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 | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf cogena.buildbin-libdir cogena.Rcheck && mkdir cogena.buildbin-libdir cogena.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cogena.buildbin-libdir cogena_1.10.0.tar.gz >cogena.Rcheck\00install.out 2>&1 && cp cogena.Rcheck\00install.out cogena-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cogena.buildbin-libdir --install="check:cogena-install.out" --force-multiarch --no-vignettes --timings cogena_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/cogena.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.10.0'
* 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 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 'C:/Users/biocbuild/bbs-3.5-bioc/meat/cogena.Rcheck/00install.out' for details.
* 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 7.52 0.58 81.47
clEnrich_one 4.71 0.10 13.28
clEnrich 3.50 0.25 17.75
upDownGene 3.12 0.21 15.69
clusterMethods 1.60 0.03 8.70
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cogena_package 7.25 0.60 89.88
clEnrich_one 4.06 0.06 14.64
clEnrich 3.36 0.25 18.71
upDownGene 2.88 0.17 18.42
clusterMethods 1.08 0.05 11.95
* 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
'C:/Users/biocbuild/bbs-3.5-bioc/meat/cogena.Rcheck/00check.log'
for details.
install for i386
* 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'
install for x64
* installing *source* package 'cogena' ...
** testing if installed package can be loaded
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
* MD5 sums
packaged installation of 'cogena' as cogena_1.10.0.zip
* DONE (cogena)