Back to Multiple platform build/check report for BioC 3.13
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-20 15:05:37 -0400 (Mon, 20 Sep 2021).

CHECK results for CeTF on machv2

To the developers/maintainers of the CeTF package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 274/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CeTF 1.4.5  (landing page)
Carlos Alberto Oliveira de Biagi Junior
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/CeTF
git_branch: RELEASE_3_13
git_last_commit: bd93884
git_last_commit_date: 2021-09-09 09:27:19 -0400 (Thu, 09 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CeTF
Version: 1.4.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CeTF.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CeTF_1.4.5.tar.gz
StartedAt: 2021-09-19 17:09:27 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 17:15:43 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 375.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CeTF.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CeTF.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CeTF_1.4.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CeTF.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.4.5’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/CeTF.Rcheck/00check.log’
for details.



Installation output

CeTF.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CeTF
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CeTF’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c PCIT.cpp -o PCIT.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.1/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)

Tests output

CeTF.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 1.4.5
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 
 19.788   0.950  21.995 

Example timings

CeTF.Rcheck/CeTF-Ex.timings

nameusersystemelapsed
CeTFdemo0.0040.0010.005
CircosTargets0.0000.0010.001
InputData-methods0.0240.0030.027
NetworkData-methods0.0270.0120.039
OutputData-methods0.0770.0350.113
PCIT0.0250.0030.030
RIF0.0050.0010.007
RIFPlot0.6160.0250.642
RIF_input0.0010.0000.002
SmearPlot1.2700.0461.319
TFs0.0010.0010.002
bivar.awk0.0010.0010.001
clustCoef0.0370.0030.039
clustCoefPercentage0.0860.0040.090
densityPlot1.9610.0702.034
diffusion000
enrichPlot0.9340.0100.945
enrichdemo0.0010.0010.002
expDiff0.4070.0130.419
getDE-methods0.0230.0030.027
getData-methods0.0160.0020.017
getEnrich0.0010.0010.001
getGroupGO000
heatPlot1.8750.0251.902
histPlot0.3620.0030.365
netConditionsPlot1.6770.0581.737
netGOTFPlot0.0000.0010.001
normExp0.1240.0100.134
pcitC0.0250.0030.028
refGenes0.0020.0020.002
runAnalysis0.4460.0310.477
simCounts0.0010.0010.002
simNorm0.0010.0010.001
tolerance0.0000.0010.001