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This page was generated on 2021-12-03 13:05:43 -0500 (Fri, 03 Dec 2021).

CHECK results for cogena on machv2

To the developers/maintainers of the cogena package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cogena.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 369/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cogena 1.28.0  (landing page)
Zhilong Jia
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/cogena
git_branch: RELEASE_3_14
git_last_commit: 639d8fb
git_last_commit_date: 2021-10-26 12:19:56 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: cogena
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cogena.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cogena_1.28.0.tar.gz
StartedAt: 2021-12-02 13:03:40 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 13:09:13 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 332.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: cogena.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cogena.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cogena_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/cogena.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogena/DESCRIPTION’ ... OK
* this is package ‘cogena’ version ‘1.28.0’
* 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-3.14-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’
heatmapPEI,cogena: no visible binding for global variable ‘clusterID’
heatmapPEI,cogena: no visible binding for global variable ‘TF’
heatmapPEI,cogena: no visible binding for global variable
  ‘clusterNumGene’
heatmapPEI,cogena: no visible binding for global variable ‘GS’
heatmapPEI,cogena: no visible binding for global variable ‘value’
heatmapPEI,cogena: no visible binding for global variable ‘GeneCount’
Undefined global functions or variables:
  GS GeneCount TF abline axis clusterID clusterNumGene cor density dist
  hist image layout legend lines median mtext order.dendrogram par
  plot.new rainbow rect reorder sd text title topo.colors value
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 LazyData ... 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 (user + system) or elapsed time > 5s
                user system elapsed
cogena_package 8.171  0.419 116.138
clEnrich_one   4.939  0.410  16.401
clEnrich       3.595  0.215  22.243
upDownGene     3.299  0.157  22.457
clusterMethods 1.949  0.028  13.930
* 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-3.14-bioc/meat/cogena.Rcheck/00check.log’
for details.



Installation output

cogena.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cogena
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
PEI0.8050.0800.886
clEnrich 3.595 0.21522.243
clEnrich_one 4.939 0.41016.401
clusterMethods 1.949 0.02813.930
coExp0.0010.0030.005
cogena_package 8.171 0.419116.138
corInCluster0.0020.0030.005
enrichment0.0020.0020.005
gene2set0.0810.0080.088
geneExpInCluster0.0030.0030.005
geneInCluster0.0020.0020.004
geneclusters000
gmt2list0.0400.0010.041
gmtlist2file0.0980.2050.303
heatmapCluster0.0030.0020.005
heatmapCmap0.0010.0030.005
heatmapPEI0.0030.0020.005
mat000
nClusters000
show0.0000.0010.001
sota2.3150.2472.563
summary000
upDownGene 3.299 0.15722.457