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This page was generated on 2024-03-04 11:38:50 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 59/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AMARETTO 1.19.0  (landing page)
Olivier Gevaert
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/AMARETTO
git_branch: devel
git_last_commit: 0d96a59
git_last_commit_date: 2023-10-24 11:12:01 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for AMARETTO on merida1


To the developers/maintainers of the AMARETTO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AMARETTO.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: AMARETTO
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AMARETTO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AMARETTO_1.19.0.tar.gz
StartedAt: 2024-03-01 23:58:48 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-02 00:08:35 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 587.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: AMARETTO.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AMARETTO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AMARETTO_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/AMARETTO.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AMARETTO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AMARETTO’ version ‘1.19.0’
* 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 ... WARNING
Codoc mismatches from Rd file 'get_firehoseData.Rd':
get_firehoseData
  Code: function(TargetDirectory = "./", TCGA_acronym_uppercase =
                 "LUAD", dataType = "stddata", dataFileTag =
                 "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType =
                 "tar.gz", gdacURL =
                 "https://gdac.broadinstitute.org/runs/", untarUngzip =
                 TRUE, printDisease_abbr = FALSE)
  Docs: function(TargetDirectory = "./", TCGA_acronym_uppercase =
                 "LUAD", dataType = "stddata", dataFileTag =
                 "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType =
                 "tar.gz", gdacURL =
                 "http://gdac.broadinstitute.org/runs/", untarUngzip =
                 TRUE, printDisease_abbr = FALSE)
  Mismatches in argument default values:
    Name: 'gdacURL' Code: "https://gdac.broadinstitute.org/runs/" Docs: "http://gdac.broadinstitute.org/runs/"

* 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 LazyData ... OK
* 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        15.679  2.485  25.499
AMARETTO_VisualizeModule  7.040  0.106   7.769
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/AMARETTO.Rcheck/00check.log’
for details.



Installation output

AMARETTO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AMARETTO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 2.19.0
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 either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

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 3.776000 seconds
Average nr of regulators per module: 9.200000 
Elapsed time is 0.299000 seconds
Nr of reassignments is: 48 
Elapsed time is 4.577000 seconds
Average nr of regulators per module: 9.100000 
Elapsed time is 0.301000 seconds
Nr of reassignments is: 9 
Elapsed time is 3.719000 seconds
Average nr of regulators per module: 9.600000 
Elapsed time is 0.344000 seconds
Nr of reassignments is: 8 
Elapsed time is 3.550000 seconds
Average nr of regulators per module: 9.700000 
Elapsed time is 0.317000 seconds
Nr of reassignments is: 8 
Elapsed time is 3.460000 seconds
Average nr of regulators per module: 9.300000 
Elapsed time is 0.323000 seconds
Nr of reassignments is: 4 
Elapsed time is 20.685000 seconds
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 35.673   1.561  40.521 

Example timings

AMARETTO.Rcheck/AMARETTO-Ex.timings

nameusersystemelapsed
AMARETTO_CreateModuleData2.4970.1383.077
AMARETTO_CreateRegulatorPrograms2.2450.0442.673
AMARETTO_Download15.679 2.48525.499
AMARETTO_EvaluateTestSet2.2740.0782.739
AMARETTO_ExportResults2.5170.1422.948
AMARETTO_HTMLreport0.0010.0010.000
AMARETTO_Initialize1.1370.0281.342
AMARETTO_Preprocess0.0000.0000.001
AMARETTO_Run2.1920.0362.411
AMARETTO_VisualizeModule7.0400.1067.769
plot_run_history3.3910.0463.710
read_gct0.0000.0000.001