Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:08:26 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for RTN on machv2


To the developers/maintainers of the RTN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTN.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 1670/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTN 2.18.0  (landing page)
Mauro Castro
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/RTN
git_branch: RELEASE_3_14
git_last_commit: cf102aa
git_last_commit_date: 2021-10-26 12:09:15 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RTN
Version: 2.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RTN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RTN_2.18.0.tar.gz
StartedAt: 2022-01-20 17:31:41 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 17:37:14 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 332.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RTN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RTN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RTN_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/RTN.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.18.0’
* 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 10.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/RTN.Rcheck/00check.log’
for details.



Installation output

RTN.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.2 (2021-11-01) -- "Bird Hippie"
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.

> 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 Jan 20 17:37:03 2022 
*********************************************** 
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 
 55.918   3.654  59.602 

Example timings

RTN.Rcheck/RTN-Ex.timings

nameusersystemelapsed
AVS-class0.0000.0000.001
RTN.data0.4060.0180.425
TNA-class000
TNI-class0.0000.0010.001
TNI.data0.4000.0120.414
avs.evse0.0000.0010.002
avs.get0.0000.0010.001
avs.pevse0.0000.0020.002
avs.plot10.0000.0000.001
avs.plot2000
avs.rvse0.0000.0010.001
avs.vse0.0000.0010.002
tna.get0.4140.0120.427
tna.gsea10.3660.0120.380
tna.gsea20.4020.0100.413
tna.mra0.3050.0090.315
tna.plot.gsea10.3830.0100.393
tna.plot.gsea20.8210.0100.831
tni.alpha.adjust0.2480.0110.259
tni.annotate.regulons0.0840.0080.091
tni.annotate.samples0.0940.0080.101
tni.area30.0850.0050.090
tni.bootstrap0.0770.0070.085
tni.conditional0.0680.0060.074
tni.constructor0.3450.0290.374
tni.dpi.filter0.0910.0100.101
tni.get0.0850.0080.093
tni.graph0.0780.0070.085
tni.gsea20.0910.0070.097
tni.overlap.genesets0.0910.0080.099
tni.permutation0.0920.0070.098
tni.plot.checks0.0990.0070.105
tni.plot.sre0.0740.0060.080
tni.preprocess0.0000.0000.001
tni.prune0.0870.0040.092
tni.regulon.summary0.0910.0070.098
tni.replace.samples0.0000.0000.001
tni.sre0.0900.0050.095
tni2tna.preprocess0.3900.0150.407
upgradeTNA0.0000.0000.001
upgradeTNI0.0000.0000.001