Package: cogena

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cogena_1.12.0.tar.gz

StartedAt: 2018-04-12 02:05:10 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:09:07 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 236.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cogena.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cogena_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cogena.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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-3.6-bioc/meat/cogena.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.1Mb
* 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 loading without being on the library search path ... 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
PEI: no visible global function definition for ‘phyper’
clEnrich: no visible global function definition for ‘data’
clEnrich : logAdjPEI: no visible global function definition for
  ‘p.adjust’
clEnrich_one: no visible global function definition for ‘data’
clEnrich_one : logAdjPEI: no visible global function definition for
  ‘p.adjust’
coExp: no visible global function definition for ‘as.dist’
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’
plot.sota: no visible global function definition for ‘legend’
plot.sota: no visible global function definition for ‘lines’
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 as.dist axis cor data density dist hist image layout legend
  lines median mtext order.dendrogram p.adjust par phyper 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", "as.dist", "cor", "density", "dist", "median",
             "order.dendrogram", "p.adjust", "phyper", "reorder", "sd")
  importFrom("utils", "data")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
cogena_package 7.408  0.385  89.555
clEnrich_one   4.997  0.446  13.381
upDownGene     3.515  0.210  16.642
clEnrich       3.137  0.236  15.305
clusterMethods 1.840  0.016   9.349
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/cogena.Rcheck/00check.log’
for details.

* installing *source* package ‘cogena’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’
* DONE (cogena)

name	user	system	elapsed
PEI	1.220	0.113	1.352
clEnrich	3.137	0.236	15.305
clEnrich_one	4.997	0.446	13.381
clusterMethods	1.840	0.016	9.349
coExp	0.002	0.001	0.004
cogena_package	7.408	0.385	89.555
corInCluster	0.003	0.001	0.003
enrichment	0.002	0.001	0.003
gene2set	0.075	0.002	0.078
geneExpInCluster	0.003	0.001	0.004
geneInCluster	0.003	0.001	0.003
geneclusters	0.001	0.000	0.001
gmt2list	0.044	0.001	0.045
gmtlist2file	0.097	0.075	0.173
heatmapCluster	0.003	0.001	0.004
heatmapCmap	0.003	0.001	0.004
heatmapPEI	0.003	0.001	0.004
mat	0.001	0.000	0.001
nClusters	0.001	0.000	0.001
show	0.000	0.000	0.001
sota	2.190	0.202	2.421
summary	0	0	0
upDownGene	3.515	0.210	16.642