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CHECK report for cellTree on tokay2

This page was generated on 2019-10-16 12:34:45 -0400 (Wed, 16 Oct 2019).

Package 236/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellTree 1.14.0
David duVerle
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/cellTree
Branch: RELEASE_3_9
Last Commit: a765f75
Last Changed Date: 2019-05-02 11:53:59 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellTree
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cellTree_1.14.0.tar.gz
StartedAt: 2019-10-16 02:32:37 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:37:26 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 289.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cellTree.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cellTree_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cellTree.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.14.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/cell.ordering.table.Rd:10: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.backbone.tree.Rd:34: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.go.enrichment.Rd:30: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.lda.Rd:25: file link 'LDA-class' in package 'topicmodels' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.lda.Rd:69: file link 'LDA' in package 'topicmodels' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.lda.Rd:69: file link 'LDA_Gibbscontrol-class' in package 'topicmodels' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.lda.Rd:69: file link 'CTM_VEMcontrol-class' in package 'topicmodels' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.go.dag.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.grouping.Rd:12: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.grouping.Rd:31: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.topics.Rd:12: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.topics.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cellTree.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 : : 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 : : 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 : : no visible global function definition
  for 'rnorm'
order.genes.by.fit : : no visible global function definition
  for 'lm'
save.per.topic.gene.distribution : : no visible global
  function definition for 'pdf'
save.per.topic.gene.distribution : : no visible global
  function definition for 'barplot'
save.per.topic.gene.distribution : : no visible global
  function definition for 'dev.off'
save.per.topic.gene.distribution : : 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
compute.lda     50.39   8.60   59.25
ct.plot.heatmap 28.13   0.32   28.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
compute.lda     31.87   8.20   40.14
ct.plot.heatmap 24.52   0.48   25.02
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/cellTree.Rcheck/00check.log'
for details.

Installation output

cellTree.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/cellTree_1.14.0.tar.gz && rm -rf cellTree.buildbin-libdir && mkdir cellTree.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellTree.buildbin-libdir cellTree_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL cellTree_1.14.0.zip && rm cellTree_1.14.0.tar.gz cellTree_1.14.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  499k  100  499k    0     0  5965k      0 --:--:-- --:--:-- --:--:-- 6487k

install for i386

* 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  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/cell.ordering.table.Rd:10: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
    cellTree-package                        html  
    compute.backbone.tree                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.backbone.tree.Rd:34: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
    compute.go.enrichment                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.go.enrichment.Rd:30: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
    compute.lda                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.lda.Rd:25: file link 'LDA-class' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.lda.Rd:69: file link 'LDA' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.lda.Rd:69: file link 'LDA_Gibbscontrol-class' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/compute.lda.Rd:69: file link 'CTM_VEMcontrol-class' in package 'topicmodels' does not exist and so has been treated as a topic
    ct.plot.go.dag                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.go.dag.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
    ct.plot.grouping                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.grouping.Rd:12: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.grouping.Rd:31: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
    ct.plot.heatmap                         html  
    ct.plot.topics                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.topics.Rd:12: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWwr3B7/R.INSTALL15a02223475/cellTree/man/ct.plot.topics.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
    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

install for x64

* installing *source* package 'cellTree' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'cellTree' as cellTree_1.14.0.zip
* DONE (cellTree)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'cellTree' successfully unpacked and MD5 sums checked

Tests output

Example timings

cellTree.Rcheck/examples_i386/cellTree-Ex.timings

nameusersystemelapsed
cell.ordering.table1.540.131.82
compute.backbone.tree1.530.061.59
compute.go.enrichment0.020.000.01
compute.lda50.39 8.6059.25
ct.plot.go.dag0.190.030.22
ct.plot.grouping2.510.112.64
ct.plot.heatmap28.13 0.3228.48
ct.plot.topics1.610.071.68
get.cell.dists0.280.000.28
go.results.to.latex000

cellTree.Rcheck/examples_x64/cellTree-Ex.timings

nameusersystemelapsed
cell.ordering.table1.200.061.27
compute.backbone.tree1.720.051.76
compute.go.enrichment0.020.000.02
compute.lda31.87 8.2040.14
ct.plot.go.dag0.130.020.14
ct.plot.grouping1.430.081.51
ct.plot.heatmap24.52 0.4825.02
ct.plot.topics1.770.101.86
get.cell.dists0.320.000.33
go.results.to.latex000