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BioC 3.5: CHECK report for cogena on malbec2

This page was generated on 2017-08-16 13:16:35 -0400 (Wed, 16 Aug 2017).

Package 260/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cogena 1.10.0
Zhilong Jia
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/cogena
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: cogena
Version: 1.10.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cogena_1.10.0.tar.gz
StartedAt: 2017-08-15 22:07:13 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:10:41 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 207.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: cogena.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cogena_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/cogena.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.10.0’
* 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-3.5-bioc/meat/cogena.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    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 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 5.976  0.560  73.706
clEnrich_one   4.068  0.252  11.231
clEnrich       3.384  0.160  15.016
upDownGene     2.596  0.180  14.579
clusterMethods 1.472  0.056   9.354
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/cogena.Rcheck/00check.log’
for details.


cogena.Rcheck/00install.out:

* 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)

cogena.Rcheck/cogena-Ex.timings:

nameusersystemelapsed
PEI1.0360.1041.141
clEnrich 3.384 0.16015.016
clEnrich_one 4.068 0.25211.231
clusterMethods1.4720.0569.354
coExp0.0000.0040.003
cogena_package 5.976 0.56073.706
corInCluster0.0000.0000.002
enrichment0.0040.0000.002
gene2set0.0520.0000.054
geneExpInCluster0.0000.0000.002
geneInCluster0.0040.0000.002
geneclusters0.0000.0000.002
gmt2list0.0320.0000.032
gmtlist2file0.0400.0240.066
heatmapCluster0.0040.0000.002
heatmapCmap0.0000.0000.001
heatmapPEI0.0000.0000.002
mat000
nClusters000
show000
sota1.7400.0281.768
summary0.0000.0000.001
upDownGene 2.596 0.18014.579