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BioC 3.4: CHECK report for cogena on moscato1

This page was generated on 2016-09-21 03:47:02 -0700 (Wed, 21 Sep 2016).

Package 237/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cogena 1.7.2
Zhilong Jia
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cogena
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cogena
Version: 1.7.2
Command: rm -rf cogena.buildbin-libdir cogena.Rcheck && mkdir cogena.buildbin-libdir cogena.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cogena.buildbin-libdir cogena_1.7.2.tar.gz >cogena.Rcheck\00install.out 2>&1 && cp cogena.Rcheck\00install.out cogena-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=cogena.buildbin-libdir --install="check:cogena-install.out" --force-multiarch --no-vignettes --timings cogena_1.7.2.tar.gz
StartedAt: 2016-09-20 06:11:52 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:18:55 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 423.7 seconds
RetCode: 0
Status:  OK  
CheckDir: cogena.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cogena.buildbin-libdir cogena.Rcheck && mkdir cogena.buildbin-libdir cogena.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cogena.buildbin-libdir cogena_1.7.2.tar.gz >cogena.Rcheck\00install.out 2>&1 && cp cogena.Rcheck\00install.out cogena-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=cogena.buildbin-libdir --install="check:cogena-install.out" --force-multiarch --no-vignettes --timings cogena_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/cogena.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cogena/DESCRIPTION' ... OK
* this is package 'cogena' version '1.7.2'
* 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 whether package 'cogena' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cogena_package 7.71   1.26   86.61
clEnrich_one   4.99   0.11   11.73
upDownGene     3.49   0.18   16.41
clEnrich       3.24   0.35   14.38
clusterMethods 2.01   0.05    8.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cogena_package 6.99   1.14   89.04
clEnrich_one   4.76   0.11   14.55
upDownGene     3.55   0.19   17.30
clEnrich       2.96   0.37   16.37
clusterMethods 1.65   0.00    9.17
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/cogena.Rcheck/00check.log'
for details.


cogena.Rcheck/00install.out:


install for i386

* installing *source* package 'cogena' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'cogena'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'cogena' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cogena' as cogena_1.7.2.zip
* DONE (cogena)

cogena.Rcheck/examples_i386/cogena-Ex.timings:

nameusersystemelapsed
PEI0.940.040.96
clEnrich 3.24 0.3514.38
clEnrich_one 4.99 0.1111.73
clusterMethods2.010.058.07
coExp0.020.000.02
cogena_package 7.71 1.2686.61
corInCluster0.000.020.01
enrichment000
gene2set0.060.000.07
geneExpInCluster0.000.020.01
geneInCluster000
geneclusters000
gmt2list0.030.000.03
gmtlist2file0.050.030.08
heatmapCluster0.010.000.02
heatmapCmap000
heatmapPEI0.020.000.01
mat000
nClusters000
show000
sota1.870.001.87
summary000
upDownGene 3.49 0.1816.41

cogena.Rcheck/examples_x64/cogena-Ex.timings:

nameusersystemelapsed
PEI1.370.081.45
clEnrich 2.96 0.3716.37
clEnrich_one 4.76 0.1114.55
clusterMethods1.650.009.17
coExp0.020.000.02
cogena_package 6.99 1.1489.04
corInCluster000
enrichment000
gene2set0.050.000.04
geneExpInCluster0.000.020.02
geneInCluster000
geneclusters000
gmt2list0.030.000.03
gmtlist2file0.060.010.08
heatmapCluster000
heatmapCmap0.000.020.01
heatmapPEI000
mat000
nClusters000
show000
sota2.110.002.11
summary000
upDownGene 3.55 0.1917.30