Vinicius Chagas
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/RTNduals |
| Branch: RELEASE_3_6 |
| Last Commit: 4948437 |
| Last Changed Date: 2017-10-30 12:41:25 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:44:21 -0400 (Thu, 12 Apr 2018).
| Package 1226/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTNduals 1.2.0 Vinicius Chagas
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: RTNduals |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTNduals_1.2.0.tar.gz |
| StartedAt: 2018-04-12 09:06:52 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 09:09:09 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 137.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTNduals.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTNduals_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/RTNduals.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTNduals/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTNduals’ version ‘1.2.0’
* 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 ‘RTNduals’ can be installed ... OK
* checking installed package size ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mbrAssociation-methods 8.699 0.326 9.218
mbrDuals-methods 6.942 0.312 7.395
mbrPlotDuals 6.886 0.276 7.305
mbrDpiFilter-methods 6.251 0.268 6.649
mbrBootstrap-methods 6.008 0.279 6.394
mbrPermutation-methods 5.150 0.198 5.480
* 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: OK
RTNduals.Rcheck/00install.out
* installing *source* package ‘RTNduals’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RTNduals)
RTNduals.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("RTNduals")
-Preprocessing TNI objects...
-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-Preprocessing 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 two TNI objects...
-Performing permutation analysis...
--For 2 regulons...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Permutation analysis 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 two TNI
objects...
-Performing bootstrap analysis...
--For 2 regulons...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Bootstrap 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 for two TNI objects...
-Applying dpi filter...
-DPI filter complete!
-Applying dpi filter...
-DPI filter complete!
-Checking expression matrix consistency...
-Checking parameter consistency...
-Checking if all TNI methods are completed...
-Selecting regulatory elements from TNI1 object...
-Selecting regulatory elements from TNI2 object...
-Extrating inferred regulatory associations...
-Computing correlation statistics between regulators and targets...
-Computing correlation statistics between regulon pairs...
-Computing quantile statistics...
-Computing Mutual Information...
-Computing Jaccard similarity...
-Running hypergeometric analysis...
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
-Sorting by the R value...
RUNIT TEST PROTOCOL -- Thu Apr 12 09:09:05 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
RTNduals RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning messages:
1: In tni.preprocess(TNI1, verbose = verbose, ... = ...) :
'gexpIDs' argument is deprected!
please use 'rowAnnotation' instead.'
2: In tni.preprocess(TNI2, verbose = verbose, ... = ...) :
'gexpIDs' argument is deprected!
please use 'rowAnnotation' instead.'
3: Only 4 regulon pair(s) is(are) being tested!
Ideally, the search space should represent all possible
combinations of a given class of regulators! For example,
all nuclear receptors annotated for a given species.
>
> proc.time()
user system elapsed
9.513 0.430 10.092
RTNduals.Rcheck/RTNduals-Ex.timings
| name | user | system | elapsed | |
| mbrAssociation-methods | 8.699 | 0.326 | 9.218 | |
| mbrBootstrap-methods | 6.008 | 0.279 | 6.394 | |
| mbrDpiFilter-methods | 6.251 | 0.268 | 6.649 | |
| mbrDuals-methods | 6.942 | 0.312 | 7.395 | |
| mbrGet-methods | 2.388 | 0.090 | 2.544 | |
| mbrPermutation-methods | 5.150 | 0.198 | 5.480 | |
| mbrPlotDuals | 6.886 | 0.276 | 7.305 | |
| mbrPreprocess-methods | 2.210 | 0.071 | 2.315 | |
| tni2mbrPreprocess-methods | 0.799 | 0.020 | 0.823 | |