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CHECK report for slinky on tokay2

This page was generated on 2019-04-09 12:40:39 -0400 (Tue, 09 Apr 2019).

Package 1511/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
slinky 1.1.1
Eric J. Kort
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/slinky
Branch: master
Last Commit: f831561
Last Changed Date: 2019-02-28 15:53:10 -0400 (Thu, 28 Feb 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: slinky
Version: 1.1.1
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_1.1.1.tar.gz
StartedAt: 2019-04-09 06:02:14 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:10:20 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 485.4 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_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/slinky.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.1.1'
* 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 9.89   0.64   11.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
     user system elapsed
rzs 12.11   0.33   13.22
* 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_1.1.1.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_1.1.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL slinky_1.1.1.zip && rm slinky_1.1.1.tar.gz slinky_1.1.1.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 1173k  100 1173k    0     0  15.6M      0 --:--:-- --:--:-- --:--:-- 17.1M

install for i386

* installing *source* package 'slinky' ...
** 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  
    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_1.1.1.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 Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  91.07   22.62  122.65 

slinky.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  84.29   18.62  114.62 

Example timings

slinky.Rcheck/examples_i386/slinky-Ex.timings

nameusersystemelapsed
Slinky-class0.500.154.94
closeAll0.020.020.08
clue0.250.010.54
clueCount0.040.000.16
clueInstances0.210.000.48
clueVehicle0.350.001.86
coerce0.260.000.30
colnames0.040.020.10
controls0.390.001.18
diffexp3.070.523.63
download000
loadL1K0.680.011.50
metadata0.030.000.07
nrow0.030.000.06
readGCTX0.090.000.14
rownames0.030.000.08
rzs 9.89 0.6411.35
subset0.050.020.11

slinky.Rcheck/examples_x64/slinky-Ex.timings

nameusersystemelapsed
Slinky-class0.420.020.94
closeAll0.020.010.06
clue0.210.000.46
clueCount0.040.000.13
clueInstances0.170.030.45
clueVehicle0.350.001.82
coerce0.900.000.93
colnames0.040.000.07
controls0.450.001.22
diffexp3.370.583.98
download000
loadL1K0.610.031.47
metadata0.000.010.05
nrow0.010.000.04
readGCTX0.080.020.11
rownames0.030.000.06
rzs12.11 0.3313.22
subset0.050.010.10