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CHECK report for CeTF on malbec1

This page was generated on 2021-04-18 12:03:42 -0400 (Sun, 18 Apr 2021).

To the developers/maintainers of the CeTF package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 263/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CeTF 1.2.4  (landing page)
Carlos Alberto Oliveira de Biagi Junior
Snapshot Date: 2021-04-17 14:51:09 -0400 (Sat, 17 Apr 2021)
URL: https://git.bioconductor.org/packages/CeTF
Branch: RELEASE_3_12
Last Commit: 2896169
Last Changed Date: 2020-11-23 09:24:27 -0400 (Mon, 23 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CeTF
Version: 1.2.4
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CeTF.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CeTF_1.2.4.tar.gz
StartedAt: 2021-04-17 23:15:46 -0400 (Sat, 17 Apr 2021)
EndedAt: 2021-04-17 23:21:07 -0400 (Sat, 17 Apr 2021)
EllapsedTime: 320.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CeTF.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CeTF.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CeTF_1.2.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CeTF.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CeTF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CeTF’ version ‘1.2.4’
* 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
* 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 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 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/CeTF.Rcheck/00check.log’
for details.



Installation output

CeTF.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CeTF
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘CeTF’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PCIT.cpp -o PCIT.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o CeTF.so PCIT.o RcppExports.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 1.2.4
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 
 16.868   0.512  18.788 

Example timings

CeTF.Rcheck/CeTF-Ex.timings

nameusersystemelapsed
CeTFdemo0.0040.0000.002
CircosTargets000
InputData-methods0.0440.0000.043
NetworkData-methods0.0320.0000.029
OutputData-methods0.0440.0120.055
PCIT0.0240.0000.025
RIF0.1080.0000.105
RIFPlot0.7160.0120.731
RIF_input0.0040.0000.001
SmearPlot2.6840.0282.714
TFs0.0040.0000.002
bivar.awk0.0000.0000.001
clustCoef0.0320.0040.034
clustCoefPercentage0.0240.0000.025
densityPlot1.6080.0521.664
diffusion000
enrichPlot0.9360.0000.942
enrichdemo0.0000.0000.001
expDiff0.3040.0000.307
getDE-methods0.0160.0040.021
getData-methods0.0240.0040.028
getEnrich000
getGroupGO000
heatPlot1.4040.0001.408
histPlot0.3640.0000.365
netConditionsPlot2.4000.0122.418
netGOTFPlot000
normExp0.0800.0080.087
pcitC0.020.000.02
refGenes0.0000.0000.001
runAnalysis0.3320.0120.344
simCounts0.0000.0000.001
simNorm0.0040.0000.001
tolerance0.0000.0000.001