Back to Multiple platform build/check report for BioC 3.9 |
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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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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... | | | 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 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 | |