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BioC experimental data: CHECK report for Fletcher2013b on malbec2

This page was generated on 2017-08-15 15:07:53 -0400 (Tue, 15 Aug 2017).

Package 101/316HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Fletcher2013b 1.12.0
Mauro Castro
Snapshot Date: 2017-08-15 09:00:06 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_5/experiment/pkgs/Fletcher2013b
Last Changed Rev: 4155 / Revision: 4227
Last Changed Date: 2017-04-24 16:09:26 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: Fletcher2013b
Version: 1.12.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Fletcher2013b_1.12.0.tar.gz
StartedAt: 2017-08-15 10:42:18 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 10:44:32 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 134.3 seconds
RetCode: 0
Status:  OK 
CheckDir: Fletcher2013b.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Fletcher2013b_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/Fletcher2013b.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Fletcher2013b/DESCRIPTION’ ... OK
* this is package ‘Fletcher2013b’ version ‘1.12.0’
* 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 ‘Fletcher2013b’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 263.1Mb
  sub-directories of 1Mb or more:
    data  262.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... 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
Fletcher2013gsea.regulons: no visible global function definition for
  ‘data’
Fletcher2013gsea.regulons: no visible binding for global variable
  ‘miscellaneous’
Fletcher2013gsea.regulons: no visible binding for global variable
  ‘Exp1limma’
Fletcher2013gsea.regulons: no visible binding for global variable
  ‘Exp2limma’
Fletcher2013gsea.regulons: no visible binding for global variable
  ‘Exp3limma’
Fletcher2013gsea.regulons: no visible global function definition for
  ‘palette’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘data’
Fletcher2013pipeline.consensusnet: no visible binding for global
  variable ‘miscellaneous’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘colorRampPalette’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘data’
Fletcher2013pipeline.enrichmap: no visible binding for global variable
  ‘miscellaneous’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘colorRampPalette’
Fletcher2013pipeline.mra1st: no visible global function definition for
  ‘data’
Fletcher2013pipeline.mra2nd: no visible global function definition for
  ‘data’
Fletcher2013pipeline.mraNormals: no visible global function definition
  for ‘data’
Fletcher2013pipeline.mraTALL: no visible global function definition for
  ‘data’
Fletcher2013pipeline.synergyShadow: no visible global function
  definition for ‘data’
Fletcher2013pipeline.synergyShadow: no visible binding for global
  variable ‘miscellaneous’
Fletcher2013pipeline.synergyShadow: no visible binding for global
  variable ‘Exp1limma’
colorscale1: no visible global function definition for ‘quantile’
colorscale1: no visible global function definition for ‘grey’
colorscale1: no visible global function definition for
  ‘colorRampPalette’
colorscale2: no visible global function definition for ‘quantile’
colorscale2: no visible global function definition for ‘grey’
colorscale2: no visible global function definition for
  ‘colorRampPalette’
plotSynergyShadow: no visible global function definition for ‘data’
plotSynergyShadow: no visible binding for global variable
  ‘miscellaneous’
plotSynergyShadow: no visible global function definition for ‘hclust’
plotSynergyShadow: no visible global function definition for ‘as.dist’
plotSynergyShadow: no visible global function definition for ‘cor’
plotSynergyShadow: no visible global function definition for
  ‘as.dendrogram’
plotSynergyShadow: no visible global function definition for ‘reorder’
plotSynergyShadow: no visible global function definition for
  ‘order.dendrogram’
plotSynergyShadow: no visible global function definition for
  ‘colorRampPalette’
plotleg1: no visible global function definition for ‘pdf’
plotleg1: no visible global function definition for ‘image’
plotleg1: no visible global function definition for ‘axis’
plotleg1: no visible global function definition for ‘box’
plotleg1: no visible global function definition for ‘mtext’
plotleg1: no visible global function definition for ‘dev.off’
plotleg2: no visible global function definition for ‘image’
plotleg2: no visible global function definition for ‘axis’
plotleg2: no visible global function definition for ‘box’
plotleg2: no visible global function definition for ‘mtext’
plotovsysh: no visible global function definition for ‘pdf’
plotovsysh: no visible global function definition for ‘layout’
plotovsysh: no visible global function definition for ‘par’
plotovsysh: no visible global function definition for ‘image’
plotovsysh: no visible global function definition for ‘axis’
plotovsysh: no visible global function definition for ‘box’
plotovsysh: no visible global function definition for ‘mtext’
plotovsysh: no visible global function definition for ‘abline’
plotovsysh: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  Exp1limma Exp2limma Exp3limma abline as.dendrogram as.dist axis box
  colorRampPalette cor data dev.off grey hclust image layout
  miscellaneous mtext order.dendrogram palette par pdf quantile reorder
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "grey",
             "palette", "pdf")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "mtext", "par")
  importFrom("stats", "as.dendrogram", "as.dist", "cor", "hclust",
             "order.dendrogram", "quantile", "reorder")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... 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-3.5-data-experiment/meat/Fletcher2013b.Rcheck/00check.log’
for details.


Fletcher2013b.Rcheck/00install.out:

* installing *source* package ‘Fletcher2013b’ ...
** 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 (Fletcher2013b)

Fletcher2013b.Rcheck/Fletcher2013b-Ex.timings:

nameusersystemelapsed
Fletcher2013b.gsea.regulons000
Fletcher2013b.pipelines000
miscellaneous0.5880.0080.596
rtni.data3.1560.8604.018
siRNA0.0040.0000.005