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This page was generated on 2024-05-18 11:38:16 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 1834/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTN 2.28.0  (landing page)
Mauro Castro
Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/RTN
git_branch: RELEASE_3_19
git_last_commit: a9f2247
git_last_commit_date: 2024-04-30 10:32:53 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for RTN on lconway


To the developers/maintainers of the RTN package:
- 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 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: RTN
Version: 2.28.0
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_2.28.0.tar.gz
StartedAt: 2024-05-17 23:35:32 -0400 (Fri, 17 May 2024)
EndedAt: 2024-05-17 23:40:35 -0400 (Fri, 17 May 2024)
EllapsedTime: 303.2 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_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RTN.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘RTN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTN’ version ‘2.28.0’
* 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  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 code 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 ... NOTE
checkRd: (-1) TNI.data.Rd:14-15: Lost braces
    14 |   \code{stni}{A TNI-class with a subset of samples and genes from 
       |              ^
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
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.

> 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 -- Fri May 17 23:40:25 2024 
*********************************************** 
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 
 43.599   3.593  47.646 

Example timings

RTN.Rcheck/RTN-Ex.timings

nameusersystemelapsed
AVS-class000
RTN.data0.3480.0160.366
TNA-class000
TNI-class0.0000.0000.001
TNI.data0.3230.0110.338
avs.evse0.0000.0010.001
avs.get000
avs.pevse0.0000.0010.002
avs.plot1000
avs.plot20.0000.0000.001
avs.rvse0.0000.0010.001
avs.vse0.0000.0000.001
tna.get0.2440.0080.254
tna.gsea10.2720.0090.282
tna.gsea20.3040.0130.322
tna.mra0.2700.0090.281
tna.plot.gsea10.3030.0130.320
tna.plot.gsea20.2560.0080.265
tni.alpha.adjust0.1400.0020.143
tni.annotate.regulons0.0580.0060.065
tni.annotate.samples0.6390.0120.655
tni.area30.0510.0060.060
tni.bootstrap0.0470.0040.052
tni.conditional0.0450.0070.054
tni.constructor0.1620.0230.186
tni.dpi.filter0.0460.0040.051
tni.get0.0490.0070.057
tni.graph0.0000.0000.001
tni.gsea20.0440.0040.047
tni.overlap.genesets0.0490.0060.056
tni.permutation0.0470.0040.052
tni.plot.checks0.0450.0040.050
tni.plot.sre0.0630.0140.078
tni.preprocess000
tni.prune0.0520.0070.063
tni.regulon.summary0.0550.0060.062
tni.replace.samples0.0010.0000.000
tni.sre0.0490.0030.054
tni2tna.preprocess0.2840.0090.297
upgradeTNA000
upgradeTNI000