Multiple platform build/check report for BioC 3.11 - CHECK report for ASSIGN on tokay2

Package: ASSIGN

Version: 1.24.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASSIGN.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ASSIGN_1.24.0.tar.gz

StartedAt: 2020-10-17 01:39:42 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 01:41:01 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 78.8 seconds

RetCode: 0

Status: OK

CheckDir: ASSIGN.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASSIGN.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ASSIGN_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ASSIGN.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ASSIGN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASSIGN' version '1.24.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ASSIGN' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/ASSIGN.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ASSIGN_1.24.0.tar.gz && rm -rf ASSIGN.buildbin-libdir && mkdir ASSIGN.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASSIGN.buildbin-libdir ASSIGN_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ASSIGN_1.24.0.zip && rm ASSIGN_1.24.0.tar.gz ASSIGN_1.24.0.zip
###
##############################################################################
##############################################################################


  % 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 1362k  100 1362k    0     0  10.1M      0 --:--:-- --:--:-- --:--:-- 10.7M

install for i386

* installing *source* package 'ASSIGN' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ASSIGN'
    finding HTML links ... done
    ComBat.step2                            html  
    assign.convergence                      html  
    assign.cv.output                        html  
    assign.mcmc                             html  
    assign.output                           html  
    assign.preprocess                       html  
    assign.summary                          html  
    assign.wrapper                          html  
    excludegenes                            html  
    gather_assign_results                   html  
    geneList1                               html  
    gfrn_geneList                           html  
    merge_drop                              html  
    optimizeGFRN                            html  
    pcaplot                                 html  
    runassignGFRN                           html  
    testData1                               html  
    trainingData1                           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 'ASSIGN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASSIGN' as ASSIGN_1.24.0.zip
* DONE (ASSIGN)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ASSIGN' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(ASSIGN)
> 
> test_check("ASSIGN")
== testthat results  ===========================================================
[ OK: 4 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   4.82    0.18    5.45


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(ASSIGN)
> 
> test_check("ASSIGN")
== testthat results  ===========================================================
[ OK: 4 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.73    0.17    3.89

name	user	system	elapsed
assign.convergence	0	0	0
assign.cv.output	2.76	0.25	3.41
assign.mcmc	0.75	0.18	0.93
assign.output	3.23	0.25	3.49
assign.preprocess	0.03	0.00	0.03
assign.summary	0.52	0.13	0.64
assign.wrapper	3.03	0.20	3.23
merge_drop	0	0	0
optimizeGFRN	0	0	0
runassignGFRN	0	0	0

name	user	system	elapsed
assign.convergence	0	0	0
assign.cv.output	1.98	0.15	2.15
assign.mcmc	0.80	0.13	0.92
assign.output	2.31	0.29	2.61
assign.preprocess	0.03	0.00	0.03
assign.summary	0.59	0.15	0.74
assign.wrapper	2.58	0.12	2.72
merge_drop	0	0	0
optimizeGFRN	0	0	0
runassignGFRN	0	0	0

CHECK report for ASSIGN on tokay2

Summary

Command output

Installation output

Tests output

Example timings