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BioC 3.5: CHECK report for CATALYST on veracruz2

This page was generated on 2017-10-18 14:35:35 -0400 (Wed, 18 Oct 2017).

Package 175/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.1.1
Helena Lucia Crowell
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/CATALYST
Branch: RELEASE_3_5
Last Commit: 1bcc68a
Last Changed Date: 2017-05-13 03:30:47 -0400 (Sat, 13 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CATALYST
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CATALYST_1.1.1.tar.gz
StartedAt: 2017-10-18 01:23:09 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:24:57 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 108.7 seconds
RetCode: 0
Status:  OK 
CheckDir: CATALYST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CATALYST_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CATALYST.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CATALYST’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    9.8Mb
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
normCytof 8.581  0.090   9.026
estTrim   4.896  0.125   5.215
plotMahal 4.881  0.081   5.110
* 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/CATALYST.Rcheck/00check.log’
for details.


CATALYST.Rcheck/00install.out:

* installing *source* package ‘CATALYST’ ...
** 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 (CATALYST)

CATALYST.Rcheck/CATALYST-Ex.timings:

nameusersystemelapsed
applyCutoffs2.8370.0713.013
assignPrelim1.8970.0522.018
compCytof2.1320.0692.277
computeSpillmat1.8490.0712.011
concatFCS0.0580.0040.064
data0.0040.0020.005
dbFrame-methods1.7900.0711.930
estCutoffs1.8760.0541.960
estTrim4.8960.1255.215
normCytof8.5810.0909.026
outFCS2.5180.0692.682
plotEvents2.7900.0582.912
plotMahal4.8810.0815.110
plotSpillmat2.0470.0732.227
plotYields3.1200.0653.312