000
Elapsed time is 0.055000 seconds
Nr of reassignments is: 3
Elapsed time is 1.188000 seconds
Average nr of regulators per module: 7.400000
Elapsed time is 0.067000 seconds
Nr of reassignments is: 1
Elapsed time is 1.166000 seconds
Average nr of regulators per module: 7.800000
Elapsed time is 0.059000 seconds
Nr of reassignments is: 3
Elapsed time is 1.219000 seconds
Average nr of regulators per module: 6.800000
Elapsed time is 0.086000 seconds
Nr of reassignments is: 7
Elapsed time is 1.451000 seconds
Average nr of regulators per module: 8.000000
Elapsed time is 0.071000 seconds
Nr of reassignments is: 7
Elapsed time is 1.209000 seconds
Average nr of regulators per module: 8.400000
Elapsed time is 0.068000 seconds
Nr of reassignments is: 4
Elapsed time is 1.179000 seconds
Average nr of regulators per module: 8.200000
Elapsed time is 0.059000 seconds
Nr of reassignments is: 2
Elapsed time is 1.194000 seconds
Average nr of regulators per module: 8.400000
Elapsed time is 0.077000 seconds
Nr of reassignments is: 0
Elapsed time is 15.326000 seconds
══ testthat results ═══════════════════════════════════════════════════════════
OK: 43 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
25.278 0.808 26.310
AMARETTO.Rcheck/AMARETTO-Ex.timings
| name | user | system | elapsed | |
| AMARETTO_CreateModuleData | 1.860 | 0.042 | 1.914 | |
| AMARETTO_CreateRegulatorPrograms | 2.226 | 0.020 | 2.271 | |
| AMARETTO_Download | 13.788 | 1.047 | 19.503 | |
| AMARETTO_EvaluateTestSet | 2.330 | 0.015 | 2.362 | |
| AMARETTO_ExportResults | 1.903 | 0.034 | 1.948 | |
| AMARETTO_HTMLreport | 0.001 | 0.000 | 0.000 | |
| AMARETTO_Initialize | 0.693 | 0.007 | 0.702 | |
| AMARETTO_Preprocess | 0 | 0 | 0 | |
| AMARETTO_Run | 1.592 | 0.016 | 1.620 | |
| AMARETTO_VisualizeModule | 4.196 | 0.039 | 4.306 | |