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BioC 3.2: CHECK report for LiquidAssociation on perceval

This page was generated on 2015-11-10 14:46:29 -0800 (Tue, 10 Nov 2015).

Package 566/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LiquidAssociation 1.24.0
Yen-Yi Ho
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/LiquidAssociation
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LiquidAssociation
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LiquidAssociation_1.24.0.tar.gz
StartedAt: 2015-11-10 06:25:51 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 06:27:43 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 112.3 seconds
RetCode: 0
Status:  OK 
CheckDir: LiquidAssociation.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LiquidAssociation_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/LiquidAssociation.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LiquidAssociation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LiquidAssociation’ version ‘1.24.0’
* 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 ‘LiquidAssociation’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘geepack’ ‘org.Sc.sgd.db’ ‘yeastCC’
  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 ... NOTE
CNM.full,matrix : .local: no visible global function definition for
  ‘geese’
CNM.full,matrix : .local: no visible binding for global variable
  ‘groupid’
CNM.full,matrix : .local: no visible binding for global variable
  ‘visit’
CNM.full,matrix : .local: no visible global function definition for
  ‘geese.control’
CNM.simple,matrix : .local: no visible global function definition for
  ‘geese’
CNM.simple,matrix : .local: no visible binding for global variable
  ‘groupid’
CNM.simple,matrix : .local: no visible binding for global variable
  ‘visit’
CNM.simple,matrix : .local: no visible global function definition for
  ‘geese.control’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/16s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getsGLA-methods 6.652  0.089   6.741
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/LiquidAssociation.Rcheck/00check.log’
for details.


LiquidAssociation.Rcheck/00install.out:

* installing *source* package ‘LiquidAssociation’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘LiquidAssociation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LiquidAssociation)

LiquidAssociation.Rcheck/LiquidAssociation-Ex.timings:

nameusersystemelapsed
CNM-class0.0010.0000.001
CNM.full-methods0.0500.0020.051
CNM.simple-methods0.0340.0010.034
GLA-methods0.0150.0000.015
LA-methods0.0020.0000.002
LiquidAssociation-package0.0380.0010.038
getsGLA-methods6.6520.0896.741
getsLA-methods3.9580.0664.024
plotGLA-methods0.0120.0021.014