Package: RNAinteractMAPK

Version: 1.22.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RNAinteractMAPK.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RNAinteractMAPK_1.22.0.tar.gz

StartedAt: 2019-10-17 13:43:32 -0400 (Thu, 17 Oct 2019)

EndedAt: 2019-10-17 13:45:42 -0400 (Thu, 17 Oct 2019)

EllapsedTime: 130.0 seconds

RetCode: 0

Status:  OK

CheckDir: RNAinteractMAPK.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RNAinteractMAPK.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RNAinteractMAPK_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/RNAinteractMAPK.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 10.4Mb
  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.cv.TPS: no visible global function definition for ‘predict’
MAPK.cv.TPS: no visible binding for global variable ‘sd’
MAPK.cv.classifier: no visible global function definition for ‘is’
MAPK.estimate.TPS: no visible global function definition for ‘Tps’
MAPK.estimate.TPS: no visible global function definition for ‘predict’
MAPK.estimate.TPS: no visible global function definition for ‘median’
MAPK.getCV: no visible global function definition for ‘predict’
MAPK.getXY: no visible global function definition for ‘rowMin’
MAPK.plot.TPS.all: no visible global function definition for
  ‘levelplot’
MAPK.plot.TPS.all: no visible global function definition for
  ‘colorRampPalette’
MAPK.plot.TPS.all : : no visible global function definition
  for ‘panel.levelplot’
MAPK.plot.TPS.all : : no visible global function definition
  for ‘panel.contourplot’
MAPK.plot.TPS.single: no visible global function definition for
  ‘colorRampPalette’
MAPK.plot.TPS.single: no visible global function definition for ‘par’
MAPK.plot.TPS.single: no visible global function definition for
  ‘contourLines’
MAPK.plot.TPS.single: no visible global function definition for
  ‘levelplot’
MAPK.plot.TPS.single : : no visible global function
  definition for ‘col2rgb’
MAPK.plot.TPS.single : : no visible global function
  definition for ‘panel.contourplot’
MAPK.plot.classification: no visible global function definition for
  ‘rainbow’
MAPK.plot.heatmap.raster: no visible global function definition for
  ‘as.dendrogram’
MAPK.plot.heatmap.raster: no visible global function definition for
  ‘order.dendrogram’
MAPK.plot.heatmap.raster: no visible global function definition for
  ‘colorRampPalette’
MAPK.plot.heatmap.raster: no visible global function definition for
  ‘col2rgb’
MAPK.plot.heatmap.raster: no visible global function definition for
  ‘mad’
MAPK.plot.heatmap.raster: no visible global function definition for
  ‘quantile’
MAPK.predict.classification: no visible global function definition for
  ‘is’
MAPK.predict.classification: no visible global function definition for
  ‘predict’
MAPK.report.gene.lists.paper: no visible global function definition for
  ‘is’
MAPK.report.gene.lists.paper: no visible global function definition for
  ‘write.table’
MAPK.smooth.scatter: no visible global function definition for
  ‘colorRampPalette’
MAPK.smooth.scatter: no visible global function definition for
  ‘col2rgb’
Undefined global functions or variables:
  Tps as.dendrogram col2rgb colorRampPalette contourLines is levelplot
  mad median order.dendrogram panel.contourplot panel.levelplot par
  predict quantile rainbow rowMin sd write.table
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "contourLines",
             "rainbow")
  importFrom("graphics", "par")
  importFrom("methods", "is")
  importFrom("stats", "as.dendrogram", "mad", "median",
             "order.dendrogram", "predict", "quantile", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/home/biocbuild/bbs-3.9-data-experiment/meat/RNAinteractMAPK.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RNAinteractMAPK
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘RNAinteractMAPK’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RNAinteractMAPK)

name	user	system	elapsed
Dmel2PPMAPK	1.215	0.031	1.248
ElpB1phenotype	0.000	0.003	0.004
Networks	0.001	0.001	0.003
PhysicalInteractions	0.000	0.001	0.001
RNAinteractMAPK-package	0.833	0.000	0.832
cellTiterGlo	0.003	0.000	0.003
dsRNAiDilutionSeriesData	0.020	0.028	0.048
mRNAdoubleKDefficiency	0.000	0.002	0.002
mRNAsingleKDefficiency	0.002	0.001	0.002
pathwayMembership	0.002	0.000	0.001
singleKDphenotype	0.006	0.000	0.005