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BioC 3.4: CHECK report for pandaR on malbec1

This page was generated on 2017-04-15 16:12:57 -0400 (Sat, 15 Apr 2017).

Package 883/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pandaR 1.6.0
Joseph N. Paulson , Dan Schlauch
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/pandaR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pandaR
Version: 1.6.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings pandaR_1.6.0.tar.gz
StartedAt: 2017-04-15 00:17:51 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:18:48 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 56.3 seconds
RetCode: 0
Status:  OK 
CheckDir: pandaR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings pandaR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/pandaR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pandaR/DESCRIPTION’ ... OK
* this is package ‘pandaR’ version ‘1.6.0’
* 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 ‘pandaR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
* checking package 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 ... NOTE
dFunction: no visible global function definition for ‘cor’
importPandaMatlab: no visible global function definition for
  ‘read.delim’
normalizeNetwork: no visible global function definition for ‘sd’
panda: no visible global function definition for ‘cor’
panda: no visible global function definition for ‘aggregate’
plot.panda: no visible global function definition for ‘hist’
plotCommunityDetection: no visible global function definition for
  ‘title’
plotZbyTF: no visible global function definition for ‘aggregate’
prepResult: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  aggregate cor hist pnorm read.delim sd title
Consider adding
  importFrom("graphics", "hist", "title")
  importFrom("stats", "aggregate", "cor", "pnorm", "sd")
  importFrom("utils", "read.delim")
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 ... NOTE
S3 methods shown with full name in documentation object 'plot.panda':
  ‘plot.panda’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
panda 5.892  0.032   5.927
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/pandaR.Rcheck/00check.log’
for details.


pandaR.Rcheck/00install.out:

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

pandaR.Rcheck/pandaR-Ex.timings:

nameusersystemelapsed
calcDegree0.6440.0120.654
calcDegreeDifference000
importPandaMatlab0.0000.0000.001
panda5.8920.0325.927
plot.panda0.0840.0040.086
plotCommunityDetection0.1120.0000.113
plotGraph0.2200.0040.224
plotZ0.8320.0000.832
plotZbyTF2.0480.0082.060
print.panda0.0960.0000.155
subnetwork0.1960.0000.241
summary.panda0.2080.0000.221
targetedGenes0.1600.0120.208
testMotif3.3600.0044.787
topedges0.1760.0000.178