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CHECK report for SigCheck on celaya2

This page was generated on 2019-10-16 12:54:20 -0400 (Wed, 16 Oct 2019).

Package 1513/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SigCheck 2.16.0
Rory Stark
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/SigCheck
Branch: RELEASE_3_9
Last Commit: ff8694e
Last Changed Date: 2019-05-02 11:53:50 -0400 (Thu, 02 May 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: SigCheck
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SigCheck.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SigCheck_2.16.0.tar.gz
StartedAt: 2019-10-16 06:52:25 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:02:33 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 607.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SigCheck.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SigCheck.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SigCheck_2.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SigCheck.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SigCheck/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SigCheck’ version ‘2.16.0’
* 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 ‘SigCheck’ 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
* 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 ... NOTE
sigCheckKnown: no visible binding for global variable ‘knownSignatures’
Undefined global functions or variables:
  knownSignatures
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
sigCheckAll      157.365 34.384 192.572
sigCheckKnown     72.629 16.010  88.648
sigCheck          22.665  3.328  26.669
sigCheckPermuted  20.375  3.846  24.222
sigCheckPlot      18.820  4.056  22.936
sigCheckRandom    12.882  2.678  15.560
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/SigCheck.Rcheck/00check.log’
for details.



Installation output

SigCheck.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SigCheck
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SigCheck’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘signature’ in package ‘SigCheck’
** 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 (SigCheck)

Tests output


Example timings

SigCheck.Rcheck/SigCheck-Ex.timings

nameusersystemelapsed
SigCheckObject-class0.0060.0020.009
classifyResults0.0700.0180.089
knownSignatures0.0320.0070.039
nkiResults0.0320.0090.060
sigCheck22.665 3.32826.669
sigCheckAll157.365 34.384192.572
sigCheckKnown72.62916.01088.648
sigCheckPermuted20.375 3.84624.222
sigCheckPlot18.820 4.05622.936
sigCheckRandom12.882 2.67815.560