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CHECK report for slinky on tokay2

This page was generated on 2019-10-16 12:41:51 -0400 (Wed, 16 Oct 2019).

Package 1541/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
slinky 1.2.2
Eric J. Kort
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/slinky
Branch: RELEASE_3_9
Last Commit: 3a53ff8
Last Changed Date: 2019-10-04 12:48:46 -0400 (Fri, 04 Oct 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: slinky
Version: 1.2.2
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:slinky.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings slinky_1.2.2.tar.gz
StartedAt: 2019-10-16 07:12:33 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:20:00 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 447.7 seconds
RetCode: 0
Status:  OK  
CheckDir: slinky.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:slinky.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings slinky_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/slinky.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'slinky/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'slinky' version '1.2.2'
* 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 'slinky' 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 or elapsed time > 5s
    user system elapsed
rzs 8.18    0.7    9.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
     user system elapsed
rzs 17.71   0.54   18.91
* 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


Installation output

slinky.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/slinky_1.2.2.tar.gz && rm -rf slinky.buildbin-libdir && mkdir slinky.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=slinky.buildbin-libdir slinky_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL slinky_1.2.2.zip && rm slinky_1.2.2.tar.gz slinky_1.2.2.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 1173k  100 1173k    0     0  14.6M      0 --:--:-- --:--:-- --:--:-- 15.9M

install for i386

* installing *source* package 'slinky' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'slinky'
    finding HTML links ... done
    Slinky-class                            html  
    chDir                                   html  
    closeAll                                html  
    clue                                    html  
    clueCount                               html  
    clueInstances                           html  
    clueVehicle                             html  
    coerce                                  html  
    colnames                                html  
    controls                                html  
    diffexp                                 html  
    download                                html  
    get_metadata                            html  
    ks                                      html  
    loadL1K                                 html  
    finding level-2 HTML links ... done

    metadata                                html  
    nrow                                    html  
    readGCTX                                html  
    rownames                                html  
    rzs                                     html  
    slinky-internal                         html  
    subset                                  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 'slinky' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'slinky' as slinky_1.2.2.zip
* DONE (slinky)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'slinky' successfully unpacked and MD5 sums checked

Tests output

slinky.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(slinky)
> 
> test_check("slinky")
== testthat results  ===========================================================
[ OK: 46 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  85.09   19.81  111.73 

slinky.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(slinky)
> 
> test_check("slinky")
== testthat results  ===========================================================
[ OK: 46 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  67.03   16.42   90.34 

Example timings

slinky.Rcheck/examples_i386/slinky-Ex.timings

nameusersystemelapsed
Slinky-class0.390.311.63
closeAll0.030.020.06
clue0.170.000.34
clueCount0.050.020.13
clueInstances0.190.010.36
clueVehicle0.280.001.78
coerce0.220.100.33
colnames0.050.000.08
controls0.360.011.01
diffexp2.640.393.06
download000
get_metadata0.030.020.08
loadL1K0.750.001.39
metadata0.030.000.04
nrow0.050.000.06
readGCTX0.060.060.14
rownames0.050.000.07
rzs8.180.709.59
subset0.110.000.12

slinky.Rcheck/examples_x64/slinky-Ex.timings

nameusersystemelapsed
Slinky-class1.090.051.42
closeAll0.060.000.09
clue0.200.030.39
clueCount0.030.020.11
clueInstances0.210.010.37
clueVehicle0.370.001.72
coerce0.240.060.33
colnames0.060.010.09
controls0.440.001.06
diffexp3.140.974.14
download000
get_metadata0.060.000.08
loadL1K0.680.031.42
metadata0.060.000.08
nrow0.060.000.07
readGCTX0.090.040.16
rownames0.080.000.09
rzs17.71 0.5418.91
subset0.100.000.11