BioC experimental data: CHECK report for RNAinteractMAPK on morelia

Package: RNAinteractMAPK

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAinteractMAPK_1.9.0.tar.gz

StartedAt: 2015-11-25 11:09:43 -0800 (Wed, 25 Nov 2015)

EndedAt: 2015-11-25 11:13:00 -0800 (Wed, 25 Nov 2015)

EllapsedTime: 196.7 seconds

RetCode: 0

Status:  OK

CheckDir: RNAinteractMAPK.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAinteractMAPK_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/RNAinteractMAPK.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAinteractMAPK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAinteractMAPK’ version ‘1.9.0’
* 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 ‘RNAinteractMAPK’ can be installed ... [17s/24s] OK
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data      6.7Mb
    extdata   3.6Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘genefilter’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘fields’ ‘methods’
  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
MAPK.cv.TPS: no visible global function definition for ‘Tps’
MAPK.estimate.TPS: no visible global function definition for ‘Tps’
MAPK.getXY: no visible global function definition for ‘rowMin’
MAPK.plot.TPS.all: no visible global function definition for
  ‘levelplot’
MAPK.plot.TPS.all : <anonymous>: no visible global function definition
  for ‘panel.levelplot’
MAPK.plot.TPS.all : <anonymous>: no visible global function definition
  for ‘panel.contourplot’
MAPK.plot.TPS.single: no visible global function definition for
  ‘levelplot’
MAPK.plot.TPS.single : <anonymous>: no visible global function
  definition for ‘panel.contourplot’
Undefined global functions or variables:
  Tps levelplot panel.contourplot panel.levelplot rowMin
* 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 ... [12s/13s] OK
* 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-3.3-data-experiment/meat/RNAinteractMAPK.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Dmel2PPMAPK	2.074	0.063	2.464
ElpB1phenotype	0.005	0.001	0.006
Networks	0.006	0.001	0.007
PhysicalInteractions	0.004	0.001	0.005
RNAinteractMAPK-package	1.335	0.047	1.381
cellTiterGlo	0.003	0.000	0.004
dsRNAiDilutionSeriesData	0.039	0.036	0.087
mRNAdoubleKDefficiency	0.004	0.000	0.005
mRNAsingleKDefficiency	0.005	0.001	0.006
pathwayMembership	0.002	0.000	0.003
singleKDphenotype	0.006	0.001	0.008