Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:07:01 -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 tokay2


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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RTN_2.18.0.tar.gz
StartedAt: 2022-01-21 02:02:33 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 02:07:56 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 322.6 seconds
RetCode: 0
Status:   OK  
CheckDir: RTN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RTN_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RTN.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'RTN' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.2Mb
  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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/RTN.Rcheck/00check.log'
for details.



Installation output

RTN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RTN_2.18.0.tar.gz && rm -rf RTN.buildbin-libdir && mkdir RTN.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTN.buildbin-libdir RTN_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RTN_2.18.0.zip && rm RTN_2.18.0.tar.gz RTN_2.18.0.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
 19 9707k   19 1907k    0     0  2509k      0  0:00:03 --:--:--  0:00:03 2509k
 58 9707k   58 5663k    0     0  3206k      0  0:00:03  0:00:01  0:00:02 3206k
100 9707k  100 9707k    0     0  3797k      0  0:00:02  0:00:02 --:--:-- 3799k

install for i386

* installing *source* package 'RTN' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTN'
    finding HTML links ... done
    AVS-class                               html  
    RTN-package                             html  
    RTN.data                                html  
    TNA-class                               html  
    TNI-class                               html  
    TNI.data                                html  
    avs.evse                                html  
    avs.get                                 html  
    avs.pevse                               html  
    avs.plot1                               html  
    avs.plot2                               html  
    avs.rvse                                html  
    avs.vse                                 html  
    tna.get                                 html  
    tna.gsea1                               html  
    tna.gsea2                               html  
    tna.mra                                 html  
    tna.plot.gsea1                          html  
    tna.plot.gsea2                          html  
    tni.alpha.adjust                        html  
    tni.annotate.regulons                   html  
    tni.annotate.samples                    html  
    tni.area3                               html  
    finding level-2 HTML links ... done

    tni.bootstrap                           html  
    tni.conditional                         html  
    tni.constructor                         html  
    tni.dpi.filter                          html  
    tni.get                                 html  
    tni.graph                               html  
    tni.gsea2                               html  
    tni.overlap.genesets                    html  
    tni.permutation                         html  
    tni.plot.checks                         html  
    tni.plot.sre                            html  
    tni.preprocess                          html  
    tni.prune                               html  
    tni.regulon.summary                     html  
    tni.replace.samples                     html  
    tni.sre                                 html  
    tni2tna.preprocess                      html  
    upgradeTNA                              html  
    upgradeTNI                              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 'RTN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTN' as RTN_2.18.0.zip
* DONE (RTN)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RTN' successfully unpacked and MD5 sums checked

Tests output

RTN.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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.

> 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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  |======================================================================| 100%
-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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  |======================================================================| 100%
-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 Jan 21 02:07:08 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 
  38.46    1.15   39.62 

RTN.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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.

> 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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  |======================================================================| 100%
-Permutation analysis complete! 

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

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  |======================================================================| 100%
-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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  |======================================================================| 100%
-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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  |======================================================================| 100%
-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 Jan 21 02:07:47 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 
  38.48    0.43   38.93 

Example timings

RTN.Rcheck/examples_i386/RTN-Ex.timings

nameusersystemelapsed
AVS-class000
RTN.data0.330.010.35
TNA-class000
TNI-class000
TNI.data0.420.030.46
avs.evse000
avs.get000
avs.pevse000
avs.plot1000
avs.plot2000
avs.rvse000
avs.vse000
tna.get0.320.030.34
tna.gsea10.290.000.30
tna.gsea20.320.000.31
tna.mra0.290.020.31
tna.plot.gsea10.330.000.33
tna.plot.gsea20.280.030.31
tni.alpha.adjust0.130.000.13
tni.annotate.regulons0.040.010.06
tni.annotate.samples0.070.020.08
tni.area30.040.010.06
tni.bootstrap0.070.000.06
tni.conditional0.510.020.54
tni.constructor0.170.000.17
tni.dpi.filter0.070.000.06
tni.get0.060.000.06
tni.graph0.060.000.06
tni.gsea20.060.020.08
tni.overlap.genesets0.050.010.07
tni.permutation0.080.000.07
tni.plot.checks0.060.000.07
tni.plot.sre0.060.000.06
tni.preprocess000
tni.prune0.050.020.07
tni.regulon.summary0.070.000.07
tni.replace.samples000
tni.sre0.050.030.08
tni2tna.preprocess0.270.030.30
upgradeTNA000
upgradeTNI000

RTN.Rcheck/examples_x64/RTN-Ex.timings

nameusersystemelapsed
AVS-class000
RTN.data0.300.010.32
TNA-class000
TNI-class000
TNI.data0.320.020.35
avs.evse000
avs.get000
avs.pevse000
avs.plot1000
avs.plot2000
avs.rvse000
avs.vse000
tna.get0.220.040.26
tna.gsea10.280.020.30
tna.gsea20.240.000.23
tna.mra0.230.020.25
tna.plot.gsea10.250.010.27
tna.plot.gsea20.250.000.25
tni.alpha.adjust0.140.000.14
tni.annotate.regulons0.100.020.11
tni.annotate.samples0.040.010.06
tni.area30.040.020.05
tni.bootstrap0.060.000.06
tni.conditional0.050.010.06
tni.constructor0.710.000.72
tni.dpi.filter0.050.020.06
tni.get0.060.000.07
tni.graph0.050.000.04
tni.gsea20.050.020.07
tni.overlap.genesets0.060.000.06
tni.permutation0.040.000.05
tni.plot.checks0.060.010.08
tni.plot.sre0.070.000.06
tni.preprocess000
tni.prune0.060.000.06
tni.regulon.summary0.060.000.07
tni.replace.samples000
tni.sre0.050.020.06
tni2tna.preprocess0.260.020.29
upgradeTNA000
upgradeTNI000