Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:07:09 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cellTree on riesling1


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 274/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellTree 1.25.0  (landing page)
David duVerle
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/cellTree
git_branch: master
git_last_commit: 0b40a89
git_last_commit_date: 2021-10-26 12:24:44 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: cellTree
Version: 1.25.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cellTree.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cellTree_1.25.0.tar.gz
StartedAt: 2022-03-17 18:41:19 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:09:37 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 1698.0 seconds
RetCode: 0
Status:   OK  
CheckDir: cellTree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cellTree.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cellTree_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/cellTree.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellTree/DESCRIPTION' ... OK
* this is package 'cellTree' version '1.25.0'
* 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 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     814.72 758.38 1576.67
ct.plot.heatmap  19.69   0.69   20.38
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/cellTree.Rcheck/00check.log'
for details.



Installation output

cellTree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cellTree
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'cellTree'
    finding HTML links ... done
    HSMM_lda_model                          html  
    cell.ordering.table                     html  
    cellTree-package                        html  
    compute.backbone.tree                   html  
    compute.go.enrichment                   html  
    compute.lda                             html  
    ct.plot.go.dag                          html  
    ct.plot.grouping                        html  
    ct.plot.heatmap                         html  
    ct.plot.topics                          html  
    get.cell.dists                          html  
    go.results.to.latex                     html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'PAIRADISE' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'universalmotif' is missing or broken
 done

Tests output


Example timings

cellTree.Rcheck/cellTree-Ex.timings

nameusersystemelapsed
cell.ordering.table0.590.080.67
compute.backbone.tree0.660.020.69
compute.go.enrichment0.000.010.02
compute.lda 814.72 758.381576.67
ct.plot.go.dag0.170.000.17
ct.plot.grouping0.920.201.12
ct.plot.heatmap19.69 0.6920.38
ct.plot.topics1.250.121.37
get.cell.dists0.310.020.33
go.results.to.latex0.010.000.02