Mauro Castro
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/RTN |
| Branch: RELEASE_3_10 |
| Last Commit: 27b801c |
| Last Changed Date: 2019-11-16 10:56:58 -0400 (Sat, 16 Nov 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:39:05 -0400 (Wed, 15 Apr 2020).
| Package 1491/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTN 2.10.1 Mauro Castro
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: RTN |
| Version: 2.10.1 |
| 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_2.10.1.tar.gz |
| StartedAt: 2020-04-15 05:22:08 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:26:38 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 269.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_2.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/RTN.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.10.1’
* 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 8.5Mb
* 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-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Permutation analysis complete!
-Performing bootstrap analysis...
--For 5 regulons...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 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...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
-Master regulatory analysis complete
-Performing overlap analysis...
--For 5 regulons...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
-Overlap analysis complete
-Performing gene set enrichment analysis...
--For 5 regulons...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
-Gene set enrichment analysis complete
-Performing two-tailed GSEA analysis...
--For 5 regulons...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
-GSEA2 analysis complete
-Performing synergy analysis...
--For 10 regulon pairs...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Synergy analysis complete
-Performing shadow analysis...
--For 3 regulon pairs...
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
-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...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Permutation analysis complete!
-Performing bootstrap analysis...
--For 2 regulons...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 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...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Performing conditional mutual information analysis...
--For 2 tfs and 2 candidate modulator(s)
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
-Conditional analysis complete!
RUNIT TEST PROTOCOL -- Wed Apr 15 05:26:28 2020
***********************************************
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
Warning messages:
1: The 'tna.overlap' function is deprecated.
For pairwise regulon analysis, please consider using the 'RTNduals' package.
2: The 'tna.synergy' function is deprecated.
For pairwise regulon analysis, please consider using the 'RTNduals' package.
3: The 'tna.shadow' function is deprecated.
For pairwise regulon analysis, please consider using the 'RTNduals' package.
>
> proc.time()
user system elapsed
46.540 2.894 49.742
RTN.Rcheck/RTN-Ex.timings
| name | user | system | elapsed | |
| AVS-class | 0.000 | 0.000 | 0.001 | |
| RTN.data | 0.323 | 0.018 | 0.342 | |
| TNA-class | 0 | 0 | 0 | |
| TNI-class | 0 | 0 | 0 | |
| TNI.data | 0.380 | 0.013 | 0.396 | |
| avs.evse | 0.000 | 0.000 | 0.001 | |
| avs.get | 0 | 0 | 0 | |
| avs.pevse | 0.001 | 0.001 | 0.001 | |
| avs.plot1 | 0.000 | 0.000 | 0.001 | |
| avs.plot2 | 0.000 | 0.001 | 0.000 | |
| avs.vse | 0.001 | 0.000 | 0.001 | |
| tna.get | 0.348 | 0.015 | 0.366 | |
| tna.gsea1 | 0.295 | 0.014 | 0.311 | |
| tna.gsea2 | 0.319 | 0.015 | 0.337 | |
| tna.mra | 0.340 | 0.012 | 0.356 | |
| tna.plot.gsea1 | 0.276 | 0.008 | 0.285 | |
| tna.plot.gsea2 | 0.294 | 0.010 | 0.305 | |
| tni.area3 | 0.550 | 0.012 | 0.565 | |
| tni.bootstrap | 0.064 | 0.004 | 0.068 | |
| tni.conditional | 0.066 | 0.006 | 0.072 | |
| tni.constructor | 0.260 | 0.024 | 0.284 | |
| tni.dpi.filter | 0.063 | 0.003 | 0.066 | |
| tni.get | 0.065 | 0.003 | 0.069 | |
| tni.graph | 0.063 | 0.007 | 0.070 | |
| tni.gsea2 | 0.055 | 0.006 | 0.061 | |
| tni.permutation | 0.067 | 0.007 | 0.074 | |
| tni.preprocess | 0.000 | 0.000 | 0.001 | |
| tni.prune | 0.073 | 0.004 | 0.080 | |
| tni.regulon.summary | 0.059 | 0.004 | 0.062 | |
| tni.replace.samples | 0 | 0 | 0 | |
| tni2tna.preprocess | 0.297 | 0.011 | 0.309 | |
| upgradeTNA | 0.001 | 0.000 | 0.001 | |
| upgradeTNI | 0 | 0 | 0 | |