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BioC 3.2: CHECK report for facopy on zin1

This page was generated on 2016-04-23 10:14:16 -0700 (Sat, 23 Apr 2016).

Package 333/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
facopy 1.4.1
David Mosen-Ansorena
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/facopy
Last Changed Rev: 112099 / Revision: 116712
Last Changed Date: 2016-01-03 05:36:06 -0800 (Sun, 03 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: facopy
Version: 1.4.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings facopy_1.4.1.tar.gz
StartedAt: 2016-04-23 00:30:13 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:33:04 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 170.9 seconds
RetCode: 0
Status:  OK 
CheckDir: facopy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings facopy_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/facopy.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘facopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘facopy’ version ‘1.4.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘cgdsr’ ‘coin’ ‘ggplot2’ ‘gridExtra’ ‘facopy.annot’ ‘grid’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘facopy’ can be installed ... [13s/13s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/31s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
facopyPlot   7.207  0.016   7.227
calculateCor 0.227  0.004   8.054
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/facopy.Rcheck/00check.log’
for details.


facopy.Rcheck/00install.out:

* installing *source* package ‘facopy’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (facopy)

facopy.Rcheck/facopy-Ex.timings:

nameusersystemelapsed
addFeatures2.1660.0162.189
addVariables0.080.000.08
alterationSummary0.9630.0040.966
calculateCor0.2270.0048.054
facopy2.2440.0082.254
facopyEnrichment0.0320.0040.036
facopyInfo-class0.0010.0000.001
facopyPlot7.2070.0167.227
getFacopyInfo0.0050.0000.014
myCalls0.0330.0000.034
myStudy0.0410.0000.041
myVariables0.0040.0000.003
plotBar0.7230.0080.731
plotHist1.1370.0041.140
plotPCA0.1130.0000.113
plotZoom0.1640.0000.164
preview0.8440.0040.850
readCNData0.0000.0000.001
variableCor0.050.000.05
variableSummary0.1130.0000.128