BioC 3.0: CHECK report for HCsnip on oaxaca

Package: HCsnip

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HCsnip_1.6.0.tar.gz

StartedAt: 2015-04-10 00:25:56 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:30:47 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 291.6 seconds

RetCode: 0

Status:  OK

CheckDir: HCsnip.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 --no-multiarch HCsnip_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/HCsnip.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.6.0’
* 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 ... [11s/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 ... 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
.test_pred: no visible global function definition for ‘coxph’
EnvioPlot: no visible global function definition for ‘exprs’
EnvioPlot: no visible global function definition for ‘hdEntropy’
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: no visible global function definition for ‘coxph’
cluster_pred: no visible global function definition for ‘exprs’
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’
* 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 ... [168s/180s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
TwoHC_perm   95.470  2.045 101.285
TwoHC_assign 53.871  0.308  60.836
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/HCsnip.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
BullingerLeukemia	0.074	0.008	0.088
EnvioPlot	0.261	0.008	0.314
HCsnipper	1.774	0.023	2.035
RSF_eval	2.455	0.031	2.800
TcgaGBM	0.118	0.013	0.151
TwoHC_assign	53.871	0.308	60.836
TwoHC_perm	95.470	2.045	101.285
cluster_pred	1.484	0.024	1.509
measure	1.288	0.019	1.308
perm_test	1.895	0.017	2.197
surv_measure	1.357	0.019	1.378