Mauro Castro
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/RTN |
| Branch: RELEASE_3_9 |
| Last Commit: b8c66dc |
| Last Changed Date: 2019-09-15 22:18:34 -0400 (Sun, 15 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:51:48 -0400 (Wed, 16 Oct 2019).
| Package 1431/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTN 2.8.5 Mauro Castro
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: RTN |
| Version: 2.8.5 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RTN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTN_2.8.5.tar.gz |
| StartedAt: 2019-10-16 06:28:00 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:33:31 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 331.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTN.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RTN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTN_2.8.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RTN.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.8.5’
* 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 9.7Mb
sub-directories of 1Mb or more:
data 8.5Mb
* 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-3.9-bioc/meat/RTN.Rcheck/00check.log’
for details.
RTN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RTN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)
RTN.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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'...
--Checking 'regulatoryElements' in '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 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 'expData' to 'rowAnnotation'...
--Checking 'regulatoryElements' in 'rowAnnotation'...
--Checking 'expData'...
--Checking 'regulatoryElements' in '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 -- Wed Oct 16 06:33:20 2019
***********************************************
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
60.233 6.047 66.257
RTN.Rcheck/RTN-Ex.timings
| name | user | system | elapsed | |
| AVS-class | 0.001 | 0.001 | 0.001 | |
| RTN.data | 0.395 | 0.043 | 0.439 | |
| TNA-class | 0.000 | 0.000 | 0.001 | |
| TNI-class | 0.001 | 0.000 | 0.001 | |
| TNI.data | 0.973 | 0.022 | 0.995 | |
| avs.evse | 0.001 | 0.002 | 0.002 | |
| avs.get | 0.000 | 0.000 | 0.001 | |
| avs.pevse | 0.002 | 0.002 | 0.004 | |
| avs.plot1 | 0.000 | 0.000 | 0.001 | |
| avs.plot2 | 0.001 | 0.001 | 0.001 | |
| avs.vse | 0.001 | 0.002 | 0.003 | |
| tna.get | 0.287 | 0.020 | 0.307 | |
| tna.graph | 0.358 | 0.026 | 0.384 | |
| tna.gsea1 | 0.304 | 0.023 | 0.327 | |
| tna.gsea2 | 0.333 | 0.026 | 0.359 | |
| tna.mra | 0.349 | 0.019 | 0.368 | |
| tna.overlap | 0.329 | 0.019 | 0.347 | |
| tna.plot.gsea1 | 0.348 | 0.025 | 0.373 | |
| tna.plot.gsea2 | 0.349 | 0.014 | 0.364 | |
| tna.shadow | 0.387 | 0.021 | 0.408 | |
| tna.synergy | 0.377 | 0.016 | 0.393 | |
| tni.area3 | 0.071 | 0.014 | 0.085 | |
| tni.bootstrap | 0.075 | 0.014 | 0.089 | |
| tni.conditional | 0.079 | 0.014 | 0.093 | |
| tni.constructor | 0.412 | 0.040 | 0.453 | |
| tni.dpi.filter | 0.096 | 0.013 | 0.110 | |
| tni.get | 0.058 | 0.005 | 0.062 | |
| tni.graph | 0.074 | 0.007 | 0.081 | |
| tni.gsea2 | 0.071 | 0.006 | 0.078 | |
| tni.permutation | 0.077 | 0.014 | 0.091 | |
| tni.preprocess | 0 | 0 | 0 | |
| tni.prune | 0.077 | 0.014 | 0.091 | |
| tni.regulon.summary | 0.087 | 0.006 | 0.093 | |
| tni.replace.samples | 0.001 | 0.000 | 0.000 | |
| tni2tna.preprocess | 0.373 | 0.022 | 0.395 | |
| upgradeTNA | 0.001 | 0.000 | 0.000 | |
| upgradeTNI | 0.000 | 0.000 | 0.001 | |