Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for AMARETTO on merida1

This page was generated on 2021-05-06 12:34:17 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the AMARETTO package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 51/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AMARETTO 1.6.0  (landing page)
Olivier Gevaert
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/AMARETTO
Branch: RELEASE_3_12
Last Commit: 0deca3f
Last Changed Date: 2020-10-27 11:43:56 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: AMARETTO
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2021-05-05 23:08:51 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:14:12 -0400 (Wed, 05 May 2021)
EllapsedTime: 320.6 seconds
RetCode: 0
Status:   OK  
CheckDir: AMARETTO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/AMARETTO.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.6.0’
* 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 ‘AMARETTO’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    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
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘knitr’
A package should be listed in only one of these fields.
'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 ... NOTE
AMARETTO_HTMLreport: no visible binding for global variable ‘ModuleNr’
AMARETTO_HTMLreport: no visible binding for global variable ‘Weights’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘RegulatorIDs’
AMARETTO_HTMLreport: no visible binding for global variable ‘TargetIDs’
AMARETTO_HTMLreport: no visible binding for global variable ‘moduleNr’
AMARETTO_HTMLreport: no visible binding for global variable ‘Testset’
AMARETTO_HTMLreport: no visible binding for global variable ‘padj’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘n_Overlapping’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘NumberGenes’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘overlap_perc’
AMARETTO_HTMLreport: no visible binding for global variable ‘Geneset’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘Description’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘Geneset_length’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘Overlapping_genes’
AMARETTO_HTMLreport: no visible binding for global variable ‘p_value’
AMARETTO_HTMLreport: no visible binding for global variable ‘p.value’
AMARETTO_HTMLreport: no visible binding for global variable ‘q.value’
AMARETTO_HTMLreport: no visible binding for global variable ‘Genes’
AMARETTO_HTMLreport: no visible binding for global variable ‘value’
AMARETTO_HTMLreport: no visible binding for global variable ‘Type’
AMARETTO_HTMLreport: no visible binding for global variable ‘Color’
AMARETTO_HTMLreport: no visible binding for global variable ‘Modules’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘dt_gensesetsall’
GeneSetDescription: no visible binding for global variable
  ‘MsigdbMapping’
GeneSetDescription : <anonymous>: no visible binding for global
  variable ‘MsigdbMapping’
GmtFromModules: no visible binding for global variable ‘value’
GmtFromModules: no visible binding for global variable ‘variable’
GmtFromModules: no visible binding for global variable ‘GeneNames’
HyperGTestGeneEnrichment: no visible binding for global variable ‘i’
HyperGTestGeneEnrichment: no visible binding for global variable ‘j’
read_gct: no visible binding for global variable ‘Description’
Undefined global functions or variables:
  Color Description GeneNames Genes Geneset Geneset_length ModuleNr
  Modules MsigdbMapping NumberGenes Overlapping_genes RegulatorIDs
  TargetIDs Testset Type Weights dt_gensesetsall i j moduleNr
  n_Overlapping overlap_perc p.value p_value padj q.value value
  variable
* 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 152 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
AMARETTO_Download 18.297  1.196  21.052
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/AMARETTO.Rcheck/00check.log’
for details.



Installation output

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/4.0/Resources/library’
* installing *source* package ‘AMARETTO’ ...
** using staged installation
** 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 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 (AMARETTO)

Tests output

AMARETTO.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> 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 2.6.2
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.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

> 
> test_check("AMARETTO")
	Found 10 CNV driver genes.
	Found 89 MethylMix driver genes.
	Found a total of 96 unique drivers with your selected method.
Running AMARETTO on 402 genes and 45 samples.
	Stopping if less then 4.02 genes reassigned.
	Autoregulation is turned ON.
Elapsed time is 2.339000 seconds
Average nr of regulators per module: 9.200000 
Elapsed time is 0.146000 seconds
Nr of reassignments is: 48 
Elapsed time is 2.210000 seconds
Average nr of regulators per module: 9.100000 
Elapsed time is 0.150000 seconds
Nr of reassignments is: 9 
Elapsed time is 2.564000 seconds
Average nr of regulators per module: 9.600000 
Elapsed time is 0.197000 seconds
Nr of reassignments is: 8 
Elapsed time is 2.184000 seconds
Average nr of regulators per module: 9.700000 
Elapsed time is 0.197000 seconds
Nr of reassignments is: 8 
Elapsed time is 1.993000 seconds
Average nr of regulators per module: 9.300000 
Elapsed time is 0.180000 seconds
Nr of reassignments is: 4 
Elapsed time is 12.166000 seconds
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 24.673   0.719  25.625 

Example timings

AMARETTO.Rcheck/AMARETTO-Ex.timings

nameusersystemelapsed
AMARETTO_CreateModuleData1.7940.0411.838
AMARETTO_CreateRegulatorPrograms1.4610.0161.478
AMARETTO_Download18.297 1.19621.052
AMARETTO_EvaluateTestSet1.7070.0211.732
AMARETTO_ExportResults1.7890.0311.823
AMARETTO_HTMLreport0.0000.0000.001
AMARETTO_Initialize0.7870.0090.798
AMARETTO_Preprocess0.0000.0000.001
AMARETTO_Run1.4740.0101.486
AMARETTO_VisualizeModule4.5610.0394.609
plot_run_history2.0540.0392.111
read_gct000