Package: cogena

Version: 1.18.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cogena.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cogena_1.18.0.tar.gz

StartedAt: 2019-10-16 00:42:06 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:46:18 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 251.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cogena.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cogena.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cogena_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/cogena.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogena/DESCRIPTION’ ... OK
* this is package ‘cogena’ version ‘1.18.0’
* 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 ‘/home/biocbuild/bbs-3.9-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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
cogena_package 7.408  0.766 104.530
clEnrich_one   4.416  0.155  13.638
clEnrich       3.081  0.184  16.765
upDownGene     2.808  0.206  18.525
clusterMethods 1.187  0.080   9.831
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/cogena.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL cogena
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

name	user	system	elapsed
PEI	0.619	0.024	0.649
clEnrich	3.081	0.184	16.765
clEnrich_one	4.416	0.155	13.638
clusterMethods	1.187	0.080	9.831
coExp	0.002	0.000	0.001
cogena_package	7.408	0.766	104.530
corInCluster	0.001	0.001	0.002
enrichment	0.000	0.002	0.002
gene2set	0.074	0.004	0.077
geneExpInCluster	0.003	0.000	0.002
geneInCluster	0.002	0.000	0.002
geneclusters	0	0	0
gmt2list	0.033	0.000	0.033
gmtlist2file	0.066	0.047	0.353
heatmapCluster	0.002	0.000	0.002
heatmapCmap	0.002	0.000	0.002
heatmapPEI	0.002	0.000	0.002
mat	0	0	0
nClusters	0	0	0
show	0.000	0.000	0.001
sota	2.072	0.022	2.367
summary	0	0	0
upDownGene	2.808	0.206	18.525