Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:26 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the RTNduals package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTNduals.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1731/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RTNduals 1.23.0 (landing page) Mauro Castro
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: RTNduals |
Version: 1.23.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RTNduals.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RTNduals_1.23.0.tar.gz |
StartedAt: 2023-02-07 14:06:37 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 14:14:33 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 475.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: RTNduals.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RTNduals.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RTNduals_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RTNduals.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘RTNduals/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RTNduals’ version ‘1.23.0’ * package encoding: UTF-8 * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘RTNduals-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: mbrAssociation,MBR-method > ### Title: Motifs analysis and inference of 'dual regulons'. > ### Aliases: mbrAssociation,MBR-method mbrAssociation > > ### ** Examples > > ##--- load a dataset for demonstration > data("tniData", package = "RTN") > gexp <- tniData$expData > annot <- tniData$rowAnnotation > tfs <- c("IRF8","IRF1","PRDM1","E2F3","STAT4","LMO4","ZNF552") > > ##--- construct a tni object > rtni <- tni.constructor(gexp, regulatoryElements = tfs, rowAnnotation=annot) -Preprocessing for input data... --Mapping 'expData' to 'rowAnnotation'... --Checking 'regulatoryElements' in 'rowAnnotation'... --Checking 'expData'... -Preprocessing complete! > > ##--- compute regulons > ## set nPermutations>=1000 > rtni <- tni.permutation(rtni, nPermutations=30) -Performing permutation analysis... --For 7 regulons... | | | 0% | |== | 3% | |===== | 7% | |======= | 10% | |========= | 13% | |============ | 17% | |============== | 20% | |================ | 23% | |=================== | 27% | |===================== | 30% | |======================= | 33% | |========================== | 37% | |============================ | 40% | |============================== | 43% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================== | 57% | |========================================== | 60% | |============================================ | 63% | |=============================================== | 67% | |================================================= | 70% | |=================================================== | 73% | |====================================================== | 77% | |======================================================== | 80% | |========================================================== | 83% | |============================================================= | 87% | |=============================================================== | 90% | |================================================================= | 93% | |==================================================================== | 97% | |======================================================================| 100% -Permutation analysis complete! > ## set nBootstrap>=100 > rtni <- tni.bootstrap(rtni, nBootstrap=30) -Performing bootstrap analysis... --For 7 regulons... | | | 0% | |== | 3% | |===== | 7% | |======= | 10% | |========= | 13% | |============ | 17% | |============== | 20% | |================ | 23% | |=================== | 27% | |===================== | 30% | |======================= | 33% | |========================== | 37% | |============================ | 40% | |============================== | 43% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================== | 57% | |========================================== | 60% | |============================================ | 63% | |=============================================== | 67% | |================================================= | 70% | |=================================================== | 73% | |====================================================== | 77%Killed * 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 ... ‘RTNduals.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/RTNduals.Rcheck/00check.log’ for details.
RTNduals.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RTNduals ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘RTNduals’ ... ** using staged installation ** R ** 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 (RTNduals)
RTNduals.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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 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! -Checking regulons and regulatory elements... -Extrating inferred regulatory associations... -Mapping network triplets between regulons... -Assessing overlap between 2 regulons... | | | 0% | |======================================================================| 100% -Assessing correlation between 2 regulons... RUNIT TEST PROTOCOL -- Tue Feb 7 14:12:04 2023 *********************************************** 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 message: No 'dual regulon' has been observed for the input parameters. > > proc.time() user system elapsed 32.993 0.695 34.509
RTNduals.Rcheck/RTNduals-Ex.timings
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