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CHECK report for sscu on malbec2

This page was generated on 2019-04-09 11:45:36 -0400 (Tue, 09 Apr 2019).

Package 1554/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sscu 2.13.0
Yu Sun
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/sscu
Branch: master
Last Commit: 072c8eb
Last Changed Date: 2018-10-30 11:54:35 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: sscu
Version: 2.13.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sscu.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sscu_2.13.0.tar.gz
StartedAt: 2019-04-09 03:52:11 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:53:47 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 96.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: sscu.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sscu.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sscu_2.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/sscu.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sscu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sscu’ version ‘2.13.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘sscu’ can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘sscu.Rmd’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/sscu.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
op_corre_CodonW  14.241  0.019  14.310
op_corre_NCprime 11.734  0.008  11.799
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/sscu.Rcheck/00check.log’
for details.



Installation output

sscu.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL sscu
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘sscu’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (sscu)

Tests output


Example timings

sscu.Rcheck/sscu-Ex.timings

nameusersystemelapsed
akashi_test0.0180.0000.125
genomic_gc30.4460.0110.862
low_frequency_op0.9370.0521.220
op_corre_CodonW14.241 0.01914.310
op_corre_NCprime11.734 0.00811.799
op_highly0.8490.0040.853
op_highly_stats1.1630.0041.176
s_index0.3560.0080.365