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

Package: ModCon

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ModCon.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ModCon_1.0.0.tar.gz

StartedAt: 2021-10-15 02:10:24 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:19:14 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 529.6 seconds

RetCode: 0

Status: OK

CheckDir: ModCon.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:ModCon.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ModCon_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ModCon.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 'ModCon/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ModCon' version '1.0.0'
* 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 whether package 'ModCon' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    data      1.1Mb
    extdata   4.0Mb
* 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
* 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
slidingWindowHZEImanipulation 23.36   0.03   23.39
ModCon                        19.26   0.33   33.56
changeSequenceHZEI             7.10   0.16    7.91
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
slidingWindowHZEImanipulation 22.15   0.00   22.14
ModCon                        20.43   0.32   34.94
changeSequenceHZEI             6.48   0.08    7.25
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/ModCon.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/ModCon_1.0.0.tar.gz && rm -rf ModCon.buildbin-libdir && mkdir ModCon.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ModCon.buildbin-libdir ModCon_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ModCon_1.0.0.zip && rm ModCon_1.0.0.tar.gz ModCon_1.0.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1778k  100 1778k    0     0  4048k      0 --:--:-- --:--:-- --:--:-- 4060k

install for i386

* installing *source* package 'ModCon' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ModCon'
    finding HTML links ... done
    Codons                                  html  
    ModCon                                  html  
    calculateHZEIint                        html  
    calculateMaxEntScanScore                html  
    cds                                     html  
    changeSequenceHZEI                      html  
    createCodonMatrix                       html  
    createFilialSequencePopulation          html  
    decreaseGTsiteStrength                  html  
    degradeSAs                              html  
    degradeSDs                              html  
    generateRandomCodonsPerAA               html  
    getOverlappingVectorsFromVector         html  
    hbg                                     html  
    hex                                     html  
    increaseGTsiteStrength                  html  
    mutatePopulation                        html  
    recombineTwoSequences                   html  
    selectBestAndMean                       html  
    selectMatingIndividuals                 html  
    slidingWindowHZEImanipulation           html  
    startModConApp                          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 'ModCon' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ModCon' as ModCon_1.0.0.zip
* DONE (ModCon)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ModCon' 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(ModCon)
Loading required package: data.table
Loading required package: parallel
> 
> test_check("ModCon")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 106.45    0.93  158.07


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(ModCon)
Loading required package: data.table
Loading required package: parallel
> 
> test_check("ModCon")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 122.14    1.89  174.48

name	user	system	elapsed
Codons	0	0	0
ModCon	19.26	0.33	33.56
calculateHZEIint	0	0	0
calculateMaxEntScanScore	0.00	0.00	0.66
cds	0	0	0
changeSequenceHZEI	7.10	0.16	7.91
createCodonMatrix	0	0	0
createFilialSequencePopulation	0	0	0
decreaseGTsiteStrength	0.40	0.09	0.50
degradeSAs	2.36	0.10	2.78
degradeSDs	1.29	0.07	1.36
generateRandomCodonsPerAA	0	0	0
getOverlappingVectorsFromVector	0	0	0
hbg	0.53	0.14	0.67
hex	0.07	0.02	0.09
increaseGTsiteStrength	0.27	0.06	0.33
mutatePopulation	0.01	0.00	0.01
recombineTwoSequences	0	0	0
selectBestAndMean	0.00	0.00	0.46
selectMatingIndividuals	0.02	0.02	0.54
slidingWindowHZEImanipulation	23.36	0.03	23.39
startModConApp	0	0	0

name	user	system	elapsed
Codons	0.01	0.00	0.02
ModCon	20.43	0.32	34.94
calculateHZEIint	0	0	0
calculateMaxEntScanScore	0.00	0.00	0.56
cds	0	0	0
changeSequenceHZEI	6.48	0.08	7.25
createCodonMatrix	0	0	0
createFilialSequencePopulation	0	0	0
decreaseGTsiteStrength	0.56	0.12	0.69
degradeSAs	2.32	0.27	2.92
degradeSDs	1.23	0.11	1.34
generateRandomCodonsPerAA	0	0	0
getOverlappingVectorsFromVector	0	0	0
hbg	0.42	0.10	0.53
hex	0.07	0.04	0.10
increaseGTsiteStrength	0.34	0.04	0.39
mutatePopulation	0	0	0
recombineTwoSequences	0	0	0
selectBestAndMean	0.00	0.02	0.50
selectMatingIndividuals	0.01	0.00	0.50
slidingWindowHZEImanipulation	22.15	0.00	22.14
startModConApp	0	0	0

CHECK results for ModCon on tokay2

Summary

Command output

Installation output

Tests output

Example timings