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BioC 3.4: CHECK report for mogsa on zin1

This page was generated on 2016-09-21 03:39:47 -0700 (Wed, 21 Sep 2016).

Package 770/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mogsa 1.7.3
Chen Meng
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mogsa
Last Changed Rev: 118206 / Revision: 121152
Last Changed Date: 2016-06-06 04:52:23 -0700 (Mon, 06 Jun 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: mogsa
Version: 1.7.3
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mogsa_1.7.3.tar.gz
StartedAt: 2016-09-20 09:31:29 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:33:15 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 106.2 seconds
RetCode: 0
Status:  OK 
CheckDir: mogsa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mogsa_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/mogsa.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.7.3’
* 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 ... 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’
plot,moa-missing: no visible global function definition for
  ‘heat.colors’
Undefined global functions or variables:
  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 ... OK
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/mogsa.Rcheck/00check.log’
for details.


mogsa.Rcheck/00install.out:

* 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)

mogsa.Rcheck/mogsa-Ex.timings:

nameusersystemelapsed
GIS0.8840.0040.889
annotate.gs0.1440.0000.147
bootMbpca000
box.gs.feature0.3920.0000.394
combine-methods0.4120.0000.414
decompose.gs.group0.3280.0040.329
decompose.gs.ind0.1280.0000.129
distMoa0.4920.0000.492
getmgsa0.1240.0040.130
matpower0.0000.0040.001
mbpca2.9400.0002.942
mgsa-class0.4160.0000.412
moGap1.1200.0041.127
moa-class0.2880.0000.289
moa0.1360.0000.134
moa.sup-class0.3040.0000.306
moaCoef0.3640.0000.366
moaScore0.3600.0040.364
mogsa-package0.4360.0000.440
mogsa0.6280.0040.636
pairwise.rv0.0160.0000.017
plotGS0.1360.0000.133
prepGraphite0.2880.0000.318
prepMsigDB0.0040.0000.003
prepSupMoa0.8080.0160.829
softK0.0000.0000.001
sup.moa0.3720.0040.377
wsvd0.0000.0000.001