Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-18 12:03:58 -0400 (Mon, 18 Oct 2021).

CHECK results for AMARETTO on riesling1

To the developers/maintainers of the AMARETTO package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 49/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AMARETTO 1.9.0  (landing page)
Olivier Gevaert
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/AMARETTO
git_branch: master
git_last_commit: 934b8e3
git_last_commit_date: 2021-05-19 12:42:00 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AMARETTO
Version: 1.9.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AMARETTO.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AMARETTO_1.9.0.tar.gz
StartedAt: 2021-10-17 23:48:04 -0400 (Sun, 17 Oct 2021)
EndedAt: 2021-10-17 23:55:14 -0400 (Sun, 17 Oct 2021)
EllapsedTime: 429.9 seconds
RetCode: 0
Status:   OK  
CheckDir: AMARETTO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AMARETTO.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AMARETTO_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/AMARETTO.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AMARETTO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AMARETTO' version '1.9.0'
* 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 whether package 'AMARETTO' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
AMARETTO_Download                10.15   1.26   15.38
AMARETTO_VisualizeModule          1.71   0.02    8.62
AMARETTO_ExportResults            0.72   0.11    7.44
plot_run_history                  0.70   0.03    7.49
AMARETTO_CreateModuleData         0.44   0.11    7.72
AMARETTO_EvaluateTestSet          0.42   0.03    7.42
AMARETTO_CreateRegulatorPrograms  0.43   0.00    7.33
AMARETTO_Run                      0.43   0.00    7.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
AMARETTO_Download                9.58   1.48   14.86
AMARETTO_VisualizeModule         1.84   0.00    9.30
AMARETTO_EvaluateTestSet         1.04   0.03    8.44
AMARETTO_CreateRegulatorPrograms 0.95   0.03    8.50
plot_run_history                 0.81   0.03    8.28
AMARETTO_ExportResults           0.66   0.16    8.13
AMARETTO_CreateModuleData        0.55   0.05    8.16
AMARETTO_Run                     0.47   0.00    8.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbuild/bbs-3.14-bioc/meat/AMARETTO.Rcheck/00check.log'
for details.



Installation output

AMARETTO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/AMARETTO_1.9.0.tar.gz && rm -rf AMARETTO.buildbin-libdir && mkdir AMARETTO.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AMARETTO.buildbin-libdir AMARETTO_1.9.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL AMARETTO_1.9.0.zip && rm AMARETTO_1.9.0.tar.gz AMARETTO_1.9.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 61 5470k   61 3343k    0     0  5991k      0 --:--:-- --:--:-- --:--:-- 5981k
100 5470k  100 5470k    0     0  7705k      0 --:--:-- --:--:-- --:--:-- 7694k

install for i386

* 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
  converting help for package 'AMARETTO'
    finding HTML links ... done
    AMARETTO_CreateModuleData               html  
    AMARETTO_CreateRegulatorPrograms        html  
    AMARETTO_Download                       html  
    AMARETTO_EvaluateTestSet                html  
    AMARETTO_ExportResults                  html  
    AMARETTO_HTMLreport                     html  
    AMARETTO_Initialize                     html  
    AMARETTO_LarsenBased                    html  
    AMARETTO_LearnRegulatoryProgramsLarsen
                                            html  
    AMARETTO_Preprocess                     html  
    AMARETTO_ReassignGenesToClusters        html  
    AMARETTO_Run                            html  
    AMARETTO_VisualizeModule                html  
    BatchData                               html  
    Beta.NA                                 html  
    ComBat_NoFiles                          html  
    CreateRegulatorData                     html  
    Driver_Genes                            html  
    FindTranscriptionallyPredictive_CNV     html  
    GeneSetDescription                      html  
    GmtFromModules                          html  
    HyperGTestGeneEnrichment                html  
    L                                       html  
    Lambda_Sequence                         html  
    MsigdbMapping                           html  
    Preprocess_MAdata                       html  
    ProcessedDataLIHC                       html  
    Save_CancerSite                         html  
    TCGA_BatchCorrection_MolecularData      html  
    TCGA_GENERIC_BatchCorrection            html  
    TCGA_GENERIC_CheckBatchEffect           html  
    TCGA_GENERIC_CleanUpSampleNames         html  
    TCGA_GENERIC_GetSampleGroups            html  
    TCGA_GENERIC_MergeData                  html  
    TCGA_Load_GISTICdata                    html  
    TCGA_Load_MolecularData                 html  
    aprior                                  html  
    bprior                                  html  
    build.design                            html  
    cacheResource                           html  
    computeGisticURL                        html  
    design.mat                              html  
    filter.absent                           html  
    geneFiltering                           html  
    get_firehoseData                        html  
    int.eprior                              html  
    it.sol                                  html  
    list.batch                              html  
    plot_run_history                        html  
    postmean                                html  
    postvar                                 html  
    printf                                  html  
    readGMT                                 html  
    read_gct                                html  
    trim.dat                                html  
    write_gct                               html  
** 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

install for x64

* installing *source* package 'AMARETTO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AMARETTO' as AMARETTO_1.9.0.zip
* DONE (AMARETTO)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'AMARETTO' successfully unpacked and MD5 sums checked

Tests output

AMARETTO.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 2.9.4
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.

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 7.280000 seconds
Average nr of regulators per module: 9.200000 
Elapsed time is 0.220000 seconds
Nr of reassignments is: 48 
Elapsed time is 0.980000 seconds
Average nr of regulators per module: 9.100000 
Elapsed time is 0.220000 seconds
Nr of reassignments is: 9 
Elapsed time is 1.080000 seconds
Average nr of regulators per module: 9.600000 
Elapsed time is 0.220000 seconds
Nr of reassignments is: 8 
Elapsed time is 1.040000 seconds
Average nr of regulators per module: 9.700000 
Elapsed time is 0.210000 seconds
Nr of reassignments is: 8 
Elapsed time is 1.030000 seconds
Average nr of regulators per module: 9.300000 
Elapsed time is 0.200000 seconds
Nr of reassignments is: 4 
Elapsed time is 12.480000 seconds
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
   8.12    0.51   20.06 

AMARETTO.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 2.9.4
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.

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 8.310000 seconds
Average nr of regulators per module: 9.200000 
Elapsed time is 0.200000 seconds
Nr of reassignments is: 48 
Elapsed time is 1.080000 seconds
Average nr of regulators per module: 9.100000 
Elapsed time is 0.640000 seconds
Nr of reassignments is: 9 
Elapsed time is 1.060000 seconds
Average nr of regulators per module: 9.600000 
Elapsed time is 0.160000 seconds
Nr of reassignments is: 8 
Elapsed time is 1.050000 seconds
Average nr of regulators per module: 9.700000 
Elapsed time is 0.150000 seconds
Nr of reassignments is: 8 
Elapsed time is 1.000000 seconds
Average nr of regulators per module: 9.300000 
Elapsed time is 0.140000 seconds
Nr of reassignments is: 4 
Elapsed time is 13.790000 seconds
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
   8.17    0.48   21.26 

Example timings

AMARETTO.Rcheck/examples_i386/AMARETTO-Ex.timings

nameusersystemelapsed
AMARETTO_CreateModuleData0.440.117.72
AMARETTO_CreateRegulatorPrograms0.430.007.33
AMARETTO_Download10.15 1.2615.38
AMARETTO_EvaluateTestSet0.420.037.42
AMARETTO_ExportResults0.720.117.44
AMARETTO_HTMLreport000
AMARETTO_Initialize0.280.000.28
AMARETTO_Preprocess000
AMARETTO_Run0.430.007.47
AMARETTO_VisualizeModule1.710.028.62
plot_run_history0.700.037.49
read_gct000

AMARETTO.Rcheck/examples_x64/AMARETTO-Ex.timings

nameusersystemelapsed
AMARETTO_CreateModuleData0.550.058.16
AMARETTO_CreateRegulatorPrograms0.950.038.50
AMARETTO_Download 9.58 1.4814.86
AMARETTO_EvaluateTestSet1.040.038.44
AMARETTO_ExportResults0.660.168.13
AMARETTO_HTMLreport000
AMARETTO_Initialize0.330.000.32
AMARETTO_Preprocess000
AMARETTO_Run0.470.008.02
AMARETTO_VisualizeModule1.840.009.30
plot_run_history0.810.038.28
read_gct000