Mauro Castro
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/RTN |
| git_branch: master |
| git_last_commit: 98b3ed5 |
| git_last_commit_date: 2021-10-26 12:09:15 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:33 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1678/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RTN 2.19.0 (landing page) Mauro Castro
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: RTN |
| Version: 2.19.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTN.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RTN_2.19.0.tar.gz |
| StartedAt: 2022-03-17 20:09:00 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:12:21 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 200.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTN.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RTN_2.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RTN.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '2.19.0'
* 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 10.1Mb
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
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/RTN.Rcheck/00check.log'
for details.
RTN.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RTN
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (RTN)
Making 'packages.html' ... done
RTN.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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...
|
| | 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 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
-Preprocessing for input data...
--Mapping 'expData' to 'rowAnnotation'...
--Checking 'regulatoryElements' in 'rowAnnotation'...
--Checking '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 -- Thu Mar 17 20:12:10 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
34.84 2.43 37.37
RTN.Rcheck/RTN-Ex.timings
| name | user | system | elapsed | |
| AVS-class | 0 | 0 | 0 | |
| RTN.data | 0.31 | 0.03 | 0.34 | |
| TNA-class | 0 | 0 | 0 | |
| TNI-class | 0 | 0 | 0 | |
| TNI.data | 0.33 | 0.02 | 0.35 | |
| avs.evse | 0 | 0 | 0 | |
| avs.get | 0 | 0 | 0 | |
| avs.pevse | 0 | 0 | 0 | |
| avs.plot1 | 0 | 0 | 0 | |
| avs.plot2 | 0 | 0 | 0 | |
| avs.rvse | 0 | 0 | 0 | |
| avs.vse | 0 | 0 | 0 | |
| tna.get | 0.30 | 0.02 | 0.32 | |
| tna.gsea1 | 0.30 | 0.00 | 0.29 | |
| tna.gsea2 | 0.28 | 0.00 | 0.28 | |
| tna.mra | 0.31 | 0.03 | 0.35 | |
| tna.plot.gsea1 | 0.27 | 0.01 | 0.28 | |
| tna.plot.gsea2 | 0.20 | 0.02 | 0.22 | |
| tni.alpha.adjust | 0.16 | 0.00 | 0.15 | |
| tni.annotate.regulons | 0.04 | 0.01 | 0.06 | |
| tni.annotate.samples | 0.05 | 0.02 | 0.07 | |
| tni.area3 | 0.06 | 0.00 | 0.06 | |
| tni.bootstrap | 0.08 | 0.00 | 0.08 | |
| tni.conditional | 0.06 | 0.00 | 0.07 | |
| tni.constructor | 0.67 | 0.02 | 0.68 | |
| tni.dpi.filter | 0.06 | 0.00 | 0.07 | |
| tni.get | 0.07 | 0.00 | 0.06 | |
| tni.graph | 0.06 | 0.01 | 0.08 | |
| tni.gsea2 | 0.05 | 0.02 | 0.06 | |
| tni.overlap.genesets | 0.04 | 0.01 | 0.06 | |
| tni.permutation | 0.05 | 0.00 | 0.05 | |
| tni.plot.checks | 0.05 | 0.00 | 0.04 | |
| tni.plot.sre | 0.04 | 0.00 | 0.05 | |
| tni.preprocess | 0 | 0 | 0 | |
| tni.prune | 0.05 | 0.00 | 0.04 | |
| tni.regulon.summary | 0.03 | 0.02 | 0.05 | |
| tni.replace.samples | 0 | 0 | 0 | |
| tni.sre | 0.03 | 0.01 | 0.05 | |
| tni2tna.preprocess | 0.22 | 0.00 | 0.22 | |
| upgradeTNA | 0 | 0 | 0 | |
| upgradeTNI | 0 | 0 | 0 | |