Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-06-17 02:38:16 -0400 (Thu, 17 Jun 2021).

CHECK results for cellTree on nebbiolo1

To the developers/maintainers of the cellTree package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellTree.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 270/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellTree 1.22.0  (landing page)
David duVerle
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/cellTree
Branch: RELEASE_3_13
Last Commit: 65701cf
Last Changed Date: 2021-05-19 12:17:25 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    TIMEOUT    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cellTree
Version: 1.22.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cellTree.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cellTree_1.22.0.tar.gz
StartedAt: 2021-06-15 11:14:28 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 11:31:13 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 1005.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cellTree.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cellTree.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cellTree_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cellTree.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.22.0’
* 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 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 ‘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 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")
  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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user  system elapsed
compute.lda     790.936 109.283 900.304
ct.plot.heatmap  12.451   0.816  13.267
* 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-3.13-bioc/meat/cellTree.Rcheck/00check.log’
for details.



Installation output

cellTree.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cellTree
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘cellTree’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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 from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (cellTree)

Tests output


Example timings

cellTree.Rcheck/cellTree-Ex.timings

nameusersystemelapsed
cell.ordering.table0.8540.0200.874
compute.backbone.tree0.8860.0040.890
compute.go.enrichment0.0010.0000.001
compute.lda790.936109.283900.304
ct.plot.go.dag0.1250.0080.133
ct.plot.grouping0.8660.0630.929
ct.plot.heatmap12.451 0.81613.267
ct.plot.topics1.1170.0191.137
get.cell.dists0.2950.0030.299
go.results.to.latex0.0000.0010.001