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CHECK report for cogena on merida1

This page was generated on 2020-04-15 12:41:46 -0400 (Wed, 15 Apr 2020).

Package 338/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cogena 1.20.0
Zhilong Jia
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/cogena
Branch: RELEASE_3_10
Last Commit: 6d9ab97
Last Changed Date: 2019-10-29 13:09:16 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cogena
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cogena.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cogena_1.20.0.tar.gz
StartedAt: 2020-04-15 01:21:59 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:26:50 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 290.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: cogena.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cogena.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cogena_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/cogena.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogena/DESCRIPTION’ ... OK
* this is package ‘cogena’ version ‘1.20.0’
* 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 ‘cogena’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/cogena.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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dist.fn: no visible global function definition for ‘cor’
heatmap.3: no visible binding for global variable ‘dist’
heatmap.3: no visible global function definition for ‘par’
heatmap.3: no visible global function definition for ‘median’
heatmap.3: no visible global function definition for ‘order.dendrogram’
heatmap.3: no visible global function definition for ‘reorder’
heatmap.3: no visible binding for global variable ‘sd’
heatmap.3: no visible global function definition for ‘layout’
heatmap.3: no visible global function definition for ‘image’
heatmap.3: no visible global function definition for ‘axis’
heatmap.3: no visible global function definition for ‘mtext’
heatmap.3: no visible global function definition for ‘rect’
heatmap.3: no visible global function definition for ‘abline’
heatmap.3: no visible global function definition for ‘lines’
heatmap.3: no visible global function definition for ‘text’
heatmap.3: no visible global function definition for ‘plot.new’
heatmap.3: no visible global function definition for ‘title’
heatmap.3: no visible global function definition for ‘density’
heatmap.3: no visible global function definition for ‘hist’
plot.sota: no visible global function definition for ‘par’
corInCluster,cogena: no visible global function definition for ‘cor’
heatmapCluster,cogena: no visible global function definition for
  ‘topo.colors’
heatmapCluster,cogena: no visible global function definition for
  ‘rainbow’
heatmapCluster,cogena: no visible global function definition for ‘par’
heatmapCluster,cogena: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  abline axis cor density dist hist image layout legend lines median
  mtext order.dendrogram par plot.new rainbow rect reorder sd text
  title topo.colors
Consider adding
  importFrom("grDevices", "rainbow", "topo.colors")
  importFrom("graphics", "abline", "axis", "hist", "image", "layout",
             "legend", "lines", "mtext", "par", "plot.new", "rect",
             "text", "title")
  importFrom("stats", "cor", "density", "dist", "median",
             "order.dendrogram", "reorder", "sd")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
cogena_package 6.946  0.516 106.784
clEnrich_one   4.555  0.544  15.717
clEnrich       3.220  0.260  20.516
upDownGene     2.954  0.271  20.539
clusterMethods 1.981  0.020  11.991
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/cogena.Rcheck/00check.log’
for details.



Installation output

cogena.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cogena
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘cogena’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’
** testing if installed package keeps a record of temporary installation path
* DONE (cogena)

Tests output


Example timings

cogena.Rcheck/cogena-Ex.timings

nameusersystemelapsed
PEI0.8530.1330.994
clEnrich 3.220 0.26020.516
clEnrich_one 4.555 0.54415.717
clusterMethods 1.981 0.02011.991
coExp0.0020.0010.003
cogena_package 6.946 0.516106.784
corInCluster0.0030.0020.004
enrichment0.0030.0020.004
gene2set0.0800.0030.083
geneExpInCluster0.0020.0010.004
geneInCluster0.0020.0010.004
geneclusters0.0000.0010.001
gmt2list0.0460.0000.046
gmtlist2file0.1130.0970.224
heatmapCluster0.0020.0020.004
heatmapCmap0.0020.0010.003
heatmapPEI0.0030.0020.005
mat000
nClusters0.0000.0010.001
show000
sota2.2880.2252.560
summary0.0000.0000.001
upDownGene 2.954 0.27120.539