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This page was generated on 2023-10-16 11:35:15 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 305/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CeTF 1.12.0  (landing page)
Carlos Alberto Oliveira de Biagi Junior
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/CeTF
git_branch: RELEASE_3_17
git_last_commit: f64ddb7
git_last_commit_date: 2023-04-25 11:14:38 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for CeTF on nebbiolo1


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.

raw results


Summary

Package: CeTF
Version: 1.12.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CeTF.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CeTF_1.12.0.tar.gz
StartedAt: 2023-10-15 19:58:43 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 20:05:24 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 400.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CeTF.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CeTF.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CeTF_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CeTF.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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 ...
  ‘CeTF.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/CeTF.Rcheck/00check.log’
for details.



Installation output

CeTF.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CeTF
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘CeTF’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PCIT.cpp -o PCIT.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o CeTF.so PCIT.o RcppExports.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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)

Tests output

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: x86_64-pc-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.

> 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 
 12.919   0.773  13.679 

Example timings

CeTF.Rcheck/CeTF-Ex.timings

nameusersystemelapsed
CeTFdemo0.0020.0000.002
CircosTargets0.0010.0000.001
InputData-methods0.0170.0000.017
NetworkData-methods0.0160.0080.024
OutputData-methods0.0220.0200.042
PCIT0.0160.0000.016
RIF0.0010.0040.004
RIFPlot0.5380.0080.546
RIF_input0.0010.0000.001
SmearPlot1.3880.0321.419
TFs0.0010.0000.001
bivar.awk0.0010.0000.001
clustCoef0.0260.0030.028
clustCoefPercentage0.8070.0200.828
densityPlot1.3250.0961.421
diffusion000
enrichPlot0.6190.0470.666
enrichdemo0.0010.0000.001
expDiff0.3080.0080.316
getDE-methods0.0140.0040.017
getData-methods0.0150.0000.015
getEnrich000
getGroupGO0.0010.0000.000
heatPlot1.0660.0481.114
histPlot0.3240.0080.332
netConditionsPlot1.1230.0361.159
netGOTFPlot0.0010.0000.001
normExp0.130.020.15
pcitC0.0190.0000.019
refGenes0.0010.0000.001
runAnalysis1.0970.0481.145
simCounts0.0010.0000.001
simNorm0.0010.0000.001
tolerance0.0010.0000.000