BioC 3.1: CHECK report for HCsnip on petty

Package: HCsnip

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HCsnip_1.8.0.tar.gz

StartedAt: 2015-10-08 23:38:17 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:44:36 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 378.9 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 HCsnip_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/HCsnip.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* 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 ... [12s/14s] 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’
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’
EnvioPlot: no visible global function definition for ‘exprs’
EnvioPlot: no visible global function definition for ‘hdEntropy’
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’
RSF_eval: no visible global function definition for ‘rfsrc’
RSF_eval: no visible global function definition for ‘predict.rfsrc’
surv_measure: no visible global function definition for ‘coxph’
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’
* 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 ... [225s/226s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
TwoHC_perm   131.956  3.699 137.060
TwoHC_assign  65.594  0.446  66.124
* 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-3.1-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	0.097	0.015	0.117
EnvioPlot	0.438	0.015	0.457
HCsnipper	2.403	0.041	2.447
RSF_eval	3.973	0.032	4.028
TcgaGBM	0.161	0.017	0.210
TwoHC_assign	65.594	0.446	66.124
TwoHC_perm	131.956	3.699	137.060
cluster_pred	2.418	0.038	2.458
measure	2.209	0.020	2.241
perm_test	3.223	0.021	3.250
surv_measure	2.312	0.019	2.335