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BioC 3.5: CHECK report for sights on oaxaca

This page was generated on 2017-03-04 16:52:39 -0500 (Sat, 04 Mar 2017).

Package 1178/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sights 1.0.1
Elika Garg
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sights
Last Changed Rev: 126695 / Revision: 127142
Last Changed Date: 2017-02-11 11:24:51 -0500 (Sat, 11 Feb 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK NO, built version is LOWER than in internal repository!!!
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: sights
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sights_1.0.1.tar.gz
StartedAt: 2017-03-04 09:10:46 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 09:13:09 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 142.3 seconds
RetCode: 0
Status:  OK 
CheckDir: sights.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sights_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/sights.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sights/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sights’ version ‘1.0.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘sights’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
* 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 loading without being on the library search path ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
plotAutoco 5.416  0.024   5.456
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/sights.Rcheck/00check.log’
for details.


sights.Rcheck/00install.out:

* installing *source* package ‘sights’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sights)

sights.Rcheck/sights-Ex.timings:

nameusersystemelapsed
ex_dataMatrix0.0400.0020.042
inglese0.1680.0080.176
normLoess0.3400.0020.342
normMedFil0.3160.0020.317
normR0.0430.0030.045
normRobZ0.0050.0010.006
normSPAWN0.1640.0010.165
normSights0.0060.0000.007
normZ0.0040.0000.005
plot3d0.9460.0180.981
plotAutoco5.4160.0245.456
plotBox1.2610.0061.283
plotHeatmap2.4860.0142.518
plotHist0.4060.0020.409
plotIGFit0.4500.0110.461
plotScatter1.4060.0081.416
plotSights1.9190.0111.931
statFDR0.0520.0010.053
statRVM0.0670.0010.069
statSights0.2110.0010.213
statT0.0720.0000.073