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CHECK report for RTN on malbec1

This page was generated on 2021-05-06 12:28:56 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RTN package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1593/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTN 2.14.1  (landing page)
Mauro Castro
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RTN
Branch: RELEASE_3_12
Last Commit: dc65d5c
Last Changed Date: 2020-11-10 14:05:51 -0400 (Tue, 10 Nov 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: RTN
Version: 2.14.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RTN.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RTN_2.14.1.tar.gz
StartedAt: 2021-05-06 05:33:11 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:37:40 -0400 (Thu, 06 May 2021)
EllapsedTime: 269.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RTN.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RTN.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RTN_2.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/RTN.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTN’ version ‘2.14.1’
* 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 ‘RTN’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   8.6Mb
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/RTN.Rcheck/00check.log’
for details.



Installation output

RTN.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL RTN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘RTN’ ...
** using staged installation
** 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 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 (RTN)

Tests output

RTN.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> BiocGenerics:::testPackage("RTN")
-Preprocessing for input data...
--Mapping 'expData' to 'rowAnnotation'...
--Checking 'regulatoryElements' in 'rowAnnotation'...
--Checking 'expData'...
-Preprocessing complete!

-Performing permutation analysis...
--For 5 regulons...

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-Permutation analysis complete! 

-Performing bootstrap analysis...
--For 5 regulons...

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-Bootstrap analysis complete! 

-Applying dpi filter...
-DPI filter complete! 

-Preprocessing for input data...
--Mapping 'phenotype' to 'phenoIDs'...
--Removing genes without names or values in 'phenotype'...
--Removing duplicated genes...
--Mapping 'hits' to 'phenoIDs'...
--Removing duplicated hits...
--Mapping 'transcriptionalNetwork' annotation to 'phenotype'...
--Checking agreement between 'transcriptionalNetwork' and 'phenotype'... 99.8% ! 
--Removing 'hits' not listed in 'transcriptionalNetwork' universe...
--Extracting regulons...
-Preprocessing complete!

-Performing master regulatory analysis...
--For 5 regulons...

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-Master regulatory analysis complete

-Performing gene set enrichment analysis...
--For 5 regulons...

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-Gene set enrichment analysis complete 

-Performing two-tailed GSEA analysis...
--For 5 regulons...

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-GSEA2 analysis complete 

-Preprocessing for input data...
--Mapping 'expData' to 'rowAnnotation'...
--Checking 'regulatoryElements' in 'rowAnnotation'...
--Checking 'expData'...
-Preprocessing complete!

-Performing permutation analysis...
--For 2 regulons...

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-Permutation analysis complete! 

-Performing bootstrap analysis...
--For 2 regulons...

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-Bootstrap analysis complete! 

-Applying dpi filter...
-DPI filter complete! 

-Preprocessing for input data...
--Checking modulators in the dataset...
--Extracting TF-targets...
--Applying modulator independence constraint...
--Applying modulator range constraint...
--Selecting subsamples...

-Estimating mutual information threshold...

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-Performing conditional mutual information analysis...
--For 2 tfs and 2 candidate modulator(s) 

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-Conditional analysis complete! 



RUNIT TEST PROTOCOL -- Thu May  6 05:37:36 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RTN RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 46.540   0.476  47.134 

Example timings

RTN.Rcheck/RTN-Ex.timings

nameusersystemelapsed
AVS-class000
RTN.data0.3880.0120.402
TNA-class000
TNI-class000
TNI.data0.3880.0040.391
avs.evse000
avs.get000
avs.pevse0.0000.0000.001
avs.plot1000
avs.plot2000
avs.vse0.0000.0000.001
tna.get0.3600.0040.366
tna.gsea10.3080.0040.312
tna.gsea20.3520.0080.362
tna.mra0.8720.0120.888
tna.plot.gsea10.2960.0200.318
tna.plot.gsea20.3000.0080.307
tni.alpha.adjust0.2000.0000.202
tni.annotate.regulons0.0640.0040.067
tni.annotate.samples0.0600.0080.066
tni.area30.0720.0080.081
tni.bootstrap0.1120.0040.115
tni.conditional0.0680.0040.072
tni.constructor0.2880.0000.288
tni.dpi.filter0.0880.0000.087
tni.get0.0960.0080.106
tni.graph0.0520.0080.064
tni.gsea20.0640.0000.065
tni.overlap.genesets0.0680.0040.074
tni.permutation0.0840.0040.089
tni.plot.checks0.0840.0040.087
tni.plot.sre0.0880.0000.087
tni.preprocess000
tni.prune0.0880.0080.098
tni.regulon.summary0.0880.0000.087
tni.replace.samples000
tni.sre0.0840.0040.089
tni2tna.preprocess0.3680.0160.385
upgradeTNA000
upgradeTNI000