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BioC 3.0: CHECK report for PANR on perceval

This page was generated on 2015-04-10 09:56:15 -0700 (Fri, 10 Apr 2015).

Package 638/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PANR 1.12.1
Xin Wang
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PANR
Last Changed Rev: 101038 / Revision: 102249
Last Changed Date: 2015-03-23 08:45:37 -0700 (Mon, 23 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: PANR
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PANR_1.12.1.tar.gz
StartedAt: 2015-04-10 04:38:16 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:39:28 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 71.8 seconds
RetCode: 0
Status:  OK 
CheckDir: PANR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PANR_1.12.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/PANR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PANR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PANR’ version ‘1.12.1’
* 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 ‘PANR’ can be installed ... [3s/4s] 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
viewNestedModules,PAN-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-logical_Or_missing:
  no visible global function definition for ‘RedPort’
viewNestedModules,PAN-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-logical_Or_missing:
  no visible global function definition for ‘calld’
viewNestedModules,PAN-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-logical_Or_missing:
  no visible global function definition for ‘addGraph’
viewNestedModules,PAN-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-logical_Or_missing:
  no visible global function definition for ‘nestNodes’
viewNestedModules,PAN-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-numeric_Or_integer_Or_missing-logical_Or_missing:
  no visible global function definition for ‘mergeOutEdges’
viewPAN,PAN-character_Or_missing-numeric_Or_integer_Or_missing-character_Or_missing-logical_Or_missing:
  no visible global function definition for ‘RedPort’
viewPAN,PAN-character_Or_missing-numeric_Or_integer_Or_missing-character_Or_missing-logical_Or_missing:
  no visible global function definition for ‘calld’
viewPAN,PAN-character_Or_missing-numeric_Or_integer_Or_missing-character_Or_missing-logical_Or_missing:
  no visible global function definition for ‘addGraph’
* 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 ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
fitNULL 25.312  0.154  25.519
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/PANR.Rcheck/00check.log’
for details.

PANR.Rcheck/00install.out:

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

PANR.Rcheck/PANR-Ex.timings:

nameusersystemelapsed
BetaMixture-class0.0010.0000.001
PAN-class0.0010.0010.002
SNR2p0.0010.0000.001
assoScore0.0670.0020.070
buildPAN1.1100.0391.156
cosineSim0.0040.0000.005
data-Bakal20070.0200.0030.024
exportPAN0.0010.0010.001
fitBM0.0010.0000.001
fitNULL25.312 0.15425.519
infer0.7500.0140.766
p2SNR0.0010.0000.001
permNULL0.0210.0030.023
pvclustModule0.0010.0010.001
sigModules0.0010.0000.002
summarize0.0270.0070.034
view0.3190.0240.350
viewLegend0.0010.0010.001
viewNestedModules0.0010.0000.001
viewPAN0.0010.0010.001