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BioC 3.5: CHECK report for cellTree on malbec2

This page was generated on 2017-08-16 13:17:13 -0400 (Wed, 16 Aug 2017).

Package 189/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellTree 1.6.0
David duVerle
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/cellTree
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellTree
Version: 1.6.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cellTree_1.6.0.tar.gz
StartedAt: 2017-08-15 21:46:59 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:49:27 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 147.5 seconds
RetCode: 0
Status:  OK 
CheckDir: cellTree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cellTree_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/cellTree.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 ‘cellTree/DESCRIPTION’ ... OK
* this is package ‘cellTree’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘cellTree’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘topGO’
  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
.format.grouping: no visible global function definition for
  ‘colorRampPalette’
.format.grouping: no visible global function definition for ‘rainbow’
.merge.backbone.node.to: no visible global function definition for
  ‘nei’
.merge.backbone.node.to: no visible global function definition for
  ‘inc’
.mixrgb : <anonymous>: no visible global function definition for
  ‘col2rgb’
.mixrgb: no visible global function definition for ‘rgb’
.normalise.data: no visible binding for global variable ‘sd’
.plot.b.tree: no visible global function definition for ‘pdf’
.plot.b.tree: no visible global function definition for ‘par’
.plot.b.tree: no visible global function definition for ‘dev.size’
.plot.b.tree: no visible global function definition for ‘legend’
.plot.b.tree: no visible global function definition for ‘rainbow’
.plot.b.tree: no visible global function definition for ‘dev.off’
.recur.merge.backbone: no visible global function definition for ‘nei’
.recur.merge.backbone: no visible global function definition for ‘inc’
.recur.ordered.branches: no visible global function definition for
  ‘nei’
.recur.shorten.backbone: no visible global function definition for
  ‘nei’
.recur.shorten.backbone: no visible global function definition for ‘to’
.recur.tree.layout: no visible global function definition for ‘nei’
cell.ordering.table: no visible global function definition for
  ‘rainbow’
cell.ordering.table: no visible global function definition for
  ‘toLatex’
compute.backbone.tree: no visible global function definition for ‘nei’
compute.backbone.tree: no visible global function definition for ‘from’
compute.backbone.tree: no visible global function definition for
  ‘density’
compute.go.enrichment: no visible global function definition for ‘new’
compute.go.enrichment: no visible global function definition for
  ‘score’
compute.go.enrichment: no visible global function definition for
  ‘getFromNamespace’
compute.go.enrichment: no visible global function definition for
  ‘ontology’
ct.plot.go.dag: no visible global function definition for ‘rainbow’
ct.plot.go.dag: no visible global function definition for ‘pdf’
ct.plot.go.dag : <anonymous>: no visible global function definition for
  ‘col2rgb’
ct.plot.go.dag: no visible global function definition for ‘nei’
ct.plot.go.dag: no visible global function definition for ‘par’
ct.plot.go.dag: no visible global function definition for ‘plot’
ct.plot.go.dag: no visible global function definition for ‘legend’
ct.plot.go.dag: no visible global function definition for ‘dev.off’
ct.plot.heatmap: no visible global function definition for
  ‘colorRampPalette’
ct.plot.heatmap: no visible global function definition for ‘dev.new’
ct.plot.heatmap: no visible binding for global variable
  ‘gene.reordering’
go.results.to.latex: no visible global function definition for
  ‘rainbow’
go.results.to.latex: no visible global function definition for
  ‘toLatex’
order.genes.by.fit : <anonymous>: no visible global function definition
  for ‘rnorm’
order.genes.by.fit : <anonymous>: no visible global function definition
  for ‘lm’
save.per.topic.gene.distribution : <anonymous>: no visible global
  function definition for ‘pdf’
save.per.topic.gene.distribution : <anonymous>: no visible global
  function definition for ‘barplot’
save.per.topic.gene.distribution : <anonymous>: no visible global
  function definition for ‘dev.off’
save.per.topic.gene.distribution : <anonymous>: no visible global
  function definition for ‘write.table’
Undefined global functions or variables:
  barplot col2rgb colorRampPalette density dev.new dev.off dev.size
  from gene.reordering getFromNamespace inc legend lm nei new ontology
  par pdf plot rainbow rgb rnorm score sd to toLatex write.table
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.new",
             "dev.off", "dev.size", "pdf", "rainbow", "rgb")
  importFrom("graphics", "barplot", "legend", "par", "plot")
  importFrom("methods", "new")
  importFrom("stats", "density", "lm", "rnorm", "sd")
  importFrom("utils", "getFromNamespace", "toLatex", "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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
compute.lda     35.828  9.096  45.218
ct.plot.heatmap 11.220  0.376  11.608
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/cellTree.Rcheck/00check.log’
for details.


cellTree.Rcheck/00install.out:

* installing *source* package ‘cellTree’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (cellTree)

cellTree.Rcheck/cellTree-Ex.timings:

nameusersystemelapsed
cell.ordering.table1.9080.0202.537
compute.backbone.tree2.1520.0202.173
compute.go.enrichment0.0040.0000.002
compute.lda35.828 9.09645.218
ct.plot.go.dag0.1720.0040.175
ct.plot.grouping2.5400.0162.559
ct.plot.heatmap11.220 0.37611.608
ct.plot.topics1.9240.0201.945
get.cell.dists0.3680.0040.370
go.results.to.latex0.0000.0000.001