Multiple platform build/check report for BioC 3.13 - CHECK results for CeTF on tokay2

Package: CeTF

Version: 1.4.5

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CeTF.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CeTF_1.4.5.tar.gz

StartedAt: 2021-10-14 20:53:17 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 21:00:42 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 445.7 seconds

RetCode: 0

Status: OK

CheckDir: CeTF.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CeTF.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CeTF_1.4.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CeTF.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/CeTF/libs/i386/CeTF.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/CeTF/libs/x64/CeTF.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/CeTF.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CeTF_1.4.5.tar.gz && rm -rf CeTF.buildbin-libdir && mkdir CeTF.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CeTF.buildbin-libdir CeTF_1.4.5.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CeTF_1.4.5.zip && rm CeTF_1.4.5.tar.gz CeTF_1.4.5.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 12 1806k   12  221k    0     0   762k      0  0:00:02 --:--:--  0:00:02  763k
100 1806k  100 1806k    0     0  2224k      0 --:--:-- --:--:-- --:--:-- 2224k

install for i386

* installing *source* package 'CeTF' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PCIT.cpp -o PCIT.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CeTF.dll tmp.def PCIT.o RcppExports.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CeTF.buildbin-libdir/00LOCK-CeTF/00new/CeTF/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CeTF'
    finding HTML links ... done
    CeTF-class                              html  
    CeTFdemo                                html  
    CircosTargets                           html  
    InputData-methods                       html  
    NetworkData-methods                     html  
    OutputData-methods                      html  
    PCIT                                    html  
    RIF                                     html  
    RIFPlot                                 html  
    RIF_input                               html  
    SmearPlot                               html  
    TFs                                     html  
    bivar.awk                               html  
    clustCoef                               html  
    clustCoefPercentage                     html  
    densityPlot                             html  
    diffusion                               html  
    enrichPlot                              html  
    enrichdemo                              html  
    expDiff                                 html  
    getDE-methods                           html  
    getData-methods                         html  
    getEnrich                               html  
    getGroupGO                              html  
    heatPlot                                html  
    histPlot                                html  
    netConditionsPlot                       html  
    netGOTFPlot                             html  
    normExp                                 html  
    pcitC                                   html  
    refGenes                                html  
    runAnalysis                             html  
    simCounts                               html  
    simNorm                                 html  
    tolerance                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CeTF' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PCIT.cpp -o PCIT.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CeTF.dll tmp.def PCIT.o RcppExports.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CeTF.buildbin-libdir/CeTF/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CeTF' as CeTF_1.4.5.zip
* DONE (CeTF)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CeTF' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  14.31    1.60   17.21


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  13.48    0.92   15.64

name	user	system	elapsed
CeTFdemo	0.00	0.01	0.02
CircosTargets	0	0	0
InputData-methods	0.04	0.02	0.05
NetworkData-methods	0.01	0.01	0.03
OutputData-methods	0.05	0.00	0.04
PCIT	0.01	0.00	0.02
RIF	0.02	0.00	0.02
RIFPlot	0.55	0.02	0.56
RIF_input	0	0	0
SmearPlot	1.47	0.08	1.55
TFs	0	0	0
bivar.awk	0	0	0
clustCoef	0.06	0.00	0.06
clustCoefPercentage	0.02	0.00	0.02
densityPlot	1.67	0.57	2.25
diffusion	0	0	0
enrichPlot	0.61	0.02	0.63
enrichdemo	0.00	0.02	0.01
expDiff	0.31	0.01	0.33
getDE-methods	0.83	0.00	0.83
getData-methods	0.01	0.00	0.02
getEnrich	0	0	0
getGroupGO	0	0	0
heatPlot	0.88	0.10	0.97
histPlot	0.26	0.03	0.29
netConditionsPlot	1.02	0.07	1.10
netGOTFPlot	0	0	0
normExp	0.14	0.02	0.15
pcitC	0.03	0.00	0.03
refGenes	0	0	0
runAnalysis	1.08	0.02	1.10
simCounts	0	0	0
simNorm	0.00	0.01	0.01
tolerance	0	0	0

name	user	system	elapsed
CeTFdemo	0.00	0.01	0.02
CircosTargets	0	0	0
InputData-methods	0.00	0.02	0.02
NetworkData-methods	0.02	0.00	0.02
OutputData-methods	0.03	0.00	0.03
PCIT	0.02	0.00	0.01
RIF	0.00	0.01	0.02
RIFPlot	0.51	0.02	0.53
RIF_input	0.00	0.01	0.02
SmearPlot	1.33	0.07	1.39
TFs	0	0	0
bivar.awk	0	0	0
clustCoef	0.03	0.00	0.03
clustCoefPercentage	0.02	0.00	0.01
densityPlot	1.5	0.0	1.5
diffusion	0	0	0
enrichPlot	0.54	0.01	0.57
enrichdemo	0	0	0
expDiff	0.25	0.02	0.26
getDE-methods	0.04	0.00	0.03
getData-methods	0.01	0.00	0.02
getEnrich	0	0	0
getGroupGO	0	0	0
heatPlot	1.22	0.03	1.25
histPlot	1.14	0.01	1.15
netConditionsPlot	1.27	0.02	1.32
netGOTFPlot	0	0	0
normExp	0.09	0.02	0.11
pcitC	0.03	0.00	0.03
refGenes	0	0	0
runAnalysis	0.36	0.01	0.37
simCounts	0	0	0
simNorm	0	0	0
tolerance	0	0	0

CHECK results for CeTF on tokay2

Summary

Command output

Installation output

Tests output

Example timings