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CHECK report for RNAinteractMAPK on malbec2

This page was generated on 2019-10-17 16:51:23 -0400 (Thu, 17 Oct 2019).

Package 294/371HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAinteractMAPK 1.22.0
Bernd Fischer
Snapshot Date: 2019-10-17 09:00:12 -0400 (Thu, 17 Oct 2019)
URL: https://git.bioconductor.org/packages/RNAinteractMAPK
Branch: RELEASE_3_9
Last Commit: eaf7b3f
Last Changed Date: 2019-05-02 11:56:23 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

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

Command output

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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.



Installation output

RNAinteractMAPK.Rcheck/00install.out

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### Running command:
###
###   /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)

Tests output


Example timings

RNAinteractMAPK.Rcheck/RNAinteractMAPK-Ex.timings

nameusersystemelapsed
Dmel2PPMAPK1.2150.0311.248
ElpB1phenotype0.0000.0030.004
Networks0.0010.0010.003
PhysicalInteractions0.0000.0010.001
RNAinteractMAPK-package0.8330.0000.832
cellTiterGlo0.0030.0000.003
dsRNAiDilutionSeriesData0.0200.0280.048
mRNAdoubleKDefficiency0.0000.0020.002
mRNAsingleKDefficiency0.0020.0010.002
pathwayMembership0.0020.0000.001
singleKDphenotype0.0060.0000.005