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BioC 3.4: CHECK report for mogsa on morelia

This page was generated on 2017-04-15 16:26:26 -0400 (Sat, 15 Apr 2017).

Package 792/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mogsa 1.8.0
Chen Meng
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/mogsa
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mogsa_1.8.0.tar.gz
StartedAt: 2017-04-15 05:15:16 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 05:17:38 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 141.4 seconds
RetCode: 0
Status:  OK 
CheckDir: mogsa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mogsa_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/mogsa.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.0’
* 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 ... 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
  ‘/Users/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
GIS0.7150.0180.733
annotate.gs0.3430.0170.361
bootMbpca0.0010.0000.000
box.gs.feature0.3510.0120.363
combine-methods0.6340.0120.646
decompose.gs.group0.1510.0100.162
decompose.gs.ind0.1430.0090.152
distMoa0.4570.0230.480
getmgsa0.0990.0100.109
matpower0.0000.0000.001
mbpca3.1610.1793.350
mgsa-class0.2330.0210.254
moGap1.4080.0261.435
moa-class0.3300.0090.339
moa0.1830.0120.197
moa.sup-class0.1460.0090.156
moaCoef0.3890.0240.413
moaScore0.3780.0210.400
mogsa-package0.2810.0210.303
mogsa0.5000.0190.519
pairwise.rv0.0160.0010.016
plotGS0.4030.0140.417
prepGraphite0.0860.0130.186
prepMsigDB0.0050.0000.005
prepSupMoa1.6100.0491.660
softK000
sup.moa0.4870.0110.499
wsvd0.0030.0000.002