| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 305/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CeTF 1.12.0 (landing page) Carlos Alberto Oliveira de Biagi Junior
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the CeTF package: - 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2023-10-17 08:26:43 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 08:35:04 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 501.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CeTF.Rcheck |
| Warnings: 0 |
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### 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CeTF.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CeTF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CeTF’ version ‘1.12.0’
* 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 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 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 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-3.17-bioc-mac-arm64/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/4.3-arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PCIT.cpp -o PCIT.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.
> library("testthat")
> library("CeTF")
========================================
CeTF version 1.12.0
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
15.473 0.797 22.451
CeTF.Rcheck/CeTF-Ex.timings
| name | user | system | elapsed | |
| CeTFdemo | 0.002 | 0.002 | 0.005 | |
| CircosTargets | 0.000 | 0.001 | 0.003 | |
| InputData-methods | 0.016 | 0.002 | 0.030 | |
| NetworkData-methods | 0.020 | 0.007 | 0.041 | |
| OutputData-methods | 0.063 | 0.018 | 0.123 | |
| PCIT | 0.018 | 0.003 | 0.036 | |
| RIF | 0.005 | 0.001 | 0.011 | |
| RIFPlot | 0.596 | 0.029 | 0.959 | |
| RIF_input | 0.000 | 0.001 | 0.002 | |
| SmearPlot | 1.520 | 0.066 | 2.448 | |
| TFs | 0.001 | 0.001 | 0.002 | |
| bivar.awk | 0.001 | 0.000 | 0.002 | |
| clustCoef | 0.050 | 0.003 | 0.081 | |
| clustCoefPercentage | 0.028 | 0.002 | 0.048 | |
| densityPlot | 1.664 | 0.053 | 2.592 | |
| diffusion | 0 | 0 | 0 | |
| enrichPlot | 0.830 | 0.014 | 1.209 | |
| enrichdemo | 0.001 | 0.001 | 0.002 | |
| expDiff | 0.372 | 0.012 | 0.528 | |
| getDE-methods | 0.014 | 0.002 | 0.022 | |
| getData-methods | 0.013 | 0.002 | 0.021 | |
| getEnrich | 0 | 0 | 0 | |
| getGroupGO | 0 | 0 | 0 | |
| heatPlot | 2.033 | 0.032 | 3.033 | |
| histPlot | 0.384 | 0.007 | 0.608 | |
| netConditionsPlot | 1.385 | 0.045 | 2.151 | |
| netGOTFPlot | 0.000 | 0.000 | 0.001 | |
| normExp | 0.092 | 0.008 | 0.147 | |
| pcitC | 0.030 | 0.003 | 0.050 | |
| refGenes | 0.000 | 0.001 | 0.001 | |
| runAnalysis | 1.043 | 0.018 | 1.619 | |
| simCounts | 0.001 | 0.001 | 0.005 | |
| simNorm | 0.001 | 0.001 | 0.003 | |
| tolerance | 0.001 | 0.001 | 0.001 | |