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 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 314/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CeTF 1.18.0 (landing page) Carlos Alberto Oliveira de Biagi Junior
| 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 CeTF package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CeTF.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: CeTF |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CeTF.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CeTF_1.18.0.tar.gz |
StartedAt: 2024-12-20 00:57:31 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:07:49 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 618.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CeTF.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CeTF.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CeTF_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CeTF.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CeTF/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CeTF’ version ‘1.18.0’ * 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 ‘CeTF’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 ... 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/CeTF.Rcheck/00check.log’ for details.
CeTF.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CeTF ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘CeTF’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PCIT.cpp -o PCIT.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CeTF.so PCIT.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-CeTF/00new/CeTF/libs ** R ** data *** moving datasets to lazyload DB ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CeTF)
CeTF.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > library("testthat") > library("CeTF") ======================================== CeTF version 1.18.0 Bioconductor page: http://bioconductor.org/packages/CeTF/ Github page: https://github.com/cbiagii/CeTF or https://cbiagii.github.io/CeTF/ Documentation: http://bioconductor.org/packages/CeTF/ If you use it in published research, please cite: Carlos Alberto Oliveira de Biagi Junior, Ricardo Perecin Nociti, Breno Osvaldo Funicheli, Patricia de Cassia Ruy, Joao Paulo Bianchi Ximenez, Wilson A Silva Jr. CeTF: an R package to Coexpression for Transcription Factors using Regulatory Impact Factors (RIF) and Partial Correlation and Information (PCIT) analysis. bioRxiv. 2020, DOI: 10.1101/2020.03.30.015784 ======================================== > test_check("CeTF") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ] > > proc.time() user system elapsed 27.707 1.607 29.765
CeTF.Rcheck/CeTF-Ex.timings
name | user | system | elapsed | |
CeTFdemo | 0.003 | 0.003 | 0.007 | |
CircosTargets | 0.000 | 0.000 | 0.001 | |
InputData-methods | 0.023 | 0.007 | 0.031 | |
NetworkData-methods | 0.189 | 0.019 | 0.208 | |
OutputData-methods | 0.051 | 0.047 | 0.098 | |
PCIT | 0.027 | 0.004 | 0.032 | |
RIF | 0.010 | 0.004 | 0.014 | |
RIFPlot | 2.127 | 0.072 | 2.220 | |
RIF_input | 0.001 | 0.002 | 0.004 | |
SmearPlot | 2.827 | 0.159 | 3.012 | |
TFs | 0.001 | 0.002 | 0.004 | |
bivar.awk | 0.002 | 0.001 | 0.003 | |
clustCoef | 0.045 | 0.006 | 0.051 | |
clustCoefPercentage | 0.041 | 0.004 | 0.046 | |
densityPlot | 2.948 | 0.125 | 3.093 | |
diffusion | 0.000 | 0.001 | 0.001 | |
enrichPlot | 1.334 | 0.103 | 1.445 | |
enrichdemo | 0.002 | 0.003 | 0.004 | |
expDiff | 1.001 | 0.082 | 1.087 | |
getDE-methods | 0.021 | 0.007 | 0.028 | |
getData-methods | 0.019 | 0.006 | 0.025 | |
getEnrich | 0.000 | 0.001 | 0.001 | |
getGroupGO | 0.001 | 0.001 | 0.001 | |
heatPlot | 2.965 | 0.051 | 3.037 | |
histPlot | 0.917 | 0.049 | 0.977 | |
netConditionsPlot | 4.006 | 0.080 | 4.122 | |
netGOTFPlot | 0.001 | 0.001 | 0.002 | |
normExp | 0.124 | 0.014 | 0.144 | |
pcitC | 0.038 | 0.004 | 0.047 | |
refGenes | 0.002 | 0.002 | 0.005 | |
runAnalysis | 0.753 | 0.044 | 0.803 | |
simCounts | 0.001 | 0.003 | 0.004 | |
simNorm | 0.002 | 0.002 | 0.005 | |
tolerance | 0.001 | 0.001 | 0.002 | |