BioC 3.3: CHECK report for mogsa on morelia

Package: mogsa

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mogsa_1.4.0.tar.gz

StartedAt: 2016-04-21 05:13:22 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 05:17:05 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 222.9 seconds

RetCode: 0

Status:  OK

CheckDir: mogsa.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mogsa_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/mogsa.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.4.0’
* 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 ‘mogsa’ can be installed ... [12s/12s] OK
* 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 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
.heatmap.rv: no visible global function definition for ‘heatmap’
.plot.eig: no visible global function definition for ‘barplot’
.plot.eig: no visible global function definition for ‘matplot’
.plot.obs: no visible global function definition for ‘abline’
.plot.obs: no visible global function definition for ‘points’
.plot.obs: no visible global function definition for ‘legend’
.plot.obs: no visible global function definition for ‘segments’
.plot.obs: no visible global function definition for ‘text’
.plot.tau: no visible global function definition for ‘barplot’
.plot.tau: no visible global function definition for ‘lines’
.plot.tau: no visible global function definition for ‘matplot’
.plot.var : <anonymous>: no visible global function definition for
  ‘abline’
.plot.var : <anonymous>: no visible global function definition for
  ‘points’
.plotGS.comb: no visible global function definition for ‘abline’
.plotGS.comb: no visible global function definition for ‘points’
.plotGS.comb: no visible global function definition for ‘text’
.plotGS.sep: no visible global function definition for ‘abline’
.plotGS.sep: no visible global function definition for ‘points’
.plotGS.sep: no visible global function definition for ‘text’
.signifGS : ff: no visible global function definition for ‘sd’
.signifGS : ff: no visible global function definition for ‘pnorm’
GIS: no visible global function definition for ‘sd’
GIS: no visible binding for global variable ‘sd’
GIS: no visible global function definition for ‘barplot’
GIS: no visible global function definition for ‘legend’
bootMbpca: no visible binding for global variable ‘sd’
bootMbpca: no visible global function definition for ‘points’
bootMbpca: no visible global function definition for ‘segments’
bootMbpca: no visible global function definition for ‘lines’
decompose.gs.group : sepc: no visible binding for global variable ‘sd’
decompose.gs.group: no visible global function definition for
  ‘gray.colors’
decompose.gs.group: no visible global function definition for ‘legend’
decompose.gs.ind: no visible global function definition for ‘layout’
decompose.gs.ind: no visible global function definition for ‘barplot’
distMoa: no visible global function definition for ‘dist’
moGap : fhclust: no visible global function definition for ‘dist’
moGap : fhclust: no visible global function definition for ‘hclust’
moGap : fhclust: no visible global function definition for ‘cutree’
moGap: no visible binding for global variable ‘kmeans’
sup.moa: no visible global function definition for ‘.ks.pval’
plot,moa-missing: no visible global function definition for
  ‘heat.colors’
Undefined global functions or variables:
  .ks.pval abline barplot cutree dist gray.colors hclust heat.colors
  heatmap kmeans layout legend lines matplot pnorm points sd segments
  text
Consider adding
  importFrom("grDevices", "gray.colors", "heat.colors")
  importFrom("graphics", "abline", "barplot", "layout", "legend",
             "lines", "matplot", "points", "segments", "text")
  importFrom("stats", "cutree", "dist", "hclust", "heatmap", "kmeans",
             "pnorm", "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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/31s] OK
Examples with CPU or elapsed time > 5s
      user system elapsed
mbpca 3.98  0.161   6.739
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/mogsa.Rcheck/00check.log’
for details.

* installing *source* package ‘mogsa’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mogsa)

name	user	system	elapsed
GIS	0.919	0.028	1.553
annotate.gs	0.463	0.017	0.788
bootMbpca	0.001	0.001	0.001
box.gs.feature	0.531	0.012	0.930
combine-methods	0.527	0.016	0.922
decompose.gs.group	0.195	0.013	0.355
decompose.gs.ind	0.172	0.010	0.333
distMoa	0.628	0.020	1.112
getmgsa	0.165	0.011	0.302
matpower	0.001	0.001	0.015
mbpca	3.980	0.161	6.739
mgsa-class	0.517	0.017	0.864
moGap	1.845	0.029	2.999
moa-class	0.119	0.004	0.198
moa	0.188	0.009	0.322
moa.sup-class	0.165	0.009	0.289
moaCoef	0.466	0.018	0.806
moaScore	0.641	0.021	1.088
mogsa-package	0.551	0.016	0.933
mogsa	0.546	0.019	0.915
pairwise.rv	0.020	0.002	0.034
plotGS	0.387	0.011	0.540
prepGraphite	0.106	0.008	0.217
prepMsigDB	0.003	0.000	0.003
prepSupMoa	1.236	0.047	1.321
softK	0.000	0.001	0.001
sup.moa	0.477	0.023	0.503
wsvd	0.002	0.000	0.002