Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1815/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RTN 2.30.0 (landing page) Mauro Castro
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the RTN package: - 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 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: RTN |
Version: 2.30.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTN.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RTN_2.30.0.tar.gz |
StartedAt: 2024-12-20 05:30:07 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:35:07 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 299.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RTN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTN.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RTN_2.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RTN.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'RTN/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'RTN' version '2.30.0' * 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 9.8Mb 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 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 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) TNI.data.Rd:14-15: Lost braces 14 | \code{stni}{A TNI-class with a subset of samples and genes from | ^ * 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 ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/RTN.Rcheck/00check.log' for details.
RTN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RTN ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 ** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 -- Fri Dec 20 05:34:54 2024 *********************************************** 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 43.71 2.98 47.03
RTN.Rcheck/RTN-Ex.timings
name | user | system | elapsed | |
AVS-class | 0 | 0 | 0 | |
RTN.data | 0.27 | 0.06 | 0.33 | |
TNA-class | 0 | 0 | 0 | |
TNI-class | 0 | 0 | 0 | |
TNI.data | 0.19 | 0.00 | 0.18 | |
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 | 0.26 | 0.02 | 0.28 | |
tna.gsea1 | 0.25 | 0.01 | 0.27 | |
tna.gsea2 | 0.24 | 0.02 | 0.25 | |
tna.mra | 0.23 | 0.00 | 0.23 | |
tna.plot.gsea1 | 0.25 | 0.01 | 0.27 | |
tna.plot.gsea2 | 0.33 | 0.00 | 0.32 | |
tni.alpha.adjust | 0.11 | 0.02 | 0.13 | |
tni.annotate.regulons | 0.06 | 0.00 | 0.06 | |
tni.annotate.samples | 0.05 | 0.00 | 0.05 | |
tni.area3 | 0.05 | 0.00 | 0.04 | |
tni.bootstrap | 0.04 | 0.00 | 0.05 | |
tni.conditional | 0.05 | 0.00 | 0.05 | |
tni.constructor | 0.16 | 0.00 | 0.15 | |
tni.dpi.filter | 0.06 | 0.00 | 0.07 | |
tni.get | 0.04 | 0.00 | 0.04 | |
tni.graph | 0 | 0 | 0 | |
tni.gsea2 | 0.04 | 0.02 | 0.05 | |
tni.overlap.genesets | 0.04 | 0.01 | 0.06 | |
tni.permutation | 0.05 | 0.01 | 0.06 | |
tni.plot.checks | 0.06 | 0.02 | 0.08 | |
tni.plot.sre | 0.05 | 0.01 | 0.06 | |
tni.preprocess | 0 | 0 | 0 | |
tni.prune | 0.06 | 0.00 | 0.06 | |
tni.regulon.summary | 0.06 | 0.02 | 0.08 | |
tni.replace.samples | 0 | 0 | 0 | |
tni.sre | 0.05 | 0.00 | 0.05 | |
tni2tna.preprocess | 0.31 | 0.02 | 0.33 | |
upgradeTNA | 0 | 0 | 0 | |
upgradeTNI | 0 | 0 | 0 | |