Multiple platform build/check report for BioC 3.12 - CHECK report for nanotatoR on tokay1

Package: nanotatoR

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nanotatoR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings nanotatoR_1.6.0.tar.gz

StartedAt: 2021-05-06 05:00:56 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 05:07:02 -0400 (Thu, 06 May 2021)

EllapsedTime: 366.4 seconds

RetCode: 0

Status: OK

CheckDir: nanotatoR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nanotatoR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings nanotatoR_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/nanotatoR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nanotatoR/DESCRIPTION' ... OK
* this is package 'nanotatoR' version '1.6.0'
* 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 'nanotatoR' 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
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
gene_list_generation 3.22   0.03     7.5
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
gene_list_generation 4.02   0.11    8.58
clinvar_gene         3.42   0.19    5.54
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/nanotatoR_1.6.0.tar.gz && rm -rf nanotatoR.buildbin-libdir && mkdir nanotatoR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nanotatoR.buildbin-libdir nanotatoR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL nanotatoR_1.6.0.zip && rm nanotatoR_1.6.0.tar.gz nanotatoR_1.6.0.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  630k  100  630k    0     0  19.8M      0 --:--:-- --:--:-- --:--:-- 20.5M

install for i386

* installing *source* package 'nanotatoR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nanotatoR'
    finding HTML links ... done
    DGV_extraction                          html  
    Decipher_extraction                     html  
    buildrunBNBedFiles                      html  
    clinvar_gene                            html  
    cohortFrequency                         html  
    compSmapbed                             html  
    gene_extraction                         html  
    gene_list_generation                    html  
    gtr_gene                                html  
    internalFrequency                       html  
    makeMergedSVData                        html  
    makeMergedSmapData                      html  
    nanotatoR                               html  
    nanotatoR_main                          html  
    nonOverlapGenes                         html  
    omim_gene                               html  
    overlapGenes                            html  
    readBNBedFiles                          html  
    readSMap                                html  
    run_bionano_filter                      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 'nanotatoR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nanotatoR' as nanotatoR_1.6.0.zip
* DONE (nanotatoR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'nanotatoR' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(nanotatoR)

> 
> test_check("nanotatoR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  12.70    0.76   13.45


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(nanotatoR)

> 
> test_check("nanotatoR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  12.56    0.34   12.90

name	user	system	elapsed
DGV_extraction	0	0	0
Decipher_extraction	0.28	0.14	0.42
buildrunBNBedFiles	0.17	0.05	0.22
clinvar_gene	2.63	0.41	4.98
cohortFrequency	0.28	0.00	0.28
compSmapbed	0.23	0.01	0.25
gene_extraction	0.27	0.00	0.89
gene_list_generation	3.22	0.03	7.50
gtr_gene	0.17	0.02	0.74
internalFrequency	0.59	0.00	1.07
makeMergedSVData	0.16	0.00	0.91
makeMergedSmapData	0	0	0
nanotatoR	0.01	0.00	0.02
nonOverlapGenes	0.44	0.00	0.43
omim_gene	0.16	0.01	1.24
overlapGenes	0.22	0.00	0.22
readBNBedFiles	0	0	0
readSMap	0.02	0.02	0.03
run_bionano_filter	0	0	0

name	user	system	elapsed
DGV_extraction	0	0	0
Decipher_extraction	0.25	0.02	0.26
buildrunBNBedFiles	0.14	0.00	0.14
clinvar_gene	3.42	0.19	5.54
cohortFrequency	0.23	0.00	0.24
compSmapbed	0.19	0.01	0.20
gene_extraction	0.26	0.00	0.87
gene_list_generation	4.02	0.11	8.58
gtr_gene	0.25	0.00	1.12
internalFrequency	0.68	0.05	0.72
makeMergedSVData	0.21	0.00	0.22
makeMergedSmapData	0	0	0
nanotatoR	0	0	0
nonOverlapGenes	0.40	0.00	0.39
omim_gene	0.28	0.00	1.44
overlapGenes	0.43	0.02	0.45
readBNBedFiles	0.02	0.00	0.02
readSMap	0.06	0.00	0.06
run_bionano_filter	0	0	0

CHECK report for nanotatoR on tokay1

Summary

Command output

Installation output

Tests output

Example timings