Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:36:18 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 |
Package 349/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CHRONOS 1.31.0 (landing page) Panos Balomenos
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the CHRONOS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CHRONOS.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: CHRONOS |
Version: 1.31.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CHRONOS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CHRONOS_1.31.0.tar.gz |
StartedAt: 2024-03-27 21:09:13 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 21:11:58 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 164.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CHRONOS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CHRONOS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CHRONOS_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CHRONOS.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘CHRONOS/DESCRIPTION’ ... OK * this is package ‘CHRONOS’ version ‘1.31.0’ * 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 ‘CHRONOS’ 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 code 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... NOTE checkRd: (-1) extractLinearSubpathways.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractLinearSubpathways.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractLinearSubpathways.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractNonLinearSubpathways.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractNonLinearSubpathways.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractNonLinearSubpathways.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly * 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 ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/CHRONOS.Rcheck/00check.log’ for details.
CHRONOS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CHRONOS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘CHRONOS’ ... ** 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 (CHRONOS)
CHRONOS.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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('CHRONOS') Testing test_CHRONOSrun...Importing entrezgene data...done. Importing miRNA data...done. Downloading files...done. Creating adjacency matrices...done. Extracting Linear Subpathways...done. #98 subpathways initially Calculating subscores...done. #21 subpathways after subscore. Calculating mirscores......end. Extracting Non Linear Subpathways...done. #24 subpathways initially Calculating subscores...done. #19 subpathways after subscore. Calculating mirscores......end. done. Testing test_pathwayToGraph...Creating adjacency matrices...done. done. Testing test_subExtractionLinear...Importing entrezgene data...done. Extracting Linear Subpathways...done. done. Testing test_subExtractionNonLinear...Importing entrezgene data...done. Extracting Non Linear Subpathways...done. done. Testing test_subRefinement...Importing entrezgene data...done. Importing miRNA data...done. #98 subpathways initially Calculating subscores...done. #21 subpathways after subscore. Calculating mirscores......end. done. Testing test_subVisualization...Importing entrezgene data...done. Summarising scores...done. Summarising scores...done. done. RUNIT TEST PROTOCOL -- Wed Mar 27 21:11:44 2024 *********************************************** Number of test functions: 6 Number of errors: 0 Number of failures: 0 1 Test Suite : CHRONOS RUnit Tests - 6 test functions, 0 errors, 0 failures Number of test functions: 6 Number of errors: 0 Number of failures: 0 > > > proc.time() user system elapsed 9.260 0.572 12.911
CHRONOS.Rcheck/CHRONOS-Ex.timings
name | user | system | elapsed | |
CHRONOSrun | 1.469 | 0.102 | 1.499 | |
convertMiRNANomenclature | 0.008 | 0.000 | 0.007 | |
convertNomenclature | 0.001 | 0.000 | 0.000 | |
createPathwayGraphs | 0.230 | 0.028 | 0.257 | |
downloadKEGGPathwayList | 0.028 | 0.000 | 0.029 | |
downloadMiRecords | 0.024 | 0.004 | 0.028 | |
downloadPathways | 0 | 0 | 0 | |
extractLinearSubpathways | 0.402 | 0.017 | 0.335 | |
extractNonLinearSubpathways | 0.191 | 0.020 | 0.230 | |
getEdgeTypes | 0.001 | 0.000 | 0.002 | |
importExpressions | 0.051 | 0.012 | 0.063 | |
pathwayMeasures | 0.118 | 0.000 | 0.117 | |
scoreSubpathways | 0.096 | 0.001 | 0.118 | |
subpathwayKEGGmap | 0.029 | 0.000 | 0.029 | |
subpathwayMiRNAs | 1.207 | 0.064 | 1.270 | |
visualizeResults | 0.126 | 0.019 | 1.291 | |