Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for SigFuge on merida1

This page was generated on 2019-04-16 11:57:00 -0400 (Tue, 16 Apr 2019).

Package 1441/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SigFuge 1.20.0
Patrick Kimes
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/SigFuge
Branch: RELEASE_3_8
Last Commit: f216ee5
Last Changed Date: 2018-11-29 14:32:54 -0400 (Thu, 29 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SigFuge
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SigFuge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SigFuge_1.20.0.tar.gz
StartedAt: 2019-04-16 02:47:53 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:50:12 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 139.1 seconds
RetCode: 0
Status:  OK 
CheckDir: SigFuge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SigFuge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SigFuge_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SigFuge.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SigFuge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SigFuge’ version ‘1.20.0’
* 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 ‘SigFuge’ 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
SFfigure: no visible binding for global variable ‘base’
SFfigure: no visible binding for global variable ‘s’
SFfigure: no visible binding for global variable ‘e’
SFfigure: no visible global function definition for ‘rgb’
SFfigure: no visible global function definition for ‘hcl’
SFfigure: no visible binding for global variable ‘cluster’
SFfigure: no visible binding for global variable ‘median’
SFfigure: no visible binding for global variable ‘x’
SFfigure: no visible binding for global variable ‘y1’
SFfigure: no visible binding for global variable ‘label’
SFfigure: no visible binding for global variable ‘value’
SFfigure: no visible binding for global variable ‘Clusters’
SFfigure: no visible binding for global variable ‘y2’
SFfigure: no visible global function definition for ‘pdf’
SFfigure: no visible global function definition for ‘dev.off’
SFlabels: no visible global function definition for ‘kmeans’
SFnormalize : <anonymous>: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  Clusters base cluster dev.off e hcl kmeans label median pdf rgb s
  value x y1 y2
Consider adding
  importFrom("grDevices", "dev.off", "hcl", "pdf", "rgb")
  importFrom("stats", "kmeans", "median")
to your NAMESPACE file.
* 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
SFfigure 23.515  1.020  25.075
SFpval   12.606  0.681  13.592
* 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-3.8-bioc/meat/SigFuge.Rcheck/00check.log’
for details.



Installation output

SigFuge.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SigFuge
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SigFuge’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SigFuge)

Tests output


Example timings

SigFuge.Rcheck/SigFuge-Ex.timings

nameusersystemelapsed
SFfigure23.515 1.02025.075
SFlabels1.1100.0491.178
SFnormalize0.4520.0240.478
SFpval12.606 0.68113.592