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BioC 3.5: CHECK report for HCsnip on veracruz2

This page was generated on 2017-06-23 13:30:22 -0400 (Fri, 23 Jun 2017).

Package 616/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HCsnip 1.16.0
Askar Obulkasim
Snapshot Date: 2017-06-22 17:17:32 -0400 (Thu, 22 Jun 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/HCsnip
Last Changed Rev: 129126 / Revision: 130624
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  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HCsnip
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HCsnip_1.16.0.tar.gz
StartedAt: 2017-06-23 03:46:41 -0400 (Fri, 23 Jun 2017)
EndedAt: 2017-06-23 03:49:49 -0400 (Fri, 23 Jun 2017)
EllapsedTime: 188.2 seconds
RetCode: 0
Status:  OK 
CheckDir: HCsnip.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HCsnip_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/HCsnip.Rcheck’
* using R version 3.4.0 (2017-04-21)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HCsnip/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HCsnip’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘survival’ ‘coin’ ‘fpc’ ‘clusterRepro’ ‘impute’ ‘randomForestSRC’
  ‘sm’ ‘sigaR’ ‘Biobase’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘HCsnip’ 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘clusterRepro’ ‘coin’ ‘fpc’ ‘impute’ ‘randomForestSRC’
  ‘sigaR’ ‘sm’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plot_KM: no visible global function definition for ‘lines’
.plot_KM: no visible global function definition for ‘plot’
.plot_KM: no visible global function definition for ‘legend’
.test_pred: no visible global function definition for ‘cor’
.test_pred: no visible global function definition for ‘coxph’
.test_pred: no visible global function definition for ‘coef’
EnvioPlot: no visible global function definition for ‘exprs’
EnvioPlot: no visible global function definition for ‘hdEntropy’
EnvioPlot: no visible global function definition for ‘quantile’
EnvioPlot: no visible global function definition for ‘median’
EnvioPlot: no visible global function definition for ‘plot.new’
EnvioPlot: no visible global function definition for ‘plot.window’
EnvioPlot: no visible global function definition for ‘axis’
EnvioPlot: no visible global function definition for ‘box’
EnvioPlot: no visible global function definition for ‘polygon’
EnvioPlot: no visible global function definition for ‘lines’
EnvioPlot: no visible global function definition for ‘rect’
EnvioPlot: no visible global function definition for ‘points’
EnvioPlot: no visible global function definition for ‘title’
HCsnipper: no visible global function definition for ‘hclust’
HCsnipper: no visible global function definition for ‘as.dist’
HCsnipper: no visible global function definition for ‘cor’
HCsnipper: no visible global function definition for ‘dist’
HCsnipper: no visible global function definition for ‘tail’
HCsnipper: no visible global function definition for ‘cutree’
RSF_eval: no visible global function definition for ‘rfsrc’
RSF_eval: no visible global function definition for ‘predict.rfsrc’
TwoHC_assign: no visible global function definition for ‘exprs’
TwoHC_perm : wrapper: no visible global function definition for ‘coxph’
TwoHC_perm : wrapper: no visible global function definition for ‘coef’
TwoHC_perm: no visible global function definition for ‘coxph’
TwoHC_perm : <anonymous>: no visible global function definition for
  ‘median’
TwoHC_perm: no visible global function definition for ‘sd’
cluster_pred: no visible global function definition for ‘exprs’
cluster_pred: no visible global function definition for ‘as.dist’
cluster_pred: no visible global function definition for ‘cor’
cluster_pred: no visible global function definition for ‘hclust’
cluster_pred : <anonymous>: no visible global function definition for
  ‘cor’
cluster_pred: no visible global function definition for ‘pvalue’
cluster_pred: no visible global function definition for ‘surv_test’
measure: no visible global function definition for ‘cluster.stats’
measure: no visible global function definition for ‘IGP.clusterRepro’
perm_test: no visible global function definition for ‘pvalue’
perm_test: no visible global function definition for ‘surv_test’
surv_measure: no visible global function definition for ‘coxph’
Undefined global functions or variables:
  IGP.clusterRepro as.dist axis box cluster.stats coef cor coxph cutree
  dist exprs hclust hdEntropy legend lines median plot plot.new
  plot.window points polygon predict.rfsrc pvalue quantile rect rfsrc
  sd surv_test tail title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot",
             "plot.new", "plot.window", "points", "polygon", "rect",
             "title")
  importFrom("stats", "as.dist", "coef", "cor", "cutree", "dist",
             "hclust", "median", "quantile", "sd")
  importFrom("utils", "tail")
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
Examples with CPU or elapsed time > 5s
               user system elapsed
TwoHC_perm   63.917  1.742  67.591
TwoHC_assign 15.889  0.239  16.594
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/HCsnip.Rcheck/00check.log’
for details.


HCsnip.Rcheck/00install.out:

* installing *source* package ‘HCsnip’ ...
** 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 (HCsnip)

HCsnip.Rcheck/HCsnip-Ex.timings:

nameusersystemelapsed
BullingerLeukemia0.0640.0080.107
EnvioPlot0.5790.0210.899
HCsnipper1.4070.0361.700
RSF_eval1.7400.0291.815
TcgaGBM0.1060.0080.117
TwoHC_assign15.889 0.23916.594
TwoHC_perm63.917 1.74267.591
cluster_pred1.3910.0271.466
measure1.1530.0151.208
perm_test2.1910.0162.310
surv_measure1.1180.0161.172