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CHECK report for RTN on tokay2

This page was generated on 2018-10-17 08:37:32 -0400 (Wed, 17 Oct 2018).

Package 1291/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTN 2.4.6
Mauro Castro
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RTN
Branch: RELEASE_3_7
Last Commit: b3fb7ce
Last Changed Date: 2018-09-03 11:48:25 -0400 (Mon, 03 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTN
Version: 2.4.6
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTN.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RTN_2.4.6.tar.gz
StartedAt: 2018-10-17 04:35:52 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:39:53 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 240.9 seconds
RetCode: 0
Status:  OK  
CheckDir: RTN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTN.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RTN_2.4.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/RTN.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.4.6'
* 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  9.5Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
* 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-3.7-bioc/meat/RTN.Rcheck/00check.log'
for details.



Installation output

RTN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/RTN_2.4.6.tar.gz && rm -rf RTN.buildbin-libdir && mkdir RTN.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTN.buildbin-libdir RTN_2.4.6.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL RTN_2.4.6.zip && rm RTN_2.4.6.tar.gz RTN_2.4.6.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
100 8541k  100 8541k    0     0  50.2M      0 --:--:-- --:--:-- --:--:-- 52.4M

install for i386

* installing *source* package 'RTN' ...
** 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.preprocess.LD1000gRel20130502       html  
    avs.preprocess.LDHapMapRel27            html  
    avs.vse                                 html  
    tna.get                                 html  
    tna.graph                               html  
    tna.gsea1                               html  
    tna.gsea2                               html  
    tna.mra                                 html  
    tna.overlap                             html  
    tna.plot.gsea1                          html  
    tna.plot.gsea2                          html  
    tna.shadow                              html  
    tna.synergy                             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.permutation                         html  
    tni.preprocess                          html  
    tni2tna.preprocess                      html  
    upgradeTNA                              html  
    upgradeTNI                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RTN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTN' as RTN_2.4.6.zip
* DONE (RTN)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'RTN' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

RTN.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-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 overlap analysis...
--For 5 regulons...

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-Overlap 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 

-Performing synergy analysis...
--For 10 regulon pairs...

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-Synergy analysis complete 

-Performing shadow analysis...
--For 3 regulon pairs...

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-Shadow analysis complete 

-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-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 -- Wed Oct 17 04:39:24 2018 
*********************************************** 
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 
  25.28    0.78   26.07 

RTN.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-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 overlap analysis...
--For 5 regulons...

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-Overlap analysis complete

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

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  |======================================================================| 100%
-Gene set enrichment analysis complete 

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

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-GSEA2 analysis complete 

-Performing synergy analysis...
--For 10 regulon pairs...

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-Synergy analysis complete 

-Performing shadow analysis...
--For 3 regulon pairs...

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-Shadow analysis complete 

-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-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 -- Wed Oct 17 04:39:46 2018 
*********************************************** 
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 
  21.23    0.62   21.92 

Example timings

RTN.Rcheck/examples_i386/RTN-Ex.timings

nameusersystemelapsed
AVS-class000
RTN.data1.020.041.06
TNA-class000
TNI-class000
TNI.data0.520.020.53
avs.evse000
avs.get000
avs.pevse000
avs.plot1000
avs.plot2000
avs.preprocess.LD1000gRel20130502000
avs.preprocess.LDHapMapRel27000
avs.vse000
tna.get0.80.00.8
tna.graph0.890.010.91
tna.gsea11.110.021.12
tna.gsea20.810.030.84
tna.mra0.810.020.83
tna.overlap0.890.010.91
tna.plot.gsea10.800.030.82
tna.plot.gsea20.780.000.79
tna.shadow0.780.020.79
tna.synergy0.770.030.80
tni.area30.920.000.92
tni.bootstrap1.040.021.06
tni.conditional0.930.000.93
tni.constructor1.500.041.54
tni.dpi.filter1.120.021.14
tni.get1.110.011.13
tni.graph0.810.020.83
tni.gsea20.750.020.76
tni.permutation1.050.001.05
tni.preprocess000
tni2tna.preprocess1.090.011.11
upgradeTNA000
upgradeTNI000

RTN.Rcheck/examples_x64/RTN-Ex.timings

nameusersystemelapsed
AVS-class000
RTN.data0.780.010.79
TNA-class000
TNI-class000
TNI.data0.490.020.50
avs.evse000
avs.get000
avs.pevse000
avs.plot1000
avs.plot20.020.000.01
avs.preprocess.LD1000gRel20130502000
avs.preprocess.LDHapMapRel27000
avs.vse000
tna.get0.730.040.78
tna.graph0.900.030.92
tna.gsea10.820.020.85
tna.gsea20.720.000.72
tna.mra0.710.020.72
tna.overlap0.730.010.75
tna.plot.gsea10.860.050.90
tna.plot.gsea20.900.010.90
tna.shadow0.930.020.96
tna.synergy0.630.020.64
tni.area30.650.030.69
tni.bootstrap1.180.011.18
tni.conditional0.780.000.78
tni.constructor2.000.052.05
tni.dpi.filter0.660.000.65
tni.get0.660.010.67
tni.graph0.670.020.69
tni.gsea20.700.000.71
tni.permutation0.70.00.7
tni.preprocess000
tni2tna.preprocess0.750.000.75
upgradeTNA000
upgradeTNI000